mayatool3_test2: docs/scripts/html/code/SimilaritySearchingFingerprints.html comparison

comparison docs/scripts/html/code/SimilaritySearchingFingerprints.html @ 0:4816e4a8ae95 draft default tip

Uploaded

author	deepakjadmin
date	Wed, 20 Jan 2016 09:23:18 -0500
parents
children

comparison

equal deleted inserted replaced

--1:000000000000
+:4816e4a8ae95
+<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 $</span>
+6 <span class="c">#</span>
+7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+8 <span class="c">#</span>
+9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+10 <span class="c">#</span>
+11 <span class="c"># This file is part of MayaChemTools.</span>
+12 <span class="c">#</span>
+13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+16 <span class="c"># later version.</span>
+17 <span class="c">#</span>
+18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+21 <span class="c"># details.</span>
+22 <span class="c">#</span>
+23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+27 <span class="c">#</span>
+28
+29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</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">$0</span><span class="s">)</span><span class="sc">;</span>
+51 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</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">&quot;$FindBin::Bin/$ScriptName&quot;</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">&quot;Processing options...\n&quot;</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">&quot;Checking and retrieving information from reference and database fingerprints files...\n&quot;</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">&quot;Performing similarity search...\n&quot;</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">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+80
+81 <span class="i">$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">$StartTime</span><span class="s">)</span><span class="sc">;</span>
+83 <span class="k">print</span> <span class="q">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</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">&quot;\nProcessing fingerprints data for reference molecules...\n&quot;</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">&quot;Processing fingerprints data for database molecules...\n&quot;</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">$DatabaseFingerprintsFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+110
+111   <span class="i">@ComparisonValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+112
+113   <span class="j">DATABASEFP:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$DatabaseFingerprintsFileIO</span><span class="i">-&gt;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">-&gt;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">$DatabaseFingerprintsFileIO</span><span class="i">-&gt;GetFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+121     <span class="i">$DatabaseCmpdID</span> = <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">-&gt;GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+122
+123     <span class="k">if</span> <span class="s">(</span><span class="i">$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">$SimilaritySearchInfo</span>{<span class="w">ReferenceCmpdIDsRef</span>}-&gt;[<span class="i">$ReferenceIndex</span>]<span class="sc">;</span>
+129       <span class="i">$ReferenceFingerprintsObject</span> = <span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceFingerprintsObjectsRef</span>}-&gt;[<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">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+153
+154   <span class="k">print</span> <span class="q">&quot;Number of fingerprints data entries in database fingerprints file: $FingerprintsCount\n&quot;</span><span class="sc">;</span>
+155   <span class="k">print</span> <span class="q">&quot;Number of fingerprints date entries processed successfully: &quot;</span><span class="cm">,</span> <span class="s">(</span><span class="i">$FingerprintsCount</span> - <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span>  <span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+156   <span class="k">print</span> <span class="q">&quot;Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n&quot;</span><span class="sc">;</span>
+157 <span class="s">}</span>
+158
+159 <span class="c"># Compare a pair of reference and database fingerprints objects corresponding to bit-vector or</span>
+160 <span class="c"># vectors using specified comparison method and comparison cutoff...</span>
+161 <span class="c">#</span>
+<a name="CompareReferenceAndDatabaseFingerprintsPair-"></a> 162 <span class="k">sub </span><span class="m">CompareReferenceAndDatabaseFingerprintsPair</span> <span class="s">{</span>
+163   <span class="k">my</span><span class="s">(</span><span class="i">$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">$ReferenceFingerprintsObject</span><span class="i">-&gt;$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">$ComparisonValue</span><span class="s">)</span> <span class="s">{</span>
