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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/code/SimilaritySearchingFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1602 @@ +<html> +<head> +<title>MayaChemTools:Code:SimilaritySearchingFingerprints.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<pre> + 1 #!/usr/bin/perl -w + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: SimilaritySearchingFingerprints.pl,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:46:21 $</span> + 5 <span class="c"># $Revision: 1.18 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> + 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> + 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span> + 38 <span class="k">use</span> <span class="w">StatisticsUtil</span><span class="sc">;</span> + 39 <span class="k">use</span> <span class="w">PseudoHeap</span><span class="sc">;</span> + 40 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsFileUtil</span><span class="sc">;</span> + 41 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsBitVector</span><span class="sc">;</span> + 42 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsVector</span><span class="sc">;</span> + 43 + 44 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span> + 45 + 46 <span class="c"># Autoflush STDOUT</span> + 47 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> + 48 + 49 <span class="c"># Starting message...</span> + 50 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> + 51 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> + 52 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 53 + 54 <span class="c"># Get the options and setup script...</span> + 55 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 56 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 57 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span> + 58 <span class="s">}</span> + 59 + 60 <span class="c"># Process reference and database file names...</span> + 61 <span class="k">my</span><span class="s">(</span><span class="i">@FingerprintsFilesList</span><span class="s">)</span><span class="sc">;</span> + 62 <span class="i">ProcessFingerprintsFileNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 63 + 64 <span class="c"># Process options...</span> + 65 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> + 66 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> + 67 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 68 + 69 <span class="c"># Setup information about fingerprints inut and SD/text output files...</span> + 70 <span class="k">my</span><span class="s">(</span><span class="i">%FingerprintsFilesInfo</span><span class="cm">,</span> <span class="i">%OutputFilesInfo</span><span class="cm">,</span> <span class="i">%SimilaritySearchInfo</span><span class="s">)</span><span class="sc">;</span> + 71 <span class="k">print</span> <span class="q">"Checking and retrieving information from reference and database fingerprints files...\n"</span><span class="sc">;</span> + 72 <span class="i">RetrieveFingerprintsFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 73 + 74 <span class="c"># Perform similarity search...</span> + 75 <span class="k">print</span> <span class="q">"Performing similarity search...\n"</span><span class="sc">;</span> + 76 <span class="k">my</span><span class="s">(</span><span class="i">%SimilaritySearchResults</span><span class="cm">,</span> <span class="i">%DatabaseFingerprintsFileData</span><span class="s">)</span><span class="sc">;</span> + 77 <span class="i">PerformSimilaritySearch</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 78 + 79 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> + 80 + 81 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 82 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span> + 83 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 84 + 85 <span class="c">###############################################################################</span> + 86 + 87 <span class="c"># Perform similarity search using fingerprints data in reference and database text files...</span> + 88 <span class="c">#</span> +<a name="PerformSimilaritySearch-"></a> 89 <span class="k">sub </span><span class="m">PerformSimilaritySearch</span> <span class="s">{</span> + 90 + 91 <span class="k">print</span> <span class="q">"\nProcessing fingerprints data for reference molecules...\n"</span><span class="sc">;</span> + 92 <span class="i">ReadReferenceFingerprintsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 93 + 94 <span class="i">InitializeSimilaritySearchResults</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 95 <span class="i">GenerateSimilaritySearchResults</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 96 <span class="i">WriteSimilaritySearchResultFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 97 <span class="s">}</span> + 98 + 99 <span class="c"># Find similar molecules from database molecules for individual or multiple reference molecules...</span> + 100 <span class="c">#</span> +<a name="GenerateSimilaritySearchResults-"></a> 101 <span class="k">sub </span><span class="m">GenerateSimilaritySearchResults</span> <span class="s">{</span> + 102 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseFingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FingerprintsCount</span><span class="cm">,</span> <span class="i">$IgnoredFingerprintsCount</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsObject</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ReferenceFingerprintsObject</span><span class="cm">,</span> <span class="i">$ReferenceIndex</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$FusedComparisonValue</span><span class="cm">,</span> <span class="i">@ComparisonValues</span><span class="s">)</span><span class="sc">;</span> + 103 + 104 <span class="k">print</span> <span class="q">"Processing fingerprints data for database molecules...\n"</span><span class="sc">;</span> + 105 + 106 <span class="s">(</span><span class="i">$FingerprintsCount</span><span class="cm">,</span> <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> + 107 + 108 <span class="i">$DatabaseFingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsFileIOParameters</span>}}<span class="s">)</span><span class="sc">;</span> + 109 <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 110 + 111 <span class="i">@ComparisonValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 112 + 113 <span class="j">DATABASEFP:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 114 <span class="i">$FingerprintsCount</span>++<span class="sc">;</span> + 115 + 116 <span class="k">if</span> <span class="s">(</span>!<span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 117 <span class="i">$IgnoredFingerprintsCount</span>++<span class="sc">;</span> + 118 <span class="k">next</span> <span class="j">DATABASEFP</span><span class="sc">;</span> + 119 <span class="s">}</span> + 120 <span class="i">$DatabaseFingerprintsObject</span> = <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->GetFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 121 <span class="i">$DatabaseCmpdID</span> = <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 122 + 123 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span> + 124 <span class="i">@ComparisonValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 125 <span class="s">}</span> + 126 + 127 <span class="j">REFERENCEFP:</span> <span class="k">for</span> <span class="i">$ReferenceIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceCmpdIDsRef</span>}}<span class="s">)</span> <span class="s">{</span> + 128 <span class="i">$ReferenceCmpdID</span> = <span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceCmpdIDsRef</span>}->[<span class="i">$ReferenceIndex</span>]<span class="sc">;</span> + 129 <span class="i">$ReferenceFingerprintsObject</span> = <span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceFingerprintsObjectsRef</span>}->[<span class="i">$ReferenceIndex</span>]<span class="sc">;</span> + 130 + 131 <span class="i">$ComparisonValue</span> = <span class="i">CompareReferenceAndDatabaseFingerprintsPair</span><span class="s">(</span><span class="i">$ReferenceFingerprintsObject</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsObject</span><span class="s">)</span><span class="sc">;</span> + 132 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ComparisonValue</span><span class="s">)</span> <span class="s">{</span> + 133 <span class="k">next</span> <span class="j">REFERENCEFP</span><span class="sc">;</span> + 134 <span class="s">}</span> + 135 + 136 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>}<span class="s">)</span> <span class="s">{</span> + 137 <span class="i">CollectSimilaritySearchResults</span><span class="s">(</span><span class="i">$DatabaseFingerprintsFileIO</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span><span class="sc">;</span> + 138 <span class="s">}</span> + 139 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span> + 140 <span class="k">push</span> <span class="i">@ComparisonValues</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="sc">;</span> + 141 <span class="s">}</span> + 142 <span class="s">}</span> + 143 + 144 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span> + 145 <span class="i">$FusedComparisonValue</span> = <span class="i">CalculateGroupFusionComparisonValue</span><span class="s">(</span>\<span class="i">@ComparisonValues</span><span class="s">)</span><span class="sc">;</span> + 146 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$FusedComparisonValue</span><span class="s">)</span> <span class="s">{</span> + 147 <span class="k">next</span> <span class="j">DATABASEFP</span><span class="sc">;</span> + 148 <span class="s">}</span> + 149 <span class="i">CollectSimilaritySearchResults</span><span class="s">(</span><span class="i">$DatabaseFingerprintsFileIO</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$FusedComparisonValue</span><span class="s">)</span><span class="sc">;</span> + 150 <span class="s">}</span> + 151 <span class="s">}</span> + 152 <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 153 + 154 <span class="k">print</span> <span class="q">"Number of fingerprints data entries in database fingerprints file: $FingerprintsCount\n"</span><span class="sc">;</span> + 155 <span class="k">print</span> <span class="q">"Number of fingerprints date entries processed successfully: "</span><span class="cm">,</span> <span class="s">(</span><span class="i">$FingerprintsCount</span> - <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> <span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 156 <span class="k">print</span> <span class="q">"Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n"</span><span class="sc">;</span> + 157 <span class="s">}</span> + 158 + 159 <span class="c"># Compare a pair of reference and database fingerprints objects corresponding to bit-vector or</span> + 160 <span class="c"># vectors using specified comparison method and comparison cutoff...</span> + 161 <span class="c">#</span> +<a name="CompareReferenceAndDatabaseFingerprintsPair-"></a> 162 <span class="k">sub </span><span class="m">CompareReferenceAndDatabaseFingerprintsPair</span> <span class="s">{</span> + 163 <span class="k">my</span><span class="s">(</span><span class="i">$ReferenceFingerprintsObject</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 164 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMethod</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="s">)</span><span class="sc">;</span> + 165 + 166 <span class="i">$ComparisonMethod</span> = <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethod</span>}<span class="sc">;</span> + 167 <span class="i">$ComparisonValue</span> = <span class="i">$ReferenceFingerprintsObject</span><span class="i">->$ComparisonMethod</span><span class="s">(</span><span class="i">$DatabaseFingerprintsObject</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethodParameters</span>}}<span class="s">)</span><span class="sc">;</span> + 168 + 169 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ComparisonValue</span><span class="s">)</span> <span class="s">{</span> + 170 <span class="k">warn</span> <span class="q">"Warning: Ignoring fingerprints data for reference compound ID "</span><span class="cm">,</span> <span class="i">$ReferenceFingerprintsObject</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">": Its comparison with database compound ID, "</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsObject</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">", failed.\n"</span><span class="sc">;</span> + 171 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 172 <span class="s">}</span> + 173 + 174 <span class="i">$ComparisonValue</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="s">)</span><span class="sc">;</span> + 175 + 176 <span class="c"># Apply any comparison cutoff...</span> + 177 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyComparisonCutoff</span>}<span class="s">)</span> <span class="s">{</span> + 178 <span class="k">return</span> <span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} ? <span class="s">(</span><span class="i">$ComparisonValue</span> >= <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonCutoff</span>} ? <span class="i">$ComparisonValue</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$ComparisonValue</span> <= <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonCutoff</span>} ? <span class="i">$ComparisonValue</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> + 179 <span class="s">}</span> + 180 <span class="k">else</span> <span class="s">{</span> + 181 <span class="k">return</span> <span class="i">$ComparisonValue</span><span class="sc">;</span> + 182 <span class="s">}</span> + 183 <span class="s">}</span> + 184 + 185 <span class="c"># Calculate group fusion comparison value...</span> + 186 <span class="c">#</span> +<a name="CalculateGroupFusionComparisonValue-"></a> 187 <span class="k">sub </span><span class="m">CalculateGroupFusionComparisonValue</span> <span class="s">{</span> + 188 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 189 <span class="k">my</span><span class="s">(</span><span class="i">$FusedComparisonValue</span><span class="cm">,</span> <span class="i">@ComparisonValues</span><span class="s">)</span><span class="sc">;</span> + 190 + 191 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$ComparisonValuesRef</span>}<span class="s">)</span> <span class="s">{</span> + 192 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 193 <span class="s">}</span> + 194 + 195 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">SortComparisonValues</span>}<span class="s">)</span> <span class="s">{</span> + 196 <span class="i">@ComparisonValues</span> = <span class="k">sort</span> <span class="s">{</span> <span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} ? <span class="s">(</span><span class="i">$b</span> <=> <span class="i">$a</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$a</span> <=> <span class="i">$b</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$ComparisonValuesRef</span>}<span class="sc">;</span> + 197 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">UsekNN</span>} && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">kNN</span>} < <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ComparisonValuesRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 198 <span class="c"># Keep only top kNN values for group fusion...</span> + 199 <span class="k">splice</span> <span class="i">@ComparisonValues</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">kNN</span>}<span class="sc">;</span> + 200 <span class="s">}</span> + 201 <span class="i">$ComparisonValuesRef</span> = \<span class="i">@ComparisonValues</span><span class="sc">;</span> + 202 <span class="s">}</span> + 203 + 204 <span class="i">$FusedComparisonValue</span> = <span class="i">&</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>}}<span class="s">(</span><span class="i">$ComparisonValuesRef</span><span class="s">)</span><span class="sc">;</span> + 205 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>}<span class="s">)</span> <span class="s">{</span> + 206 <span class="i">$FusedComparisonValue</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$FusedComparisonValue</span><span class="s">)</span><span class="sc">;</span> + 207 <span class="s">}</span> + 208 + 209 <span class="k">return</span> <span class="i">$FusedComparisonValue</span><span class="sc">;</span> + 210 <span class="s">}</span> + 211 + 212 <span class="c"># Collect similarity results for individual reference and multiple references search...</span> + 213 <span class="c">#</span> +<a name="CollectSimilaritySearchResults-"></a> 214 <span class="k">sub </span><span class="m">CollectSimilaritySearchResults</span> <span class="s">{</span> + 215 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseFingerprintsFileIO</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 216 + 217 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span> <span class="s">{</span> + 218 <span class="i">$SimilaritySearchResults</span>{<span class="i">$ReferenceCmpdID</span>}<span class="i">->AddKeyValuePair</span><span class="s">(</span><span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="s">)</span><span class="sc">;</span> + 219 <span class="s">}</span> + 220 <span class="k">else</span> <span class="s">{</span> + 221 <span class="i">$SimilaritySearchResults</span>{<span class="w">ResultsPseudoHeap</span>}<span class="i">->AddKeyValuePair</span><span class="s">(</span><span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="s">)</span><span class="sc">;</span> + 222 <span class="s">}</span> + 223 + 224 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectInputFileData</span>}<span class="s">)</span> <span class="s">{</span> + 225 <span class="i">CollectDatabaseFileData</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsFileIO</span><span class="s">)</span><span class="sc">;</span> + 226 <span class="s">}</span> + 227 <span class="s">}</span> + 228 + 229 <span class="c"># Initialize similarity results for individual or multiple reference molecules...</span> + 230 <span class="c">#</span> +<a name="InitializeSimilaritySearchResults-"></a> 231 <span class="k">sub </span><span class="m">InitializeSimilaritySearchResults</span> <span class="s">{</span> + 232 <span class="k">my</span><span class="s">(</span><span class="i">$ReferenceCmpdID</span><span class="s">)</span><span class="sc">;</span> + 233 + 234 <span class="i">%SimilaritySearchResults</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 235 + 236 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>}<span class="s">)</span> <span class="s">{</span> + 237 <span class="k">for</span> <span class="i">$ReferenceCmpdID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceCmpdIDsRef</span>}}<span class="s">)</span> <span class="s">{</span> + 238 <span class="i">$SimilaritySearchResults</span>{<span class="i">$ReferenceCmpdID</span>} = <span class="w">new</span> <span class="i">PseudoHeap</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} ? <span class="q">'KeepTopN'</span> <span class="co">:</span> <span class="q">'KeepBottomN'</span><span class="s">)</span><span class="cm">,</span> <span class="q">'KeyType'</span> <span class="cm">=></span> <span class="q">'Numeric'</span><span class="cm">,</span> <span class="q">'MaxSize'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSimilarMolecules</span>}<span class="s">)</span><span class="sc">;</span> + 239 <span class="s">}</span> + 240 <span class="s">}</span> + 241 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span> + 242 <span class="i">$SimilaritySearchResults</span>{<span class="w">ResultsPseudoHeap</span>} = <span class="w">new</span> <span class="i">PseudoHeap</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} ? <span class="q">'KeepTopN'</span> <span class="co">:</span> <span class="q">'KeepBottomN'</span><span class="s">)</span><span class="cm">,</span> <span class="q">'KeyType'</span> <span class="cm">=></span> <span class="q">'Numeric'</span><span class="cm">,</span> <span class="q">'MaxSize'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSimilarMolecules</span>}<span class="s">)</span><span class="sc">;</span> + 243 <span class="s">}</span> + 244 + 245 <span class="i">%DatabaseFingerprintsFileData</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 246 <span class="s">}</span> + 247 + 248 <span class="c"># Write out results SD and/or CSV/TSV text files for individual or multiple reference molecules...</span> + 249 <span class="c">#</span> +<a name="WriteSimilaritySearchResultFiles-"></a> 250 <span class="k">sub </span><span class="m">WriteSimilaritySearchResultFiles</span> <span class="s">{</span> + 251 <span class="k">my</span><span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="s">)</span><span class="sc">;</span> + 252 + 253 <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">SetupAndOpenOutputFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 254 + 255 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>}<span class="s">)</span> <span class="s">{</span> + 256 <span class="k">for</span> <span class="i">$ReferenceCmpdID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceCmpdIDsRef</span>}}<span class="s">)</span> <span class="s">{</span> + 257 <span class="k">for</span> <span class="i">$ComparisonValue</span> <span class="s">(</span><span class="i">$SimilaritySearchResults</span>{<span class="i">$ReferenceCmpdID</span>}<span class="i">->GetSortedKeys</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 258 <span class="k">for</span> <span class="i">$DatabaseCmpdID</span> <span class="s">(</span><span class="i">$SimilaritySearchResults</span>{<span class="i">$ReferenceCmpdID</span>}<span class="i">->GetKeyValues</span><span class="s">(</span><span class="i">$ComparisonValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 259 <span class="i">WriteDataToOutputFiles</span><span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span><span class="sc">;</span> + 260 <span class="s">}</span> + 261 <span class="s">}</span> + 262 <span class="s">}</span> + 263 <span class="s">}</span> + 264 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span> + 265 <span class="k">for</span> <span class="i">$ComparisonValue</span> <span class="s">(</span><span class="i">$SimilaritySearchResults</span>{<span class="w">ResultsPseudoHeap</span>}<span class="i">->GetSortedKeys</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 266 <span class="k">for</span> <span class="i">$DatabaseCmpdID</span> <span class="s">(</span><span class="i">$SimilaritySearchResults</span>{<span class="w">ResultsPseudoHeap</span>}<span class="i">->GetKeyValues</span><span class="s">(</span><span class="i">$ComparisonValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 267 <span class="i">WriteDataToOutputFiles</span><span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="s">)</span><span class="sc">;</span> + 268 <span class="s">}</span> + 269 <span class="s">}</span> + 270 <span class="s">}</span> + 271 + 272 <span class="k">if</span> <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="s">)</span> <span class="s">{</span> + 273 <span class="k">close</span> <span class="i">$NewSDFileRef</span><span class="sc">;</span> + 274 <span class="s">}</span> + 275 <span class="k">if</span> <span class="s">(</span><span class="i">$NewTextFileRef</span><span class="s">)</span> <span class="s">{</span> + 276 <span class="k">close</span> <span class="i">$NewTextFileRef</span><span class="sc">;</span> + 277 <span class="s">}</span> + 278 <span class="s">}</span> + 279 + 280 <span class="c"># Write individual reference or multiple references similarity results along with any other data to output files...</span> + 281 <span class="c">#</span> +<a name="WriteDataToOutputFiles-"></a> 282 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span> + 283 <span class="k">my</span><span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 284 + 285 <span class="k">if</span> <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="s">)</span> <span class="s">{</span> + 286 <span class="i">WriteMolStringDataToSDOutputFile</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="s">)</span><span class="sc">;</span> + 287 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span> <span class="s">{</span> + 288 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <ReferenceCmpdID>\n$ReferenceCmpdID\n\n"</span><span class="sc">;</span> + 289 <span class="s">}</span> + 290 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <DatabaseCmpdID>\n$DatabaseCmpdID\n\n> <ComparisonValue>\n$ComparisonValue\n\n"</span><span class="sc">;</span> + 291 <span class="i">WriteDatabaseDataToSDOutputFile</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="s">)</span><span class="sc">;</span> + 292 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"\$\$\$\$\n"</span><span class="sc">;</span> + 293 <span class="s">}</span> + 294 + 295 <span class="k">if</span> <span class="s">(</span><span class="i">$NewTextFileRef</span><span class="s">)</span> <span class="s">{</span> + 296 <span class="k">my</span><span class="s">(</span><span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span> + 297 + 298 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 299 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span> <span class="s">{</span> + 300 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="sc">;</span> + 301 <span class="s">}</span> + 302 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="s">)</span><span class="sc">;</span> + 303 + 304 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>} || <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>}<span class="s">)</span> <span class="s">{</span> + 305 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">RetrieveDatabaseDataForTextOutputFile</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="s">)</span><span class="sc">;</span> + 306 <span class="s">}</span> + 307 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 308 <span class="s">}</span> + 309 <span class="s">}</span> + 310 + 311 <span class="c"># Open output files...</span> + 312 <span class="c">#</span> +<a name="SetupAndOpenOutputFiles-"></a> 313 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span> + 314 <span class="k">my</span><span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$NewSDFile</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="s">)</span><span class="sc">;</span> + 315 + 316 <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">2</span><span class="sc">;</span> + 317 + 318 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> + 319 <span class="i">$NewSDFile</span> = <span class="i">$OutputFilesInfo</span>{<span class="w">SDOutFileName</span>}<span class="sc">;</span> + 320 <span class="k">print</span> <span class="q">"Generating SD file $NewSDFile...\n"</span><span class="sc">;</span> + 321 <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">">$NewSDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewSDFile: $! \n"</span><span class="sc">;</span> + 322 <span class="i">$NewSDFileRef</span> = \<span class="i">*NEWSDFILE</span><span class="sc">;</span> + 323 <span class="s">}</span> + 324 + 325 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span> + 326 <span class="i">$NewTextFile</span> = <span class="i">$OutputFilesInfo</span>{<span class="w">TextOutFileName</span>}<span class="sc">;</span> + 327 <span class="k">print</span> <span class="q">"Generating text file $NewTextFile...\n"</span><span class="sc">;</span> + 328 <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">">$NewTextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewTextFile: $! \n"</span><span class="sc">;</span> + 329 <span class="i">$NewTextFileRef</span> = \<span class="i">*NEWTEXTFILE</span><span class="sc">;</span> + 330 + 331 <span class="i">WriteTextFileCoulmnLabels</span><span class="s">(</span>\<span class="i">*NEWTEXTFILE</span><span class="s">)</span><span class="sc">;</span> + 332 <span class="s">}</span> + 333 + 334 <span class="k">return</span> <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span> + 335 <span class="s">}</span> + 336 + 337 <span class="c"># Write out approriate column labels to text file...</span> + 338 <span class="c">#</span> +<a name="WriteTextFileCoulmnLabels-"></a> 339 <span class="k">sub </span><span class="m">WriteTextFileCoulmnLabels</span> <span class="s">{</span> + 340 <span class="k">my</span><span class="s">(</span><span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 341 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span> + 342 + 343 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 344 + 345 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>}<span class="s">)</span> <span class="s">{</span> + 346 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">qw(ReferenceCompoundID DatabaseCompoundID ComparisonValue)</span><span class="sc">;</span> + 347 <span class="s">}</span> + 348 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span> + 349 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">qw(DatabaseCompoundID ComparisonValue)</span><span class="sc">;</span> + 350 <span class="s">}</span> + 351 + 352 <span class="c"># Add columns for other database fingerprints file data to be written to output file...</span> + 353 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>}<span class="s">)</span> <span class="s">{</span> + 354 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataFieldsToOutput</span>}}<span class="sc">;</span> + 355 <span class="s">}</span> + 356 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>}<span class="s">)</span> <span class="s">{</span> + 357 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabelsToOutput</span>}}<span class="sc">;</span> + 358 <span class="s">}</span> + 359 + 360 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 361 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 362 <span class="s">}</span> + 363 + 364 <span class="c"># Write molecule string data to SD output file...</span> + 365 <span class="c">#</span> +<a name="WriteMolStringDataToSDOutputFile-"></a> 366 <span class="k">sub </span><span class="m">WriteMolStringDataToSDOutputFile</span> <span class="s">{</span> + 367 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 368 + 369 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectCmpdStringData</span>}<span class="s">)</span> <span class="s">{</span> + 370 <span class="k">my</span><span class="s">(</span><span class="i">$MolString</span><span class="s">)</span><span class="sc">;</span> + 371 + 372 <span class="s">(</span><span class="i">$MolString</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/M END/</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}<span class="sc">;</span> + 373 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"$MolString\nM END\n"</span><span class="sc">;</span> + 374 <span class="s">}</span> + 375 <span class="k">else</span> <span class="s">{</span> + 376 <span class="c"># Just write out an empty molecule data string...</span> + 377 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="i">SDFileUtil::GenerateEmptyCtabBlockLines</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 378 <span class="s">}</span> + 379 <span class="s">}</span> + 380 + 381 <span class="c"># Write database data from SD or Text database file to SD output file...</span> + 382 <span class="c">#</span> +<a name="WriteDatabaseDataToSDOutputFile-"></a> 383 <span class="k">sub </span><span class="m">WriteDatabaseDataToSDOutputFile</span> <span class="s">{</span> + 384 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 385 + 386 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>}<span class="s">)</span> <span class="s">{</span> + 387 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabel</span><span class="cm">,</span> <span class="i">$DataFieldValue</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldLabelAndValues</span><span class="s">)</span><span class="sc">;</span> + 388 + 389 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">/\n/</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}<span class="sc">;</span> + 390 <span class="i">%DataFieldLabelAndValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span> + 391 + 392 <span class="k">for</span> <span class="i">$DataFieldLabel</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputCurrentDataFields</span>} ? <span class="i">GetCmpdDataHeaderLabels</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span> <span class="co">:</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataFieldsToOutput</span>}}<span class="s">)</span> <span class="s">{</span> + 393 <span class="i">$DataFieldValue</span> = <span class="k">exists</span> <span class="i">$DataFieldLabelAndValues</span>{<span class="i">$DataFieldLabel</span>} ? <span class="i">$DataFieldLabelAndValues</span>{<span class="i">$DataFieldLabel</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> + 394 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <$DataFieldLabel>\n$DataFieldValue\n\n"</span><span class="sc">;</span> + 395 <span class="s">}</span> + 396 <span class="s">}</span> + 397 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>}<span class="s">)</span> <span class="s">{</span> + 398 <span class="k">my</span><span class="s">(</span><span class="i">$DataColNum</span><span class="cm">,</span> <span class="i">$DataFieldLabel</span><span class="cm">,</span> <span class="i">$DataFieldValue</span><span class="s">)</span><span class="sc">;</span> + 399 + 400 <span class="k">for</span> <span class="i">$DataColNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumsToOutput</span>}}<span class="s">)</span> <span class="s">{</span> + 401 <span class="i">$DataFieldLabel</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumToLabelMap</span>}{<span class="i">$DataColNum</span>}<span class="sc">;</span> + 402 <span class="i">$DataFieldValue</span> = <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}->[<span class="i">$DataColNum</span>]<span class="sc">;</span> + 403 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <$DataFieldLabel>\n$DataFieldValue\n\n"</span><span class="sc">;</span> + 404 <span class="s">}</span> + 405 <span class="s">}</span> + 406 <span class="s">}</span> + 407 + 408 <span class="c"># Retriebe database data from SD or Text database file for text output file...</span> + 409 <span class="c">#</span> +<a name="RetrieveDatabaseDataForTextOutputFile-"></a> 410 <span class="k">sub </span><span class="m">RetrieveDatabaseDataForTextOutputFile</span> <span class="s">{</span> + 411 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 412 + 413 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>}<span class="s">)</span> <span class="s">{</span> + 414 <span class="k">my</span><span class="s">(</span><span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldLabelAndValues</span><span class="s">)</span><span class="sc">;</span> + 415 + 416 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">/\n/</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}<span class="sc">;</span> + 417 <span class="i">%DataFieldLabelAndValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span> + 418 + 419 <span class="k">return</span> <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValues</span>{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValues</span>{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataFieldsToOutput</span>}}<span class="sc">;</span> + 420 <span class="s">}</span> + 421 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>}<span class="s">)</span> <span class="s">{</span> + 422 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}<span class="s">)</span> <span class="s">{</span> + 423 <span class="k">return</span> <span class="k">map</span> <span class="s">{</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}->[<span class="i">$_</span>] <span class="s">}</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumsToOutput</span>}}<span class="s">)</span><span class="sc">;</span> + 424 <span class="s">}</span> + 425 <span class="k">else</span> <span class="s">{</span> + 426 <span class="k">return</span> <span class="s">(</span><span class="q">''</span><span class="s">)</span> x <span class="i">$#</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumsToOutput</span>}}<span class="sc">;</span> + 427 <span class="s">}</span> + 428 <span class="s">}</span> + 429 <span class="s">}</span> + 430 + 431 <span class="c"># Collect database file SD compound string or CSV/TSV data line for generating results</span> + 432 <span class="c"># files..