+170     <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring fingerprints data for reference compound ID &quot;</span><span class="cm">,</span>  <span class="i">$ReferenceFingerprintsObject</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;: Its comparison with database compound ID, &quot;</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsObject</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;, failed.\n&quot;</span><span class="sc">;</span>
+171     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+172   <span class="s">}</span>
+173
+174   <span class="i">$ComparisonValue</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.$OptionsInfo{Precision}f&quot;</span><span class="cm">,</span> <span class="i">$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">$ComparisonValue</span> &gt;= <span class="i">$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> &lt;= <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">$b</span> &lt;=&gt; <span class="i">$a</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$a</span> &lt;=&gt; <span class="i">$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>} &amp;&amp; <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">kNN</span>} &lt; <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$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">$FusedComparisonValue</span> = <span class="i">&amp;</span>{<span class="i">$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">$FusedComparisonValue</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.$OptionsInfo{Precision}f&quot;</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">$ReferenceCmpdID</span>}<span class="i">-&gt;AddKeyValuePair</span><span class="s">(</span><span class="i">$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">-&gt;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">$ReferenceCmpdID</span>} = <span class="w">new</span> <span class="i">PseudoHeap</span><span class="s">(</span><span class="q">&#39;Type&#39;</span> <span class="cm">=&gt;</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} ? <span class="q">&#39;KeepTopN&#39;</span> <span class="co">:</span> <span class="q">&#39;KeepBottomN&#39;</span><span class="s">)</span><span class="cm">,</span> <span class="q">&#39;KeyType&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Numeric&#39;</span><span class="cm">,</span> <span class="q">&#39;MaxSize&#39;</span> <span class="cm">=&gt;</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">$SimilaritySearchResults</span>{<span class="w">ResultsPseudoHeap</span>} = <span class="w">new</span> <span class="i">PseudoHeap</span><span class="s">(</span><span class="q">&#39;Type&#39;</span> <span class="cm">=&gt;</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} ? <span class="q">&#39;KeepTopN&#39;</span> <span class="co">:</span> <span class="q">&#39;KeepBottomN&#39;</span><span class="s">)</span><span class="cm">,</span> <span class="q">&#39;KeyType&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Numeric&#39;</span><span class="cm">,</span> <span class="q">&#39;MaxSize&#39;</span> <span class="cm">=&gt;</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">-&gt;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">$ReferenceCmpdID</span>}<span class="i">-&gt;GetKeyValues</span><span class="s">(</span><span class="i">$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">-&gt;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">-&gt;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">$NewSDFileRef</span>  <span class="q">&quot;&gt;  &lt;ReferenceCmpdID&gt;\n$ReferenceCmpdID\n\n&quot;</span><span class="sc">;</span>
+289     <span class="s">}</span>
+290     <span class="k">print</span> <span class="i">$NewSDFileRef</span>  <span class="q">&quot;&gt;  &lt;DatabaseCmpdID&gt;\n$DatabaseCmpdID\n\n&gt;  &lt;ComparisonValue&gt;\n$ComparisonValue\n\n&quot;</span><span class="sc">;</span>
+291     <span class="i">WriteDatabaseDataToSDOutputFile</span><span class="s">(</span><span class="i">$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">&quot;\$\$\$\$\n&quot;</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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+308   <span class="s">}</span>
+309 <span class="s">}</span>
+310
+311 <span class="c"># Open output files...</span>
+312 <span class="c">#</span>
+<a name="SetupAndOpenOutputFiles-"></a> 313 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span>
+314   <span class="k">my</span><span class="s">(</span><span class="i">$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">&quot;Generating SD file $NewSDFile...\n&quot;</span><span class="sc">;</span>
+321     <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewSDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $NewSDFile: $! \n&quot;</span><span class="sc">;</span>
+322     <span class="i">$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">&quot;Generating text file $NewTextFile...\n&quot;</span><span class="sc">;</span>
+328     <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewTextFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $NewTextFile: $! \n&quot;</span><span class="sc">;</span>
+329     <span class="i">$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">&quot;$Line\n&quot;</span><span class="sc">;</span>
+362 <span class="s">}</span>
+363
+364 <span class="c"># Write molecule string data to SD output file...</span>
+365 <span class="c">#</span>
+<a name="WriteMolStringDataToSDOutputFile-"></a> 366 <span class="k">sub </span><span class="m">WriteMolStringDataToSDOutputFile</span> <span class="s">{</span>