</span> + 433 <span class="c">#</span> +<a name="CollectDatabaseFileData-"></a> 434 <span class="k">sub </span><span class="m">CollectDatabaseFileData</span> <span class="s">{</span> + 435 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsFileIO</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 436 + 437 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}<span class="s">)</span> <span class="s">{</span> + 438 <span class="k">return</span><span class="sc">;</span> + 439 <span class="s">}</span> + 440 + 441 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectCmpdStringData</span>}<span class="s">)</span> <span class="s">{</span> + 442 <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>} = <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->GetCompoundString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 443 <span class="s">}</span> + 444 + 445 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectDataLine</span>}<span class="s">)</span> <span class="s">{</span> + 446 <span class="k">my</span><span class="s">(</span><span class="i">@DataLineWords</span><span class="s">)</span><span class="sc">;</span> + 447 <span class="i">@DataLineWords</span> = <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->GetDataLineWords</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 448 <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>} = \<span class="i">@DataLineWords</span><span class="sc">;</span> + 449 <span class="s">}</span> + 450 + 451 <span class="s">}</span> + 452 + 453 <span class="c"># Read fingerprints data from reference fingerprints file...</span> + 454 <span class="c">#</span> +<a name="ReadReferenceFingerprintsData-"></a> 455 <span class="k">sub </span><span class="m">ReadReferenceFingerprintsData</span> <span class="s">{</span> + 456 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="s">)</span><span class="sc">;</span> + 457 + 458 <span class="i">$FingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsFileIOParameters</span>}}<span class="s">)</span><span class="sc">;</span> + 459 <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceCmpdIDsRef</span>}<span class="cm">,</span> <span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceFingerprintsObjectsRef</span>}<span class="s">)</span> = <span class="i">Fingerprints::FingerprintsFileUtil::ReadAndProcessFingerpritsData</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="s">)</span><span class="sc">;</span> + 460 + 461 <span class="s">}</span> + 462 + 463 <span class="c"># Retrieve information about fingerprints files...</span> + 464 <span class="c">#</span> +<a name="RetrieveFingerprintsFilesInfo-"></a> 465 <span class="k">sub </span><span class="m">RetrieveFingerprintsFilesInfo</span> <span class="s">{</span> + 466 + 467 <span class="i">%FingerprintsFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 468 <span class="i">%OutputFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 469 <span class="i">%SimilaritySearchInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 470 + 471 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 472 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 473 + 474 <span class="c"># Set up reference and database file names...</span> + 475 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FileName</span>} = <span class="i">$FingerprintsFilesList</span>[<span class="n">0</span>]<span class="sc">;</span> + 476 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FileName</span>} = <span class="i">$FingerprintsFilesList</span>[<span class="n">1</span>]<span class="sc">;</span> + 477 + 478 <span class="c"># Retrieve information about reference and database fingerprints file...</span> + 479 <span class="i">RetrieveReferenceFingerprintsFileInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 480 <span class="i">RetrieveDatabaseFingerprintsFileInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 481 + 482 <span class="c"># Setup fingerprints comparison method and associated method parameters...</span> + 483 <span class="i">SetupReferenceAndDatabaseFingerprintsComparisonInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 484 + 485 <span class="c"># Retrieve information for output files...</span> + 486 <span class="i">RetrieveOutputFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 487 <span class="s">}</span> + 488 + 489 <span class="c"># Setup refrerence and database fingerprints comparison method and associated method parameters...</span> + 490 <span class="c">#</span> +<a name="SetupReferenceAndDatabaseFingerprintsComparisonInfo-"></a> 491 <span class="k">sub </span><span class="m">SetupReferenceAndDatabaseFingerprintsComparisonInfo</span> <span class="s">{</span> + 492 + 493 <span class="c"># Make sure reference and database fingerprints string match...</span> + 494 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FirstFingerprintsStringType</span>} !~ <span class="q">/^$FingerprintsFilesInfo{Database}{FirstFingerprintsStringType}$/i</span><span class="s">)</span> || + 495 <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsBitVectorStringMode</span>} != <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsBitVectorStringMode</span>}<span class="s">)</span> || + 496 <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsVectorStringMode</span>} != <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsVectorStringMode</span>}<span class="s">)</span> <span class="s">)</span> <span class="s">{</span> + 497 <span class="k">die</span> <span class="q">"Error: First reference fingerprints string type, $FingerprintsFilesInfo{Reference}{FirstFingerprintsStringType}, must match first database fingerprints type, $FingerprintsFilesInfo{Database}{FirstFingerprintsStringType}.\n"</span><span class="sc">;</span> + 498 <span class="s">}</span> + 499 + 500 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FirstFingerprintsStringDescription</span>} !~ <span class="q">/^$FingerprintsFilesInfo{Database}{FirstFingerprintsStringDescription}$/i</span><span class="s">)</span> <span class="s">{</span> + 501 <span class="k">warn</span> <span class="q">"Warning: First reference fingerprints string description, $FingerprintsFilesInfo{Reference}{FirstFingerprintsStringDescription}, doesn't match first database fingerprints string description, $FingerprintsFilesInfo{Database}{FirstFingerprintsStringDescription}.\n"</span><span class="sc">;</span> + 502 <span class="s">}</span> + 503 + 504 <span class="c"># Setup individual reference and multiple references search mode...</span> + 505 <span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>} = <span class="k">undef</span><span class="sc">;</span> + 506 <span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>} = <span class="k">undef</span><span class="sc">;</span> + 507 + 508 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^IndividualReference$/i</span><span class="s">)</span> <span class="s">{</span> + 509 <span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>} = <span class="n">1</span><span class="sc">;</span> + 510 <span class="s">}</span> + 511 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^MultipleReferences$/i</span><span class="s">)</span> <span class="s">{</span> + 512 <span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>} = <span class="n">1</span><span class="sc">;</span> + 513 <span class="s">}</span> + 514 <span class="k">else</span> <span class="s">{</span> + 515 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: IndividualReference, MultipleReferences\n"</span><span class="sc">;</span> + 516 <span class="s">}</span> + 517 + 518 <span class="c"># Set up reference and database fingerprints similarity search method and paramaters...</span> + 519 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="cm">,</span> <span class="i">$ComparisonMethod</span><span class="cm">,</span> <span class="i">$ApplyComparisonCutoff</span><span class="cm">,</span> <span class="i">$ComparisonCutoff</span><span class="cm">,</span> <span class="i">$KeepTop</span><span class="cm">,</span> <span class="i">@ComparisonMethodParameters</span><span class="s">)</span><span class="sc">;</span> + 520 + 521 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethod</span>} = <span class="q">''</span><span class="sc">;</span> + 522 <span class="i">@</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethodParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 523 + 524 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonCutoff</span>} = <span class="q">''</span><span class="sc">;</span> + 525 <span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} = <span class="q">''</span><span class="sc">;</span> + 526 + 527 <span class="i">$ComparisonMeasure</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$ComparisonMethod</span> = <span class="q">''</span><span class="sc">;</span> + 528 <span class="i">@ComparisonMethodParameters</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 529 + 530 <span class="j">FINGERPRINTSTYPE:</span> <span class="s">{</span> + 531 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsBitVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span> + 532 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonMeasure</span>}<span class="sc">;</span> + 533 <span class="i">$ComparisonMethod</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonMeasureMethod</span>}<span class="sc">;</span> + 534 + 535 <span class="k">if</span> <span class="s">(</span><span class="i">$ComparisonMeasure</span> =~ <span class="q">/^TverskySimilarity$/i</span><span class="s">)</span> <span class="s">{</span> + 536 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>}<span class="sc">;</span> + 537 <span class="s">}</span> + 538 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ComparisonMeasure</span> =~ <span class="q">/^WeightedTverskySimilarity$/i</span><span class="s">)</span> <span class="s">{</span> + 539 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>}<span class="sc">;</span> + 540 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>}<span class="sc">;</span> + 541 <span class="s">}</span> + 542 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ComparisonMeasure</span> =~ <span class="q">/^WeightedTanimotoSimilarity$/i</span><span class="s">)</span> <span class="s">{</span> + 543 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>}<span class="sc">;</span> + 544 <span class="s">}</span> + 545 + 546 <span class="k">last</span> <span class="j">FINGERPRINTSTYPE</span><span class="sc">;</span> + 547 <span class="s">}</span> + 548 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span> + 549 <span class="k">my</span><span class="s">(</span><span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span> + 550 + 551 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMeasure</span>}<span class="sc">;</span> + 552 <span class="i">$ComparisonMethod</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMeasuresMethod</span>}<span class="sc">;</span> + 553 + 554 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMode</span>}<span class="sc">;</span> + 555 + 556 <span class="i">$SkipValuesCheck</span> = <span class="i">$OptionsInfo</span>{<span class="w">Fast</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 557 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="sc">;</span> + 558 + 559 <span class="k">last</span> <span class="j">FINGERPRINTSTYPE</span><span class="sc">;</span> + 560 <span class="s">}</span> + 561 <span class="k">die</span> <span class="q">"Error: Uknown fingerprints string type. Supported values: FingerprintsBitVectorString or FingerprintsVectorString.\n"</span><span class="sc">;</span> + 562 <span class="s">}</span> + 563 + 564 <span class="i">$ApplyComparisonCutoff</span> = <span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>} && <span class="i">$OptionsInfo</span>{<span class="w">GroupFusionApplyCutoff</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> + 565 + 566 <span class="i">$ComparisonCutoff</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$KeepTop</span> = <span class="q">''</span><span class="sc">;</span> + 567 <span class="k">if</span> <span class="s">(</span><span class="i">$ComparisonMethod</span> =~ <span class="q">/Distance/i</span><span class="s">)</span> <span class="s">{</span> + 568 <span class="i">$ComparisonCutoff</span> = <span class="i">$OptionsInfo</span>{<span class="w">DistanceCutoff</span>}<span class="sc">;</span> + 569 <span class="i">$KeepTop</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SearchMode</span>} =~ <span class="q">/^SimilaritySearch$/i</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> + 570 <span class="s">}</span> + 571 <span class="k">else</span> <span class="s">{</span> + 572 <span class="i">$ComparisonCutoff</span> = <span class="i">$OptionsInfo</span>{<span class="w">SimilarityCutoff</span>}<span class="sc">;</span> + 573 <span class="i">$KeepTop</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SearchMode</span>} =~ <span class="q">/^SimilaritySearch$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 574 <span class="s">}</span> + 575 + 576 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethod</span>} = <span class="i">$ComparisonMethod</span><span class="sc">;</span> + 577 <span class="i">@</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethodParameters</span>}} = <span class="i">@ComparisonMethodParameters</span><span class="sc">;</span> + 578 + 579 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonCutoff</span>} = <span class="i">$ComparisonCutoff</span><span class="sc">;</span> + 580 <span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} = <span class="i">$KeepTop</span><span class="sc">;</span> + 581 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyComparisonCutoff</span>} = <span class="i">$ApplyComparisonCutoff</span><span class="sc">;</span> + 582 + 583 <span class="c"># Setup references to group fusion methods...</span> + 584 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = <span class="k">undef</span><span class="sc">;</span> + 585 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>} = <span class="k">undef</span><span class="sc">;</span> + 586 + 587 <span class="j">FUSIONRULE:</span> <span class="s">{</span> + 588 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Max$/i</span><span class="s">)</span> <span class="s">{</span> + 589 <span class="c"># It's always the first value in the appropriated sorted list using value of KeepTop...</span> + 590 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = <span class="k">sub</span> <span class="s">{</span> <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> <span class="k">return</span> <span class="i">$ComparisonValuesRef</span>->[<span class="n">0</span>]<span class="sc">;</span> <span class="s">}</span><span class="sc">;</span> + 591 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span> + 592 <span class="s">}</span> + 593 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Min$/i</span><span class="s">)</span> <span class="s">{</span> + 594 <span class="c"># It's always the last value in the appropriated sorted list using value of KeepTop...</span> + 595 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = <span class="k">sub</span> <span class="s">{</span> <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> <span class="k">return</span> <span class="i">$ComparisonValuesRef</span>->[<span class="i">$#</span>{<span class="i">$ComparisonValuesRef</span>}]<span class="sc">;</span> <span class="s">}</span><span class="sc">;</span> + 596 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span> + 597 <span class="s">}</span> + 598 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Mean$/i</span><span class="s">)</span> <span class="s">{</span> + 599 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = \<span class="i">&StatisticsUtil::Mean</span><span class="sc">;</span> + 600 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>} = <span class="n">1</span><span class="sc">;</span> + 601 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span> + 602 <span class="s">}</span> + 603 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Median$/i</span><span class="s">)</span> <span class="s">{</span> + 604 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = \<span class="i">&StatisticsUtil::Median</span><span class="sc">;</span> + 605 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>} = <span class="n">1</span><span class="sc">;</span> + 606 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span> + 607 <span class="s">}</span> + 608 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Sum$/i</span><span class="s">)</span> <span class="s">{</span> + 609 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = \<span class="i">&StatisticsUtil::Sum</span><span class="sc">;</span> + 610 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>} = <span class="n">1</span><span class="sc">;</span> + 611 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span> + 612 <span class="s">}</span> + 613 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Euclidean$/i</span><span class="s">)</span> <span class="s">{</span> + 614 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = \<span class="i">&StatisticsUtil::Euclidean</span><span class="sc">;</span> + 615 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>} = <span class="n">1</span><span class="sc">;</span> + 616 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span> + 617 <span class="s">}</span> + 618 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{groupfusionrule}, for option \"-g, --GroupFusionRule\" is not valid. Allowed values: Max, Min, Mean, Median, Sum, Euclidean\n"</span><span class="sc">;</span> + 619 <span class="s">}</span> + 620 + 621 <span class="i">$SimilaritySearchInfo</span>{<span class="w">UsekNN</span>} = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">kNN</span>} !~ <span class="q">/^All$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 622 <span class="i">$SimilaritySearchInfo</span>{<span class="w">SortComparisonValues</span>} = <span class="s">(</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^(Max|Min)$/i</span><span class="s">)</span> || <span class="i">$SimilaritySearchInfo</span>{<span class="w">UsekNN</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 623 <span class="s">}</span> + 624 + 625 <span class="c"># Retrieve information about reference fingerprints file...</span> + 626 <span class="c">#</span> +<a name="RetrieveReferenceFingerprintsFileInfo-"></a> 627 <span class="k">sub </span><span class="m">RetrieveReferenceFingerprintsFileInfo</span> <span class="s">{</span> + 628 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span><span class="sc">;</span> + 629 + 630 <span class="i">$FingerprintsFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FileName</span>}<span class="sc">;</span> + 631 <span class="s">(</span><span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span> = <span class="i">RetrieveFingerprintsFileInfo</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 632 + 633 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FileType</span>} = <span class="i">$FileType</span><span class="sc">;</span> + 634 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">InDelim</span>} = <span class="i">$InDelim</span><span class="sc">;</span> + 635 + 636 <span class="c"># Setup reference FingerprintsFileIO parameters...</span> + 637 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsFileIOParameters</span>}} = <span class="i">RetrieveFingerprintsFileIOParameters</span><span class="s">(</span><span class="q">'Reference'</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 638 + 639 <span class="c"># Make sure reference fingerprints data file contains valid and retrieve fingerprints string mode information...</span> + 640 <span class="s">(</span><span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span> = <span class="i">RetrieveFingerprintsFileFingerprintsStringInfo</span><span class="s">(</span><span class="q">'Reference'</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 641 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsStringMode</span>} = <span class="i">$FingerprintsStringMode</span><span class="sc">;</span> + 642 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="i">$FingerprintsBitVectorStringMode</span><span class="sc">;</span> + 643 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsVectorStringMode</span>} = <span class="i">$FingerprintsVectorStringMode</span><span class="sc">;</span> + 644 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FirstFingerprintsStringType</span>} = <span class="i">$FirstFingerprintsStringType</span><span class="sc">;</span> + 645 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FirstFingerprintsStringDescription</span>} = <span class="i">$FirstFingerprintsStringDescription</span><span class="sc">;</span> + 646 + 647 <span class="s">}</span> + 648 + 649 <span class="c"># Retrieve information about database fingerprints file...</span> + 650 <span class="c">#</span> +<a name="RetrieveDatabaseFingerprintsFileInfo-"></a> 651 <span class="k">sub </span><span class="m">RetrieveDatabaseFingerprintsFileInfo</span> <span class="s">{</span> + 652 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span><span class="sc">;</span> + 653 + 654 <span class="i">$FingerprintsFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FileName</span>}<span class="sc">;</span> + 655 <span class="s">(</span><span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span> = <span class="i">RetrieveFingerprintsFileInfo</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 656 + 657 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FileType</span>} = <span class="i">$FileType</span><span class="sc">;</span> + 658 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">InDelim</span>} = <span class="i">$InDelim</span><span class="sc">;</span> + 659 + 660 <span class="c"># Setup reference FingerprintsFileIO parameters...</span> + 661 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsFileIOParameters</span>}} = <span class="i">RetrieveFingerprintsFileIOParameters</span><span class="s">(</span><span class="q">'Database'</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 662 + 663 <span class="c"># Make sure database fingerprints data file contains valid and retrieve fingerprints string mode information...</span> + 664 <span class="s">(</span><span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span> = <span class="i">RetrieveFingerprintsFileFingerprintsStringInfo</span><span class="s">(</span><span class="q">'Database'</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 665 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsStringMode</span>} = <span class="i">$FingerprintsStringMode</span><span class="sc">;</span> + 666 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="i">$FingerprintsBitVectorStringMode</span><span class="sc">;</span> + 667 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsVectorStringMode</span>} = <span class="i">$FingerprintsVectorStringMode</span><span class="sc">;</span> + 668 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FirstFingerprintsStringType</span>} = <span class="i">$FirstFingerprintsStringType</span><span class="sc">;</span> + 669 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FirstFingerprintsStringDescription</span>} = <span class="i">$FirstFingerprintsStringDescription</span><span class="sc">;</span> + 670 + 671 <span class="c"># Retrieve database fingerprints data field information for output file...</span> + 672 <span class="c">#</span> + 673 <span class="i">RetrieveDatabaseFingerprintsDataFieldsInfo</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span> + 674 + 675 <span class="c"># Retrieve database fingerprints text file data columns information for output file...</span> + 676 <span class="c">#</span> + 677 <span class="i">RetrieveDatabaseFingerprintsDataColsInfo</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span> + 678 + 679 <span class="c"># Any need to collect database compound string or data line for generation of results files...</span> + 680 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectCmpdStringData</span>} = <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 681 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectDataLine</span>} = <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^Text$/i</span> && <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataColsMode</span>} =~ <span class="q">/^(All|Specify)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 682 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectInputFileData</span>} = <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectCmpdStringData</span>} || <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectDataLine</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 683 + 684 <span class="c"># Set maximum number of similar compounds to find for individual reference of set of multiple</span> + 685 <span class="c"># reference compounds...</span> + 686 <span class="c">#</span> + 687 <span class="i">SetMaximumSimilarMoleculesToRetrieve</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span> + 688 <span class="s">}</span> + 689 + 690 <span class="c"># Retrieve database fingerprints data field information...</span> + 691 <span class="c">#</span> +<a name="RetrieveDatabaseFingerprintsDataFieldsInfo-"></a> 692 <span class="k">sub </span><span class="m">RetrieveDatabaseFingerprintsDataFieldsInfo</span> <span class="s">{</span> + 693 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 694 <span class="k">my</span><span class="s">(</span><span class="i">$CollectDataFields</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="cm">,</span> <span class="i">@DataFieldsToOutput</span><span class="s">)</span><span class="sc">;</span> + 695 + 696 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>} = <span class="n">0</span><span class="sc">;</span> + 697 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataFieldsToOutput</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 698 + 699 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputCurrentDataFields</span>} = <span class="n">0</span><span class="sc">;</span> + 700 + 701 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">AllDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 702 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CommonDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 703 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">SpecifiedDatabaseDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 704 + 705 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> !~ <span class="q">/^SD$/i</span><span class="s">)</span> <span class="s">{</span> + 706 <span class="k">return</span><span class="sc">;</span> + 707 <span class="s">}</span> + 708 + 709 <span class="c"># No need to go over SD file and collect data fields for SD file during All DatabaseDataFieldsMode as</span> + 710 <span class="c"># they would be retrieved from database SD file compound string during generation of output files...</span> + 711 <span class="c">#</span> + 712 <span class="i">$CollectDataFields</span> = <span class="s">(</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} =~ <span class="q">/^(All|Common)$/i</span><span class="s">)</span> || <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} && <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 713 + 714 <span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">2</span><span class="sc">;</span> + 715 + 716 <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span> + 717 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$FingerprintsFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $FingerprintsFile: $! \n"</span><span class="sc">;</span> + 718 <span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span> = <span class="i">GetAllAndCommonCmpdDataHeaderLabels</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span> + 719 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> + 720 <span class="s">}</span> + 721 + 722 <span class="i">@DataFieldsToOutput</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 723 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> + 724 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AllDataFieldsRef</span><span class="s">)</span> <span class="s">{</span> + 725 <span class="k">push</span> <span class="i">@DataFieldsToOutput</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AllDataFieldsRef</span>}<span class="sc">;</span> + 726 <span class="k">push</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">AllDataFields</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$AllDataFieldsRef</span>}<span class="sc">;</span> + 727 <span class="s">}</span> + 728 <span class="k">else</span> <span class="s">{</span> + 729 <span class="c"># Retrieve and output data fields and values dynamically...</span> + 730 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputCurrentDataFields</span>} = <span class="n">1</span><span class="sc">;</span> + 731 <span class="s">}</span> + 732 <span class="s">}</span> + 733 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span> + 734 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span> <span class="s">{</span> + 735 <span class="k">push</span> <span class="i">@DataFieldsToOutput</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$CommonDataFieldsRef</span>}<span class="sc">;</span> + 736 <span class="k">push</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CommonDataFields</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$CommonDataFieldsRef</span>}<span class="sc">;</span> + 737 <span class="s">}</span> + 738 <span class="s">}</span> + 739 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> + 740 <span class="k">push</span> <span class="i">@DataFieldsToOutput</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataFields</span>}}<span class="sc">;</span> + 741 <span class="k">push</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">SpecifiedDatabaseDataFields</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataFields</span>}}<span class="sc">;</span> + 742 <span class="s">}</span> + 743 + 744 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} !~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span> + 745 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>} = <span class="n">1</span><span class="sc">;</span> + 746 <span class="s">}</span> + 747 + 748 <span class="k">push</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataFieldsToOutput</span>}}<span class="cm">,</span> <span class="i">@DataFieldsToOutput</span><span class="sc">;</span> + 749 + 750 <span class="s">}</span> + 751 + 752 <span class="c"># Retrieve database fingerprints data columns information...</span> + 753 <span class="c">#</span> +<a name="RetrieveDatabaseFingerprintsDataColsInfo-"></a> 754 <span class="k">sub </span><span class="m">RetrieveDatabaseFingerprintsDataColsInfo</span> <span class="s">{</span> + 755 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 756 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="cm">,</span> <span class="i">$ColLabel</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">@DataColLabels</span><span class="cm">,</span> <span class="i">@DataColLabelsToOutput</span><span class="cm">,</span> <span class="i">@DataColNumsToOutput</span><span class="cm">,</span> <span class="i">%DataColLabelToNumMap</span><span class="cm">,</span> <span class="i">%DataColNumToLabelMap</span><span class="s">)</span><span class="sc">;</span> + 757 + 758 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>} = <span class="n">0</span><span class="sc">;</span> + 759 + 760 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 761 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabelToNumMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 762 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumToLabelMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 763 + 764 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumsToOutput</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 765 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabelsToOutput</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 766 + 767 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> !~ <span class="q">/^Text$/i</span><span class="s">)</span> <span class="s">{</span> + 768 <span class="k">return</span><span class="sc">;</span> + 769 <span class="s">}</span> + 770 + 771 <span class="i">@DataColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 772 <span class="i">@DataColLabelsToOutput</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 773 <span class="i">@DataColNumsToOutput</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 774 + 775 <span class="i">%DataColLabelToNumMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 776 <span class="i">%DataColNumToLabelMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 777 + 778 <span class="c"># Get column label line...</span> + 779 <span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">"$FingerprintsFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $FingerprintsFile: $! \n"</span><span class="sc">;</span> + 780 <span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span> + 781 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span> + 782 + 783 <span class="i">$InDelim</span> = <span class="s">(</span><span class="i">$InDelim</span> =~ <span class="q">/^Tab$/i</span><span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="i">$InDelim</span> =~ <span class="q">/semicolon/i</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span> + 784 + 785 <span class="i">@DataColLabels</span> = <span class="i">TextUtil::SplitWords</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span> + 786 <span class="i">$NumOfCols</span> = <span class="k">scalar</span> <span class="i">@DataColLabels</span><span class="sc">;</span> + 787 + 788 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#DataColLabels</span><span class="s">)</span> <span class="s">{</span> + 789 <span class="i">$ColLabel</span> = <span class="i">$DataColLabels</span>[<span class="i">$ColNum</span>]<span class="sc">;</span> + 790 <span class="i">$DataColLabelToNumMap</span>{<span class="i">$ColLabel</span>} = <span class="i">$ColNum</span><span class="sc">;</span> + 791 <span class="i">$DataColNumToLabelMap</span>{<span class="i">$ColNum</span>} = <span class="i">$ColLabel</span><span class="sc">;</span> + 792 <span class="s">}</span> + 793 + 794 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataColsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> + 795 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseColMode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span> + 796 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataCols</span>}}<span class="s">)</span> <span class="s">{</span> + 797 <span class="k">if</span> <span class="s">(</span><span class="i">$ColNum</span> > <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span> + 798 <span class="k">die</span> <span class="q">"Error: Column number, $ColNum, specified using \"--DatabaseDataCols\" is not valid: It must be <= $NumOfCols\n"</span><span class="sc">;</span> + 799 <span class="s">}</span> + 800 <span class="k">push</span> <span class="i">@DataColNumsToOutput</span><span class="cm">,</span> <span class="s">(</span><span class="i">$ColNum</span> - <span class="n">1</span><span class="s">)</span><span class="sc">;</span> + 801 <span class="s">}</span> + 802 <span class="s">}</span> + 803 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseColMode</span>} =~ <span class="q">/^ColLabel$/i</span><span class="s">)</span> <span class="s">{</span> + 804 <span class="k">for</span> <span class="i">$ColLabel</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataCols</span>}}<span class="s">)</span> <span class="s">{</span> + 805 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataColLabelToNumMap</span>{<span class="i">$ColLabel</span>}<span class="s">)</span> <span class="s">{</span> + 806 <span class="k">die</span> <span class="q">"Error: Column label, $ColLabel, specified using \"--DatabaseDataCols\" is not valid: It doesn't exist\n"</span><span class="sc">;</span> + 807 <span class="s">}</span> + 808 <span class="k">push</span> <span class="i">@DataColNumsToOutput</span><span class="cm">,</span> <span class="i">$DataColLabelToNumMap</span>{<span class="i">$ColLabel</span>}<span class="sc">;</span> + 809 <span class="s">}</span> + 810 <span class="s">}</span> + 811 <span class="s">}</span> + 812 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataColsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> + 813 <span class="i">@DataColNumsToOutput</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span> <span class="s">}</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#DataColLabels</span><span class="s">)</span><span class="sc">;</span> + 814 <span class="s">}</span> + 815 + 816 <span class="c"># Setup data column labels to output...