+367   <span class="k">my</span><span class="s">(</span><span class="i">$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">$NewSDFileRef</span> <span class="q">&quot;$MolString\nM  END\n&quot;</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">$NewSDFileRef</span> <span class="i">SDFileUtil::GenerateEmptyCtabBlockLines</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+378   <span class="s">}</span>
+379 <span class="s">}</span>
+380
+381 <span class="c"># Write database data from SD or Text database file to SD output file...</span>
+382 <span class="c">#</span>
+<a name="WriteDatabaseDataToSDOutputFile-"></a> 383 <span class="k">sub </span><span class="m">WriteDatabaseDataToSDOutputFile</span> <span class="s">{</span>
+384   <span class="k">my</span><span class="s">(</span><span class="i">$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">&#39;&#39;</span><span class="sc">;</span>
+394       <span class="k">print</span> <span class="i">$NewSDFileRef</span>  <span class="q">&quot;&gt;  &lt;$DataFieldLabel&gt;\n$DataFieldValue\n\n&quot;</span><span class="sc">;</span>
+395     <span class="s">}</span>
+396   <span class="s">}</span>
+397   <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">$DatabaseCmpdID</span>}-&gt;[<span class="i">$DataColNum</span>]<span class="sc">;</span>
+403       <span class="k">print</span> <span class="i">$NewSDFileRef</span>  <span class="q">&quot;&gt;  &lt;$DataFieldLabel&gt;\n$DataFieldValue\n\n&quot;</span><span class="sc">;</span>
+404     <span class="s">}</span>
+405   <span class="s">}</span>
+406 <span class="s">}</span>
+407
+408 <span class="c"># Retriebe database data from SD or Text database file for text output file...</span>
+409 <span class="c">#</span>
+<a name="RetrieveDatabaseDataForTextOutputFile-"></a> 410 <span class="k">sub </span><span class="m">RetrieveDatabaseDataForTextOutputFile</span> <span class="s">{</span>
+411   <span class="k">my</span><span class="s">(</span><span class="i">$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">$_</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$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">$DatabaseCmpdID</span>}-&gt;[<span class="i">$_</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">&#39;&#39;</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">-&gt;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">-&gt;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">&quot;Error: First reference fingerprints string type, $FingerprintsFilesInfo{Reference}{FirstFingerprintsStringType}, must match first database fingerprints type, $FingerprintsFilesInfo{Database}{FirstFingerprintsStringType}.\n&quot;</span><span class="sc">;</span>
+498   <span class="s">}</span>
+499
+500   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Warning: First reference fingerprints string description, $FingerprintsFilesInfo{Reference}{FirstFingerprintsStringDescription}, doesn&#39;t match first database fingerprints string description, $FingerprintsFilesInfo{Database}{FirstFingerprintsStringDescription}.\n&quot;</span><span class="sc">;</span>
+502   <span class="s">}</span>
+503
+504   <span class="c"># Setup individual reference and multiple references search mode...</span>
+505   <span class="i">$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">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m, --mode\&quot; is not valid. Allowed values: IndividualReference, MultipleReferences\n&quot;</span><span class="sc">;</span>
+516   <span class="s">}</span>
+517
+518   <span class="c"># Set up reference and database fingerprints similarity search method and paramaters...</span>
+519   <span class="k">my</span><span class="s">(</span><span class="i">$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">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethod</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+522   <span class="i">@</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethodParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+523
+524   <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonCutoff</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+525   <span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+526
+527   <span class="i">$ComparisonMeasure</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span> <span class="i">$ComparisonMethod</span> = <span class="q">&#39;&#39;</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">$SkipValuesCheck</span><span class="sc">;</span>
+558
+559       <span class="k">last</span> <span class="j">FINGERPRINTSTYPE</span><span class="sc">;</span>
+560     <span class="s">}</span>
+561     <span class="k">die</span> <span class="q">&quot;Error: Uknown fingerprints string type. Supported values: FingerprintsBitVectorString or FingerprintsVectorString.\n&quot;</span><span class="sc">;</span>
+562   <span class="s">}</span>
+563
+564   <span class="i">$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>} &amp;&amp; <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">&#39;&#39;</span><span class="sc">;</span> <span class="i">$KeepTop</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+567   <span class="k">if</span> <span class="s">(</span><span class="i">$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$/i</span><span class="s">)</span> <span class="s">{</span>