</span> + 817 <span class="k">if</span> <span class="s">(</span><span class="k">scalar</span> <span class="i">@DataColNumsToOutput</span><span class="s">)</span> <span class="s">{</span> + 818 <span class="i">@DataColLabelsToOutput</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$DataColNumToLabelMap</span>{<span class="i">$_</span>} <span class="s">}</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#DataColNumsToOutput</span><span class="s">)</span><span class="sc">;</span> + 819 <span class="s">}</span> + 820 + 821 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>} = <span class="k">scalar</span> <span class="i">@DataColNumsToOutput</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 822 + 823 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabels</span>}} = <span class="i">@DataColLabels</span><span class="sc">;</span> + 824 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabelToNumMap</span>}} = <span class="i">%DataColLabelToNumMap</span><span class="sc">;</span> + 825 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumToLabelMap</span>}} = <span class="i">%DataColNumToLabelMap</span><span class="sc">;</span> + 826 + 827 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumsToOutput</span>}} = <span class="i">@DataColNumsToOutput</span><span class="sc">;</span> + 828 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabelsToOutput</span>}} = <span class="i">@DataColLabelsToOutput</span><span class="sc">;</span> + 829 <span class="s">}</span> + 830 + 831 <span class="c"># Set maximum number of similar compounds to find for individual reference of set of multiple</span> + 832 <span class="c"># reference compounds...</span> + 833 <span class="c">#</span> +<a name="SetMaximumSimilarMoleculesToRetrieve-"></a> 834 <span class="k">sub </span><span class="m">SetMaximumSimilarMoleculesToRetrieve</span> <span class="s">{</span> + 835 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 836 <span class="k">my</span><span class="s">(</span><span class="i">$MaxSimilarMolecules</span><span class="cm">,</span> <span class="i">$NumOfDatabaseMolecules</span><span class="cm">,</span> <span class="i">$PercentSimilarMolecules</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> + 837 + 838 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SimilarCountMode</span>} !~ <span class="q">/^PercentSimilar$/i</span><span class="s">)</span> <span class="s">{</span> + 839 <span class="k">return</span><span class="sc">;</span> + 840 <span class="s">}</span> + 841 + 842 <span class="i">$PercentSimilarMolecules</span> = <span class="i">$OptionsInfo</span>{<span class="w">PercentSimilarMolecules</span>}<span class="sc">;</span> + 843 + 844 <span class="c"># Count database entries to figure out MaxSimilarMolecules using PercentSimilarMolecules</span> + 845 <span class="c"># value...</span> + 846 <span class="i">$NumOfDatabaseMolecules</span> = <span class="n">0</span><span class="sc">;</span> + 847 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span> && <span class="k">exists</span><span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">NumOfDatabaseMolecules</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 848 <span class="c"># It might already be counted for SD file...</span> + 849 <span class="i">$NumOfDatabaseMolecules</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">NumOfDatabaseMolecules</span>}<span class="sc">;</span> + 850 <span class="s">}</span> + 851 <span class="k">else</span> <span class="s">{</span> + 852 <span class="k">print</span> <span class="q">"Calculating maximum number of similar molecules to retrieve for \"PercentSimilar\" value of \"--SimilarCountMode\" option by counting number of molecules in database fingerprints file...\n"</span><span class="sc">;</span> + 853 <span class="k">open</span> <span class="w">FINGERPRINTSFILE</span><span class="cm">,</span> <span class="q">"$FingerprintsFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $FingerprintsFile: $! \n"</span><span class="sc">;</span> + 854 <span class="j">FILETYPE:</span> <span class="s">{</span> + 855 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span><span class="s">)</span> <span class="s">{</span> + 856 <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*FINGERPRINTSFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 857 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span> + 858 <span class="i">$NumOfDatabaseMolecules</span>++<span class="sc">;</span> + 859 <span class="s">}</span> + 860 <span class="s">}</span> + 861 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 862 <span class="s">}</span> + 863 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^Text$/i</span><span class="s">)</span> <span class="s">{</span> + 864 <span class="c"># Ignore column label line...</span> + 865 <span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*FINGERPRINTSFILE</span><span class="s">)</span><span class="sc">;</span> + 866 <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*FINGERPRINTSFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 867 <span class="i">$NumOfDatabaseMolecules</span>++<span class="sc">;</span> + 868 <span class="s">}</span> + 869 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 870 <span class="s">}</span> + 871 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^FP$/i</span><span class="s">)</span> <span class="s">{</span> + 872 <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*FINGERPRINTSFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 873 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> + 874 <span class="i">$NumOfDatabaseMolecules</span>++<span class="sc">;</span> + 875 <span class="s">}</span> + 876 <span class="s">}</span> + 877 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 878 <span class="s">}</span> + 879 <span class="i">$NumOfDatabaseMolecules</span> = <span class="n">0</span><span class="sc">;</span> + 880 <span class="s">}</span> + 881 <span class="k">close</span> <span class="w">FINGERPRINTSFILE</span><span class="sc">;</span> + 882 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">NumOfDatabaseMolecules</span>} = <span class="i">$NumOfDatabaseMolecules</span><span class="sc">;</span> + 883 <span class="s">}</span> + 884 + 885 <span class="i">$MaxSimilarMolecules</span> = <span class="k">int</span> <span class="s">(</span><span class="s">(</span><span class="i">$NumOfDatabaseMolecules</span> * <span class="i">$PercentSimilarMolecules</span><span class="s">)</span>/<span class="n">100</span><span class="s">)</span><span class="sc">;</span> + 886 <span class="k">if</span> <span class="s">(</span><span class="i">$MaxSimilarMolecules</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 887 <span class="i">$MaxSimilarMolecules</span> = <span class="n">1</span><span class="sc">;</span> + 888 <span class="s">}</span> + 889 + 890 <span class="i">$OptionsInfo</span>{<span class="w">MaxSimilarMolecules</span>} = <span class="i">$MaxSimilarMolecules</span><span class="sc">;</span> + 891 <span class="s">}</span> + 892 + 893 <span class="c"># Retrieve information about fingerprints file...</span> + 894 <span class="c">#</span> +<a name="RetrieveFingerprintsFileInfo-"></a> 895 <span class="k">sub </span><span class="m">RetrieveFingerprintsFileInfo</span> <span class="s">{</span> + 896 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 897 <span class="k">my</span><span class="s">(</span><span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$FileName</span><span class="s">)</span><span class="sc">;</span> + 898 + 899 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 900 <span class="k">die</span> <span class="q">"Error: Input fingerprints file, $FingerprintsFile, doesn't exist.\n"</span><span class="sc">;</span> + 901 <span class="s">}</span> + 902 + 903 <span class="i">$FileType</span> = <span class="i">Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 904 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$FileType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 905 <span class="k">die</span> <span class="q">"Error: Input file, $FingerprintsFile, is not a fingerprints file.\n"</span><span class="sc">;</span> + 906 <span class="s">}</span> + 907 + 908 <span class="i">$InDelim</span> = <span class="q">''</span><span class="sc">;</span> + 909 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^Text$/i</span><span class="s">)</span> <span class="s">{</span> + 910 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> + 911 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 912 <span class="i">$InDelim</span> = <span class="s">(</span><span class="i">$FileExt</span> =~ <span class="q">/^tsv$/i</span><span class="s">)</span> ? <span class="q">'Tab'</span> <span class="co">:</span> <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>}<span class="sc">;</span> + 913 <span class="s">}</span> + 914 + 915 <span class="k">return</span> <span class="s">(</span><span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span> + 916 <span class="s">}</span> + 917 + 918 <span class="c"># Retrieve fingerprints file IO parameters...</span> + 919 <span class="c">#</span> +<a name="RetrieveFingerprintsFileIOParameters-"></a> 920 <span class="k">sub </span><span class="m">RetrieveFingerprintsFileIOParameters</span> <span class="s">{</span> + 921 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileMode</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 922 <span class="k">my</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span> + 923 + 924 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFileMode</span> !~ <span class="q">/^(Reference|Database)$/</span><span class="s">)</span> <span class="s">{</span> + 925 <span class="k">die</span> <span class="q">"Error: Unknown fingerprints file mode: $FingerprintsFileMode. Supported values: Reference or Database\n"</span><span class="sc">;</span> + 926 <span class="s">}</span> + 927 + 928 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 929 + 930 <span class="j">FILETYPE:</span> <span class="s">{</span> + 931 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span><span class="s">)</span> <span class="s">{</span> + 932 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsMode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">'FingerprintsFieldLabel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}FingerprintsField"</span>}<span class="cm">,</span> <span class="q">'CompoundIDMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}CompoundIDMode"</span>}<span class="cm">,</span> <span class="q">'CompoundIDFieldLabel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}CompoundIDField"</span>}<span class="cm">,</span> <span class="q">'CompoundIDPrefix'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}CompoundIDPrefix"</span>}<span class="s">)</span><span class="sc">;</span> + 933 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 934 <span class="s">}</span> + 935 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^FP$/i</span><span class="s">)</span> <span class="s">{</span> + 936 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsMode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="s">)</span><span class="sc">;</span> + 937 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 938 <span class="s">}</span> + 939 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^Text$/i</span><span class="s">)</span> <span class="s">{</span> + 940 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsMode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">'FingerprintsCol'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}FingerprintsCol"</span>}<span class="cm">,</span> <span class="q">'ColMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}ColMode"</span>}<span class="cm">,</span> <span class="q">'CompoundIDCol'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}CompoundIDCol"</span>}<span class="cm">,</span> <span class="q">'CompoundIDPrefix'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}CompoundIDPrefix"</span>}<span class="cm">,</span> <span class="q">'InDelim'</span> <span class="cm">=></span> <span class="i">$FingerprintsFilesInfo</span>{<span class="i">$FingerprintsFileMode</span>}{<span class="w">InDelim</span>}<span class="s">)</span><span class="sc">;</span> + 941 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 942 <span class="s">}</span> + 943 <span class="k">die</span> <span class="q">"Error: Fingerprints file type, $FileType, is not valid. Supported file types: SD, FP or Text\n"</span><span class="sc">;</span> + 944 <span class="s">}</span> + 945 + 946 <span class="k">return</span> <span class="i">%FingerprintsFileIOParams</span><span class="sc">;</span> + 947 <span class="s">}</span> + 948 + 949 <span class="c"># Make sure fingerprints data file contains valid dta and retrieve fingerprints string mode information...</span> + 950 <span class="c">#</span> +<a name="RetrieveFingerprintsFileFingerprintsStringInfo-"></a> 951 <span class="k">sub </span><span class="m">RetrieveFingerprintsFileFingerprintsStringInfo</span> <span class="s">{</span> + 952 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileMode</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 953 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span><span class="sc">;</span> + 954 + 955 <span class="i">$FingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="i">$FingerprintsFileMode</span>}{<span class="w">FingerprintsFileIOParameters</span>}}<span class="s">)</span><span class="sc">;</span> + 956 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="s">)</span> <span class="s">{</span> + 957 <span class="k">die</span> <span class="q">"Error: Reference fingerprints file, $FingerprintsFile, contains invalid fingerprints data.\n"</span><span class="sc">;</span> + 958 <span class="s">}</span> + 959 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->IsFingerprintsFileDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 960 <span class="k">die</span> <span class="q">"Error: Reference fingerprints file, $FingerprintsFile, contains invalid fingerprints data.\n"</span><span class="sc">;</span> + 961 <span class="s">}</span> + 962 + 963 <span class="i">$FingerprintsStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprintsStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 964 <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprintsBitVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 965 <span class="i">$FingerprintsVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprintsVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 966 + 967 <span class="i">$FirstFingerprintsStringType</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFirstFingerprintsStringType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 968 <span class="i">$FirstFingerprintsStringDescription</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFirstFingerprintsStringDescription</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 969 + 970 <span class="i">$FingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 971 + 972 <span class="k">return</span> <span class="s">(</span><span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span><span class="sc">;</span> + 973 <span class="s">}</span> + 974 + 975 <span class="c"># Retrieve output files names using reference fingerprints file name...</span> + 976 <span class="c">#</span> +<a name="RetrieveOutputFilesInfo-"></a> 977 <span class="k">sub </span><span class="m">RetrieveOutputFilesInfo</span> <span class="s">{</span> + 978 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$SDOutFileName</span><span class="cm">,</span> <span class="i">$TextOutFileName</span><span class="cm">,</span> <span class="i">$SDOutFileExt</span><span class="cm">,</span> <span class="i">$TextOutFileExt</span><span class="cm">,</span> <span class="i">$ReferenceFileName</span><span class="cm">,</span> <span class="i">$DatabaseFileName</span><span class="s">)</span><span class="sc">;</span> + 979 + 980 <span class="i">$OutputFilesInfo</span>{<span class="w">OutFileRoot</span>} = <span class="q">''</span><span class="sc">;</span> + 981 <span class="i">$OutputFilesInfo</span>{<span class="w">SDOutFileName</span>} = <span class="q">''</span><span class="sc">;</span> + 982 <span class="i">$OutputFilesInfo</span>{<span class="w">TextOutFileName</span>} = <span class="q">''</span><span class="sc">;</span> + 983 + 984 <span class="i">$FingerprintsFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FileName</span>}<span class="sc">;</span> + 985 + 986 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> + 987 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 988 + 989 <span class="i">$SDOutFileExt</span> = <span class="q">"sdf"</span><span class="sc">;</span> + 990 <span class="i">$TextOutFileExt</span> = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> ? <span class="q">"tsv"</span> <span class="co">:</span> <span class="q">"csv"</span><span class="sc">;</span> + 991 + 992 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span> <span class="s">{</span> + 993 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> + 994 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> + 995 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> + 996 <span class="s">}</span> + 997 <span class="k">else</span> <span class="s">{</span> + 998 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> + 999 <span class="s">}</span> +1000 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> +1001 <span class="s">}</span> +1002 <span class="k">else</span> <span class="s">{</span> +1003 <span class="i">$OutFileRoot</span> = <span class="q">"${FileName}SimilaritySearching"</span><span class="sc">;</span> +1004 <span class="s">}</span> +1005 +1006 <span class="i">$SDOutFileName</span> = <span class="q">"${OutFileRoot}.${SDOutFileExt}"</span><span class="sc">;</span> +1007 <span class="i">$TextOutFileName</span> = <span class="q">"${OutFileRoot}.${TextOutFileExt}"</span><span class="sc">;</span> +1008 +1009 <span class="i">$ReferenceFileName</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FileName</span>}<span class="sc">;</span> +1010 <span class="i">$DatabaseFileName</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FileName</span>}<span class="sc">;</span> +1011 +1012 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> +1013 <span class="k">if</span> <span class="s">(</span><span class="i">$SDOutFileName</span> =~ <span class="q">/^$ReferenceFileName$/i</span><span class="s">)</span> <span class="s">{</span> +1014 <span class="k">die</span> <span class="q">"Error: Same output, $SDOutFileName, and reference input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span> +1015 <span class="s">}</span> +1016 <span class="k">if</span> <span class="s">(</span><span class="i">$SDOutFileName</span> =~ <span class="q">/^$DatabaseFileName$/i</span><span class="s">)</span> <span class="s">{</span> +1017 <span class="k">die</span> <span class="q">"Error: Same output, $SDOutFileName, and database input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span> +1018 <span class="s">}</span> +1019 <span class="s">}</span> +1020 +1021 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span> +1022 <span class="k">if</span> <span class="s">(</span><span class="i">$TextOutFileName</span> =~ <span class="q">/^$ReferenceFileName$/i</span><span class="s">)</span> <span class="s">{</span> +1023 <span class="k">die</span> <span class="q">"Error: Same output, $TextOutFileName, and reference input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span> +1024 <span class="s">}</span> +1025 <span class="k">if</span> <span class="s">(</span><span class="i">$TextOutFileName</span> =~ <span class="q">/^$DatabaseFileName$/i</span><span class="s">)</span> <span class="s">{</span> +1026 <span class="k">die</span> <span class="q">"Error: Same output, $TextOutFileName, and database input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span> +1027 <span class="s">}</span> +1028 <span class="s">}</span> +1029 +1030 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span> +1031 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> +1032 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$SDOutFileName</span><span class="s">)</span> <span class="s">{</span> +1033 <span class="k">die</span> <span class="q">"Error: The output file $SDOutFileName already exists.\n"</span><span class="sc">;</span> +1034 <span class="s">}</span> +1035 <span class="s">}</span> +1036 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span> +1037 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$TextOutFileName</span><span class="s">)</span> <span class="s">{</span> +1038 <span class="k">die</span> <span class="q">"Error: The output file $TextOutFileName already exists.\n"</span><span class="sc">;</span> +1039 <span class="s">}</span> +1040 <span class="s">}</span> +1041 <span class="s">}</span> +1042 +1043 <span class="i">$OutputFilesInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$OutFileRoot</span><span class="sc">;</span> +1044 <span class="i">$OutputFilesInfo</span>{<span class="w">SDOutFileName</span>} = <span class="i">$SDOutFileName</span><span class="sc">;</span> +1045 <span class="i">$OutputFilesInfo</span>{<span class="w">TextOutFileName</span>} = <span class="i">$TextOutFileName</span><span class="sc">;</span> +1046 +1047 <span class="s">}</span> +1048 +1049 <span class="c"># Process input fingerprints file names...</span> +1050 <span class="c">#</span> +<a name="ProcessFingerprintsFileNames-"></a>1051 <span class="k">sub </span><span class="m">ProcessFingerprintsFileNames</span> <span class="s">{</span> +1052 <span class="i">@FingerprintsFilesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1053 +1054 <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> +1055 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span> +1056 <span class="s">}</span> +1057 +1058 <span class="c"># Reference fingerprints file name...</span> +1059 <span class="k">push</span> <span class="i">@FingerprintsFilesList</span><span class="cm">,</span> <span class="i">$ARGV</span>[<span class="n">0</span>]<span class="sc">;</span> +1060 +1061 <span class="c"># Database fingerprints file name...</span> +1062 <span class="k">push</span> <span class="i">@FingerprintsFilesList</span><span class="cm">,</span> <span class="i">$ARGV</span>[<span class="n">1</span>]<span class="sc">;</span> +1063 +1064 <span class="s">}</span> +1065 +1066 <span class="c"># Process option values...</span> +<a name="ProcessOptions-"></a>1067 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> +1068 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1069 +1070 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> +1071 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsMode</span>} = <span class="i">$Options</span>{<span class="w">fingerprintsmode</span>}<span class="sc">;</span> +1072 +1073 <span class="i">$OptionsInfo</span>{<span class="w">SearchMode</span>} = <span class="i">$Options</span>{<span class="w">searchmode</span>}<span class="sc">;</span> +1074 +1075 <span class="i">ProcessBitVectorComparisonOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1076 <span class="i">ProcessVectorComparisonOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1077 +1078 <span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} = <span class="i">$Options</span>{<span class="w">groupfusionrule</span>}<span class="sc">;</span> +1079 <span class="i">$OptionsInfo</span>{<span class="w">GroupFusionApplyCutoff</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">groupfusionapplycutoff</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span><span class="sc">;</span> +1080 +1081 <span class="i">$OptionsInfo</span>{<span class="w">SimilarCountMode</span>} = <span class="i">$Options</span>{<span class="w">similarcountmode</span>}<span class="sc">;</span> +1082 <span class="i">$OptionsInfo</span>{<span class="w">NumOfSimilarMolecules</span>} = <span class="i">$Options</span>{<span class="w">numofsimilarmolecules</span>}<span class="sc">;</span> +1083 <span class="i">$OptionsInfo</span>{<span class="w">PercentSimilarMolecules</span>} = <span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>}<span class="sc">;</span> +1084 +1085 <span class="c"># Set MaxSimilarMolecules to NumOfSimilarMolecules. For PercentSimilar value of SimilarCountMode,</span> +1086 <span class="c"># it'll be overwritten using number of entries in database fingerprints file and value of PercentSimilarMolecules...</span> +1087 <span class="c">#</span> +1088 <span class="i">$OptionsInfo</span>{<span class="w">MaxSimilarMolecules</span>} = <span class="i">$OptionsInfo</span>{<span class="w">NumOfSimilarMolecules</span>}<span class="sc">;</span> +1089 +1090 <span class="i">$OptionsInfo</span>{<span class="w">SimilarityCutoff</span>} = <span class="i">$Options</span>{<span class="w">similaritycutoff</span>}<span class="sc">;</span> +1091 <span class="i">$OptionsInfo</span>{<span class="w">DistanceCutoff</span>} = <span class="i">$Options</span>{<span class="w">distancecutoff</span>}<span class="sc">;</span> +1092 +1093 <span class="i">$OptionsInfo</span>{<span class="w">kNN</span>} = <span class="i">$Options</span>{<span class="w">knn</span>}<span class="sc">;</span> +1094 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">knn</span>} !~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> +1095 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">knn</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1096 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{knn}, for option \"-k, --KNN\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> +1097 <span class="s">}</span> +1098 <span class="s">}</span> +1099 +1100 <span class="i">ProcessReferenceFingerprintsDataOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1101 <span class="i">ProcessDatabaseFingerprintsDataOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1102 +1103 <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span> +1104 +1105 <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>} = <span class="i">$Options</span>{<span class="w">indelim</span>}<span class="sc">;</span> +1106 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/tab/i</span> <span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span><span class="s">)</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span> +1107 <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> +1108 +1109 <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span> +1110 <span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(SD|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> +1111 <span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(Text|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> +1112 +1113 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> +1114 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> +1115 +1116 <span class="i">$OptionsInfo</span>{<span class="w">Fast</span>} = <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> +1117 <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>} = <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> +1118 +1119 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span> +1120 <span class="s">}</span> +1121 +1122 <span class="c"># Process options related to comparion of bit vector strings...</span> +1123 <span class="c">#</span> +<a name="ProcessBitVectorComparisonOptions-"></a>1124 <span class="k">sub </span><span class="m">ProcessBitVectorComparisonOptions</span> <span class="s">{</span> +1125 <span class="c"># Setup supported bit vector similarity coefficients for bit vector strings...</span> +1126 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="cm">,</span> <span class="i">$SupportedComparisonMeasure</span><span class="cm">,</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresNameMap</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresMethodMap</span><span class="s">)</span><span class="sc">;</span> +1127 +1128 <span class="i">@SupportedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1129 <span class="i">%SupportedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1130 <span class="i">%SupportedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1131 +1132 <span class="k">for</span> <span class="i">$SupportedComparisonMeasure</span> <span class="s">(</span><span class="i">Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1133 <span class="c"># Similarity coefficient function/method names contain "Coefficient" in their names.</span> +1134 <span class="c"># So take 'em out and setup a map to original function/method name...</span> +1135 <span class="i">$ComparisonMeasure</span> = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span> +1136 <span class="i">$ComparisonMeasure</span> =~ <span class="q">s/Coefficient$//</span><span class="sc">;</span> +1137 +1138 <span class="k">push</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="sc">;</span> +1139 <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$ComparisonMeasure</span><span class="sc">;</span> +1140 <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span> +1141 <span class="s">}</span> +1142 +1143 <span class="c"># Setup similarity coefficient to use for calculating similarity matrices for bit vector strings...</span> +1144 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="cm">,</span> <span class="i">$SpecifiedComparisonMeasureName</span><span class="cm">,</span> <span class="i">$SpecifiedComparisonMeasureMethod</span><span class="s">)</span><span class="sc">;</span> +1145 +1146 <span class="i">$SpecifiedComparisonMeasureName</span> = <span class="q">''</span><span class="sc">;</span> +1147 <span class="i">$SpecifiedComparisonMeasureMethod</span> = <span class="q">''</span><span class="sc">;</span> +1148 +1149 <span class="i">$SpecifiedMeasure</span> = <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>}<span class="sc">;</span> +1150 +1151 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>} <span class="s">)</span> <span class="s">{</span> +1152 <span class="k">die</span> <span class="q">"Error: The value specified, $SpecifiedMeasure, for option \"-b --BitVectorComparisonMode\" is not valid.\nAllowed values:"</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> +1153 <span class="s">}</span> +1154 +1155 <span class="i">$SpecifiedComparisonMeasureMethod</span> = <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span> +1156 <span class="i">$SpecifiedComparisonMeasureName</span> = <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span> +1157 +1158 <span class="i">$OptionsInfo</span>{<span class="w">BitVectorComparisonMode</span>} = <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>}<span class="sc">;</span> +1159 +1160 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonMeasure</span>} = <span class="i">$SpecifiedMeasure</span><span class="sc">;</span> +1161 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonMeasureName</span>} = <span class="i">$SpecifiedComparisonMeasureName</span><span class="sc">;</span> +1162 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonMeasureMethod</span>} = <span class="i">$SpecifiedComparisonMeasureMethod</span><span class="sc">;</span> +1163 +1164 <span class="c"># Make sure valid alpha parameter is specified for Tversky calculation...</span> +1165 <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>} = <span class="q">''</span><span class="sc">;</span> +1166 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedMeasure</span> =~ <span class="q">/^(TverskySimilarity|WeightedTverskySimilarity)$/i</span><span class="s">)</span> <span class="s">{</span> +1167 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">alpha</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1168 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"-a, --alpha\" option in \"TverskySimilarity or WeightedTverskySimilarity\" \"-m --mode\". \n"</span><span class="sc">;</span> +1169 <span class="s">}</span> +1170 <span class="k">my</span><span class="s">(</span><span class="i">$Alpha</span><span class="s">)</span><span class="sc">;</span> +1171 <span class="i">$Alpha</span> = <span class="i">$Options</span>{<span class="w">alpha</span>}<span class="sc">;</span> +1172 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$Alpha</span><span class="s">)</span> && <span class="i">$Alpha</span> >=<span class="n">0</span> && <span class="i">$Alpha</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1173 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{alpha}, for option \"-a, --alpha\" is not valid. Allowed values: >= 0 and <= 1\n"</span><span class="sc">;</span> +1174 <span class="s">}</span> +1175 <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>} = <span class="i">$Alpha</span><span class="sc">;</span> +1176 <span class="s">}</span> +1177 +1178 <span class="c"># Make sure valid beta parameter is specified for WeightedTanimoto and WeightedTversky</span> +1179 <span class="c"># calculations...</span> +1180 <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>} = <span class="q">''</span><span class="sc">;</span> +1181 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedMeasure</span> =~ <span class="q">/^(WeightedTverskySimilarity|WeightedTanimotoSimilarity)$/i</span><span class="s">)</span> <span class="s">{</span> +1182 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">beta</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1183 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"-b, --beta\" option in \"WeightedTverskySimilarity or WeightedTanimotoSimilarity\" \"-m --mode\". \n"</span><span class="sc">;</span> +1184 <span class="s">}</span> +1185 <span class="k">my</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span><span class="sc">;</span> +1186 <span class="i">$Beta</span> = <span class="i">$Options</span>{<span class="w">beta</span>}<span class="sc">;</span> +1187 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span> && <span class="i">$Beta</span> >=<span class="n">0</span> && <span class="i">$Beta</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1188 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{beta}, for option \"-b, --beta\" is not valid. Allowed values: >= 0 and <= 1\n"</span><span class="sc">;</span> +1189 <span class="s">}</span> +1190 <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>} = <span class="i">$Beta</span><span class="sc">;</span> +1191 <span class="s">}</span> +1192 <span class="s">}</span> +1193 +1194 <span class="c"># Process options related to comparion of vector strings...</span> +1195 <span class="c">#</span> +<a name="ProcessVectorComparisonOptions-"></a>1196 <span class="k">sub </span><span class="m">ProcessVectorComparisonOptions</span> <span class="s">{</span> +1197 <span class="c"># Setup specified similarity coefficients for vector strings..</span> +1198 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="cm">,</span> <span class="i">$SupportedComparisonMeasure</span><span class="cm">,</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresNameMap</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresMethodMap</span><span class="s">)</span><span class="sc">;</span> +1199 +1200 <span class="i">@SupportedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1201 <span class="i">%SupportedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1202 <span class="i">%SupportedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1203 <span class="k">for</span> <span class="i">$SupportedComparisonMeasure</span> <span class="s">(</span><span class="i">Fingerprints::FingerprintsVector::GetSupportedDistanceAndSimilarityCoefficients</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1204 <span class="c"># Similarity and distance coefficient function/method names contain "Coefficient" in their names.</span> +1205 <span class="c"># So take 'em out and setup a map to original function/method name...</span> +1206 <span class="i">$ComparisonMeasure</span> = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span> +1207 <span class="k">if</span> <span class="s">(</span><span class="i">$ComparisonMeasure</span> =~ <span class="q">/Coefficient$/i</span><span class="s">)</span> <span class="s">{</span> +1208 <span class="i">$ComparisonMeasure</span> =~ <span class="q">s/Coefficient$//i</span><span class="sc">;</span> +1209 <span class="s">}</span> +1210 <span class="k">push</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="sc">;</span> +1211 <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$ComparisonMeasure</span><span class="sc">;</span> +1212 <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span> +1213 <span class="s">}</span> +1214 +1215 <span class="c"># Setup a list of similarity coefficients to use for calculating similarity matrices for bit vector strings...</span> +1216 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="cm">,</span> <span class="i">$SpecifiedComparisonMeasureName</span><span class="cm">,</span> <span class="i">$SpecifiedComparisonMeasureMethod</span><span class="s">)</span><span class="sc">;</span> +1217 +1218 <span class="i">$SpecifiedComparisonMeasureName</span> = <span class="q">''</span><span class="sc">;</span> +1219 <span class="i">$SpecifiedComparisonMeasureMethod</span> = <span class="q">''</span><span class="sc">;</span> +1220 +1221 <span class="i">$SpecifiedMeasure</span> = <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>}<span class="sc">;</span> +1222 <span class="i">$SpecifiedMeasure</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> +1223 +1224 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span><span class="s">(</span><span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1225 <span class="k">die</span> <span class="q">"Error: The value specified, $SpecifiedMeasure, for option \"-v --VectorComparisonMode\" is not valid.\nAllowed values:"</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> +1226 <span class="s">}</span> +1227 +1228 <span class="i">$SpecifiedComparisonMeasureMethod</span> = <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span> +1229 <span class="i">$SpecifiedComparisonMeasureName</span> = <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span> +1230 +1231 <span class="i">$OptionsInfo</span>{<span class="w">VectorComparisonMode</span>} = <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>}<span class="sc">;</span> +1232 +1233 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMeasure</span>} = <span class="i">$SpecifiedMeasure</span><span class="sc">;</span> +1234 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMeasuresName</span>} = <span class="i">$SpecifiedComparisonMeasureName</span><span class="sc">;</span> +1235 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMeasuresMethod</span>} = <span class="i">$SpecifiedComparisonMeasureMethod</span><span class="sc">;</span> +1236 +1237 <span class="c"># Setup specified vector comparison calculation modes...</span> +1238 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedFormulism</span><span class="s">)</span><span class="sc">;</span> +1239 +1240 <span class="i">$SpecifiedFormulism</span> = <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>}<span class="sc">;</span> +1241 <span class="i">$SpecifiedFormulism</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> +1242 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedFormulism</span> !~ <span class="q">/^(AlgebraicForm|BinaryForm|SetTheoreticForm)$/i</span><span class="s">)</span> <span class="s">{</span> +1243 <span class="k">die</span> <span class="q">"Error: The value specified, $SpecifiedFormulism, for option \"--VectorComparisonFormulism\" is not valid. Allowed values: AlgebraicForm, BinaryForm or SetTheoreticForm\n"</span><span class="sc">;</span> +1244 <span class="s">}</span> +1245 +1246 <span class="i">$OptionsInfo</span>{<span class="w">VectorComparisonFormulism</span>} = <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>}<span class="sc">;</span> +1247 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMode</span>} = <span class="i">$SpecifiedFormulism</span><span class="sc">;</span> +1248 +1249 <span class="s">}</span> +1250 +1251 <span class="c"># Process options related to data retrieval from reference fingerprints SD and CSV/TSV</span> +1252 <span class="c"># text files...</span> +1253 <span class="c">#</span> +<a name="ProcessReferenceFingerprintsDataOptions-"></a>1254 <span class="k">sub </span><span class="m">ProcessReferenceFingerprintsDataOptions</span> <span class="s">{</span> +1255 +1256 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDPrefix</span>} = <span class="i">$Options</span>{<span class="w">referencecompoundidprefix</span>} ? <span class="i">$Options</span>{<span class="w">referencecompoundidprefix</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span> +1257 +1258 <span class="c"># Compound ID and fingerprints column options for text files...</span> +1259 +1260 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceColMode</span>} = <span class="i">$Options</span>{<span class="w">referencecolmode</span>}<span class="sc">;</span> +1261 +1262 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1263 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecolmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span> +1264 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1265 <span class="k">die</span> <span class="q">"Error: Column value, $Options{referencecompoundidcol}, specified using \"--ReferenceCompoundIDCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span> +1266 <span class="s">}</span> +1267 <span class="s">}</span> +1268 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDCol</span>} = <span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="sc">;</span> +1269 <span class="s">}</span> +1270 <span class="k">else</span> <span class="s">{</span> +1271 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> +1272 <span class="s">}</span> +1273 +1274 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1275 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecolmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span> +1276 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1277 <span class="k">die</span> <span class="q">"Error: Column value, $Options{referencefingerprintscol}, specified using \"--ReferenceFingerprintsCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span> +1278 <span class="s">}</span> +1279 <span class="s">}</span> +1280 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceFingerprintsCol</span>} = <span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="sc">;</span> +1281 <span class="s">}</span> +1282 <span class="k">else</span> <span class="s">{</span> +1283 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceFingerprintsCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> +1284 <span class="s">}</span> +1285 +1286 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="s">)</span> && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1287 <span class="k">if</span> <span class="s">(</span><span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="s">)</span> && <span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1288 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>} == <span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1289 <span class="k">die</span> <span class="q">"Error: Values specified using \"--ReferenceCompoundIDCol\" and \"--ReferenceFingerprintsCol\", $Options{referencecompoundidcol}, must be different.\n"</span><span class="sc">;</span> +1290 <span class="s">}</span> +1291 <span class="s">}</span> +1292 <span class="k">else</span> <span class="s">{</span> +1293 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>} <span class="k">eq</span> <span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1294 <span class="k">die</span> <span class="q">"Error: Values specified using \"--ReferenceCompoundIDCol\" and \"--ReferenceFingerprintsCol\", $Options{referencecompoundidcol}, must be different.\n"</span><span class="sc">;</span> +1295 <span class="s">}</span> +1296 <span class="s">}</span> +1297 <span class="s">}</span> +1298 +1299 <span class="c"># Compound ID and fingerprints field options for SD files...</span> +1300 +1301 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">referencecompoundidmode</span>}<span class="sc">;</span> +1302 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDField</span>} = <span class="q">''</span><span class="sc">;</span> +1303 +1304 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidmode</span>} =~ <span class="q">/^DataField$/i</span> && !<span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>}<span class="s">)</span> <span class="s">{</span> +1305 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--ReferenceCompoundIDField\" option in \"DataField\" \"--ReferenceCompoundIDMode\". \n"</span><span class="sc">;</span> +1306 <span class="s">}</span> +1307 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>}<span class="s">)</span> <span class="s">{</span> +1308 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDField</span>} = <span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>}<span class="sc">;</span> +1309 <span class="s">}</span> +1310 +1311 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1312 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceFingerprintsField</span>} = <span class="i">$Options</span>{<span class="w">referencefingerprintsfield</span>}<span class="sc">;</span> +1313 <span class="s">}</span> +1314 <span class="k">else</span> <span class="s">{</span> +1315 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceFingerprintsField</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> +1316 <span class="s">}</span> +1317 +1318 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>} && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1319 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>} <span class="k">eq</span> <span class="i">$Options</span>{<span class="w">referencefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1320 <span class="k">die</span> <span class="q">"Error: Values specified using \"--ReferenceCompoundIDField\" and \"--ReferenceFingerprintsfield\", $Options{referencecompoundidfield}, must be different.\n"</span><span class="sc">;</span> +1321 <span class="s">}</span> +1322 <span class="s">}</span> +1323 +1324 <span class="s">}</span> +1325 +1326 <span class="c"># Process options related to data retrieval from database fingerprints SD and CSV/TSV</span> +1327 <span class="c"># text files...</span> +1328 <span class="c">#</span> +<a name="ProcessDatabaseFingerprintsDataOptions-"></a>1329 <span class="k">sub </span><span class="m">ProcessDatabaseFingerprintsDataOptions</span> <span class="s">{</span> +1330 +1331 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDPrefix</span>} = <span class="i">$Options</span>{<span class="w">databasecompoundidprefix</span>} ? <span class="i">$Options</span>{<span class="w">databasecompoundidprefix</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span> +1332 +1333 <span class="c"># Compound ID and fingerprints column options for text files...</span> +1334 +1335 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseColMode</span>} = <span class="i">$Options</span>{<span class="w">databasecolmode</span>}<span class="sc">;</span> +1336 +1337 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1338 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecolmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span> +1339 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1340 <span class="k">die</span> <span class="q">"Error: Column value, $Options{databasecompoundidcol}, specified using \"--DatabaseCompoundIDCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span> +1341 <span class="s">}</span> +1342 <span class="s">}</span> +1343 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDCol</span>} = <span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="sc">;</span> +1344 <span class="s">}</span> +1345 <span class="k">else</span> <span class="s">{</span> +1346 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> +1347 <span class="s">}</span> +1348 +1349 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1350 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecolmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span> +1351 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1352 <span class="k">die</span> <span class="q">"Error: Column value, $Options{databasefingerprintscol}, specified using \"--DatabaseFingerprintsCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span> +1353 <span class="s">}</span> +1354 <span class="s">}</span> +1355 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseFingerprintsCol</span>} = <span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="sc">;</span> +1356 <span class="s">}</span> +1357 <span class="k">else</span> <span class="s">{</span> +1358 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseFingerprintsCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> +1359 <span class="s">}</span> +1360 +1361 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="s">)</span> && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1362 <span class="k">if</span> <span class="s">(</span><span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="s">)</span> && <span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1363 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>} == <span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1364 <span class="k">die</span> <span class="q">"Error: Values specified using \"--DatabaseCompoundIDCol\" and \"--DatabaseFingerprintsCol\", $Options{databasecompoundidcol}, must be different.\n"</span><span class="sc">;</span> +1365 <span class="s">}</span> +1366 <span class="s">}</span> +1367 <span class="k">else</span> <span class="s">{</span> +1368 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>} <span class="k">eq</span> <span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1369 <span class="k">die</span> <span class="q">"Error: Values specified using \"--DatabaseCompoundIDCol\" and \"--DatabaseFingerprintsCol\", $Options{databasecompoundidcol}, must be different.\n"</span><span class="sc">;</span> +1370 <span class="s">}</span> +1371 <span class="s">}</span> +1372 <span class="s">}</span> +1373 +1374 <span class="c"># Database data column options for text files...</span> +1375 +1376 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataColsMode</span>} = <span class="i">$Options</span>{<span class="w">databasedatacolsmode</span>}<span class="sc">;</span> +1377 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataCols</span>} = <span class="q">''</span><span class="sc">;</span> +1378 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataCols</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1379 +1380 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatacolsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> +1381 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseDataCols</span><span class="cm">,</span> <span class="i">$DatabaseColNum</span><span class="cm">,</span> <span class="i">@SpecifiedDataCols</span><span class="s">)</span><span class="sc">;</span> +1382 +1383 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">databasedatacols</span>}<span class="s">)</span> <span class="s">{</span> +1384 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DatabaseDataCols\" option in \"Specify\" \"--DatabaseDataColsMode\". \n"</span><span class="sc">;</span> +1385 <span class="s">}</span> +1386 <span class="i">$DatabaseDataCols</span> = <span class="i">$Options</span>{<span class="w">databasedatacols</span>}<span class="sc">;</span> +1387 +1388 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecolmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span> +1389 <span class="i">$DatabaseDataCols</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> +1390 <span class="i">@SpecifiedDataCols</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$DatabaseDataCols</span><span class="sc">;</span> +1391 <span class="k">for</span> <span class="i">$DatabaseColNum</span> <span class="s">(</span><span class="i">@SpecifiedDataCols</span><span class="s">)</span> <span class="s">{</span> +1392 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$DatabaseColNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1393 <span class="k">die</span> <span class="q">"Error: Column value, $DatabaseColNum, specified using \"--DatabaseDataCols\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span> +1394 <span class="s">}</span> +1395 <span class="s">}</span> +1396 <span class="s">}</span> +1397 <span class="k">else</span> <span class="s">{</span> +1398 <span class="i">@SpecifiedDataCols</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$DatabaseDataCols</span><span class="sc">;</span> +1399 <span class="s">}</span> +1400 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataCols</span>} = <span class="i">$DatabaseDataCols</span><span class="sc">;</span> +1401 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataCols</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataCols</span><span class="sc">;</span> +1402 <span class="s">}</span> +1403 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatacolsmode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> +1404 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataCols</span>} = <span class="q">'All'</span><span class="sc">;</span> +1405 <span class="s">}</span> +1406 +1407 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataColsMode</span>} =~ <span class="q">/^Specify$/i</span> && !<span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataCols</span>}<span class="s">)</span> <span class="s">{</span> +1408 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DatabaseDataCols\" option in \"Specify\" \"--DatabaseDataColsMode\". \n"</span><span class="sc">;</span> +1409 <span class="s">}</span> +1410 +1411 <span class="c"># Compound ID and fingerprints field options for SD files...</span> +1412 +1413 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">databasecompoundidmode</span>}<span class="sc">;</span> +1414 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDField</span>} = <span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>} ? <span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> +1415 +1416 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span> +1417 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>}<span class="s">)</span> <span class="s">{</span> +1418 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DatabaseCompoundIDField\" option in \"DataField\" \"--DatabaseCompoundIDMode\". \n"</span><span class="sc">;</span> +1419 <span class="s">}</span> +1420 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDField</span>} = <span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>}<span class="sc">;</span> +1421 <span class="s">}</span> +1422 +1423 +1424 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1425 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseFingerprintsField</span>} = <span class="i">$Options</span>{<span class="w">databasefingerprintsfield</span>}<span class="sc">;</span> +1426 <span class="s">}</span> +1427 <span class="k">else</span> <span class="s">{</span> +1428 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseFingerprintsField</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> +1429 <span class="s">}</span> +1430 +1431 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>} && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1432 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>} <span class="k">eq</span> <span class="i">$Options</span>{<span class="w">databasefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1433 <span class="k">die</span> <span class="q">"Error: Values specified using \"--DatabaseCompoundIDField\" and \"--DatabaseFingerprintsfield\", $Options{databasecompoundidfield}, must be different.\n"</span><span class="sc">;</span> +1434 <span class="s">}</span> +1435 <span class="s">}</span> +1436 +1437 <span class="c"># Database data field options for SD files...</span> +1438 +1439 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">databasedatafieldsmode</span>}<span class="sc">;</span> +1440 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFields</span>} = <span class="q">''</span><span class="sc">;</span> +1441 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1442 +1443 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatafieldsmode</span>} =~ <span class="q">/^Specify$/i</span> && !<span class="i">$Options</span>{<span class="w">databasedatafields</span>}<span class="s">)</span> <span class="s">{</span> +1444 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DatabaseDataFields\" option in \"Specify\" \"--DatabaseDataFieldsMode\". \n"</span><span class="sc">;</span> +1445 <span class="s">}</span> +1446 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatafields</span>}<span class="s">)</span> <span class="s">{</span> +1447 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span> +1448 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFields</span>} = <span class="i">$Options</span>{<span class="w">databasedatafields</span>}<span class="sc">;</span> +1449 +1450 <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">databasedatafields</span>}<span class="sc">;</span> +1451 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span> +1452 <span class="s">}</span> +1453 <span class="s">}</span> +1454 +1455 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> +<a name="SetupScriptUsage-"></a>1456 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> +1457 +1458 <span class="c"># Retrieve all the options...</span> +1459 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1460 +1461 <span class="i">$Options</span>{<span class="w">alpha</span>} = <span class="n">0.5</span><span class="sc">;</span> +1462 <span class="i">$Options</span>{<span class="w">beta</span>} = <span class="n">1</span><span class="sc">;</span> +1463 +1464 <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>} = <span class="q">"TanimotoSimilarity"</span><span class="sc">;</span> +1465 +1466 <span class="i">$Options</span>{<span class="w">databasecolmode</span>} = <span class="q">'colnum'</span><span class="sc">;</span> +1467 +1468 <span class="i">$Options</span>{<span class="w">databasecompoundidprefix</span>} = <span class="q">'Cmpd'</span><span class="sc">;</span> +1469 <span class="i">$Options</span>{<span class="w">databasecompoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span> +1470 +1471 <span class="i">$Options</span>{<span class="w">databasedatacolsmode</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span> +1472 <span class="i">$Options</span>{<span class="w">databasedatafieldsmode</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span> +1473 +1474 <span class="i">$Options</span>{<span class="w">distancecutoff</span>} = <span class="n">10</span><span class="sc">;</span> +1475 +1476 <span class="i">$Options</span>{<span class="w">referencecolmode</span>} = <span class="q">'colnum'</span><span class="sc">;</span> +1477 +1478 <span class="i">$Options</span>{<span class="w">referencecompoundidprefix</span>} = <span class="q">'Cmpd'</span><span class="sc">;</span> +1479 <span class="i">$Options</span>{<span class="w">referencecompoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span> +1480 +1481 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span> +1482 +1483 <span class="i">$Options</span>{<span class="w">fingerprintsmode</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> +1484 <span class="i">$Options</span>{<span class="w">groupfusionrule</span>} = <span class="q">'Max'</span><span class="sc">;</span> +1485 <span class="i">$Options</span>{<span class="w">groupfusionapplycutoff</span>} = <span class="q">'Yes'</span><span class="sc">;</span> +1486 +1487 <span class="i">$Options</span>{<span class="w">knn</span>} = <span class="q">'All'</span><span class="sc">;</span> +1488 +1489 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'MultipleReferences'</span><span class="sc">;</span> +1490 +1491 <span class="i">$Options</span>{<span class="w">numofsimilarmolecules</span>} = <span class="n">10</span><span class="sc">;</span> +1492 <span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>} = <span class="n">1</span><span class="sc">;</span> +1493 +1494 <span class="i">$Options</span>{<span class="w">indelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> +1495 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> +1496 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span> +1497 +1498 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">'text'</span><span class="sc">;</span> +1499 +1500 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span> +1501 +1502 <span class="i">$Options</span>{<span class="w">searchmode</span>} = <span class="q">'SimilaritySearch'</span><span class="sc">;</span> +1503 +1504 <span class="i">$Options</span>{<span class="w">similarcountmode</span>} = <span class="q">'NumOfSimilar'</span><span class="sc">;</span> +1505 +1506 <span class="i">$Options</span>{<span class="w">similaritycutoff</span>} = <span class="n">0.75</span><span class="sc">;</span> +1507 +1508 <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>} = <span class="q">'TanimotoSimilarity'</span><span class="sc">;</span> +1509 <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>} = <span class="q">'AlgebraicForm'</span><span class="sc">;</span> +1510 +1511 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"alpha=f"</span><span class="cm">,</span> <span class="q">"beta=f"</span><span class="cm">,</span> <span class="q">"bitvectorcomparisonmode|b=s"</span><span class="cm">,</span> <span class="q">"databasecolmode=s"</span><span class="cm">,</span> <span class="q">"databasecompoundidcol=s"</span><span class="cm">,</span> <span class="q">"databasecompoundidprefix=s"</span><span class="cm">,</span> <span class="q">"databasecompoundidfield=s"</span><span class="cm">,</span> <span class="q">"databasecompoundidmode=s"</span><span class="cm">,</span> <span class="q">"databasedatacols=s"</span><span class="cm">,</span> <span class="q">"databasedatacolsmode=s"</span><span class="cm">,</span> <span class="q">"databasedatafields=s"</span><span class="cm">,</span> <span class="q">"databasedatafieldsmode=s"</span><span class="cm">,</span> <span class="q">"databasefingerprintscol=s"</span><span class="cm">,</span> <span class="q">"databasefingerprintsfield=s"</span><span class="cm">,</span> <span class="q">"distancecutoff=f"</span><span class="cm">,</span> <span class="q">"detail|d=i"</span><span class="cm">,</span> <span class="q">"fast|f"</span><span class="cm">,</span> <span class="q">"fingerprintsmode=s"</span><span class="cm">,</span> <span class="q">"groupfusionrule|g=s"</span><span class="cm">,</span> <span class="cm">,</span> <span class="q">"groupfusionapplycutoff=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"indelim=s"</span><span class="cm">,</span> <span class="q">"knn|k=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"numofsimilarmolecules|n=i"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"output=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"percentsimilarmolecules|p=f"</span><span class="cm">,</span> <span class="q">"precision=s"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"referencecolmode=s"</span><span class="cm">,</span> <span class="q">"referencecompoundidcol=s"</span><span class="cm">,</span> <span class="q">"referencecompoundidprefix=s"</span><span class="cm">,</span> <span class="q">"referencecompoundidfield=s"</span><span class="cm">,</span> <span class="q">"referencecompoundidmode=s"</span><span class="cm">,</span> <span class="q">"referencefingerprintscol=s"</span><span class="cm">,</span> <span class="q">"referencefingerprintsfield=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"searchmode|s=s"</span><span class="cm">,</span> <span class="q">"similarcountmode=s"</span><span class="cm">,</span> <span class="q">"similaritycutoff=f"</span><span class="cm">,</span> <span class="q">"vectorcomparisonmode|v=s"</span><span class="cm">,</span> <span class="q">"vectorcomparisonformulism=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1512 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> +1513 <span class="s">}</span> +1514 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> +1515 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> +1516 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> +1517 <span class="s">}</span> +1518 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span> +1519 <span class="s">}</span> +1520 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecolmode</span>} !~ <span class="q">/^(ColNum|ColLabel)$/i</span><span class="s">)</span> <span class="s">{</span> +1521 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{databasecolmode}, for option \"--DatabaseColMode\" is not valid. Allowed values: ColNum, or ColLabel\n"</span><span class="sc">;</span> +1522 <span class="s">}</span> +1523 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span> +1524 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{databasecompoundidmode}, for option \"--DatabaseCompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span> +1525 <span class="s">}</span> +1526 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatacolsmode</span>} !~ <span class="q">/^(All|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span> +1527 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{databasedatacolsmode}, for option \"--DatabaseDataColsMode\" is not valid. Allowed values: All, Specify, or CompoundID\n"</span><span class="sc">;</span> +1528 <span class="s">}</span> +1529 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span> +1530 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{databasedatafieldsmode}, for option \"--DatabaseDataFieldsMode\" is not valid. Allowed values: All, Common, Specify, or CompoundID\n"</span><span class="sc">;</span> +1531 <span class="s">}</span> +1532 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1533 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{detail}, for option \"-d, --detail\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> +1534 <span class="s">}</span> +1535 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintsmode</span>} !~ <span class="q">/^(AutoDetect|FingerprintsBitVectorString|FingerprintsVectorString)$/i</span><span class="s">)</span> <span class="s">{</span> +1536 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{fingerprintsmode}, for option \"--FingerprintsMode\" is not valid. Allowed values: AutoDetect, FingerprintsBitVectorString or FingerprintsVectorString \n"</span><span class="sc">;</span> +1537 <span class="s">}</span> +1538 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">groupfusionrule</span>} !~ <span class="q">/^(Max|Min|Mean|Median|Sum|Euclidean)$/i</span><span class="s">)</span> <span class="s">{</span> +1539 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{groupfusionrule}, for option \"-g, --GroupFusionRule\" is not valid. Allowed values: Max, Min, Mean, Median, Sum, Euclidean\n"</span><span class="sc">;</span> +1540 <span class="s">}</span> +1541 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">groupfusionapplycutoff</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> +1542 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"--GroupFusionApplyCutoff\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> +1543 <span class="s">}</span> +1544 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} !~ <span class="q">/^(comma|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span> +1545 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{indelim}, for option \"--InDelim\" is not valid. Allowed values: comma, or semicolon\n"</span><span class="sc">;</span> +1546 <span class="s">}</span> +1547 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(IndividualReference|MultipleReferences)$/i</span><span class="s">)</span> <span class="s">{</span> +1548 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: IndividualReference, MultipleReferences\n"</span><span class="sc">;</span> +1549 <span class="s">}</span> +1550 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">numofsimilarmolecules</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1551 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{numofsimilarmolecules}, for option \"-n, --NumOfSimilarMolecules\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> +1552 <span class="s">}</span> +1553 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span> +1554 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--OutDelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span> +1555 <span class="s">}</span> +1556 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|text|both)$/i</span><span class="s">)</span> <span class="s">{</span> +1557 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, text, or both\n"</span><span class="sc">;</span> +1558 <span class="s">}</span> +1559 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>}<span class="s">)</span> && <span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>} > <span class="n">0</span> && <span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>} <= <span class="n">100</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1560 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{percentsimilarmolecules}, for option \"-p, --PercentSimilarMolecules\" is not valid. Allowed values: > 0 and <= 100 \n"</span><span class="sc">;</span> +1561 <span class="s">}</span> +1562 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> +1563 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> +1564 <span class="s">}</span> +1565 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1566 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{precision}, for option \"--precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> +1567 <span class="s">}</span> +1568 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecolmode</span>} !~ <span class="q">/^(ColNum|ColLabel)$/i</span><span class="s">)</span> <span class="s">{</span> +1569 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{referencecolmode}, for option \"--ReferenceColMode\" is not valid. Allowed values: ColNum, or ColLabel\n"</span><span class="sc">;</span> +1570 <span class="s">}</span> +1571 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span> +1572 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{referencecompoundidmode}, for option \"--ReferenceCompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span> +1573 <span class="s">}</span> +1574 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">searchmode</span>} !~ <span class="q">/^(SimilaritySearch|DissimilaritySearch)$/i</span><span class="s">)</span> <span class="s">{</span> +1575 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{searchmode}, for option \"-s, --SearchMode\" is not valid. Allowed values: SimilaritySearch, DissimilaritySearch \n"</span><span class="sc">;</span> +1576 <span class="s">}</span> +1577 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">similarcountmode</span>} !~ <span class="q">/^(NumOfSimilar|PercentSimilar)$/i</span><span class="s">)</span> <span class="s">{</span> +1578 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{similarcountmode}, for option \"--SimilarCountMode\" is not valid. Allowed values: NumOfSimilar, PercentSimilar \n"</span><span class="sc">;</span> +1579 <span class="s">}</span> +1580 <span class="s">}</span> +1581 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>