+589       <span class="c"># It&#39;s always the first value in the appropriated sorted list using value of KeepTop...</span>
+590       <span class="i">$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>-&gt;[<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&#39;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">$ComparisonValuesRef</span>-&gt;[<span class="i">$#</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">&amp;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">&amp;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">&amp;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">&amp;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">&quot;Error: The value specified, $Options{groupfusionrule}, for option \&quot;-g, --GroupFusionRule\&quot; is not valid. Allowed values: Max, Min, Mean, Median, Sum, Euclidean\n&quot;</span><span class="sc">;</span>
+619   <span class="s">}</span>
+620
+621   <span class="i">$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">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsFileIOParameters</span>}} = <span class="i">RetrieveFingerprintsFileIOParameters</span><span class="s">(</span><span class="q">&#39;Reference&#39;</span><span class="cm">,</span> <span class="i">$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">&#39;Reference&#39;</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">&#39;Database&#39;</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">$FirstFingerprintsStringDescription</span><span class="s">)</span> = <span class="i">RetrieveFingerprintsFileFingerprintsStringInfo</span><span class="s">(</span><span class="q">&#39;Database&#39;</span><span class="cm">,</span> <span class="i">$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> &amp;&amp; <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">$OptionsInfo</span>{<span class="w">TextOutput</span>} &amp;&amp; <span class="i">$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>} &amp;&amp; <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">&quot;$FingerprintsFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $FingerprintsFile: $! \n&quot;</span><span class="sc">;</span>
+718     <span class="s">(</span><span class="i">$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$/i</span><span class="s">)</span> <span class="s">{</span>
+768     <span class="k">return</span><span class="sc">;</span>
+769   <span class="s">}</span>
+770
+771   <span class="i">@DataColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+772   <span class="i">@DataColLabelsToOutput</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+773   <span class="i">@DataColNumsToOutput</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+774
+775   <span class="i">%DataColLabelToNumMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+776   <span class="i">%DataColNumToLabelMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+777
+778   <span class="c"># Get column label line...</span>
+779   <span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">&quot;$FingerprintsFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $FingerprintsFile: $! \n&quot;</span><span class="sc">;</span>
+780   <span class="i">$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$/i</span><span class="s">)</span> ? <span class="q">&quot;\t&quot;</span> <span class="co">:</span> <span class="s">(</span><span class="i">$InDelim</span> =~ <span class="q">/semicolon/i</span> ? <span class="q">&quot;\;&quot;</span> <span class="co">:</span> <span class="q">&quot;\,&quot;</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">$ColNum</span> &gt; <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span>
+798           <span class="k">die</span> <span class="q">&quot;Error: Column number, $ColNum, specified using \&quot;--DatabaseDataCols\&quot; is not valid: It must be &lt;= $NumOfCols\n&quot;</span><span class="sc">;</span>
+799         <span class="s">}</span>
+800         <span class="k">push</span> <span class="i">@DataColNumsToOutput</span><span class="cm">,</span> <span class="s">(</span><span class="i">$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">&quot;Error: Column label, $ColLabel, specified using \&quot;--DatabaseDataCols\&quot; is not valid: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+807         <span class="s">}</span>
+808         <span class="k">push</span> <span class="i">@DataColNumsToOutput</span><span class="cm">,</span> <span class="i">$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> &amp;&amp; <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">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">NumOfDatabaseMolecules</span>}<span class="sc">;</span>
+850   <span class="s">}</span>
+851   <span class="k">else</span> <span class="s">{</span>
+852     <span class="k">print</span> <span class="q">&quot;Calculating maximum number of similar molecules to retrieve for \&quot;PercentSimilar\&quot; value of \&quot;--SimilarCountMode\&quot; option by counting number of molecules in database fingerprints file...\n&quot;</span><span class="sc">;</span>
+853     <span class="k">open</span> <span class="w">FINGERPRINTSFILE</span><span class="cm">,</span> <span class="q">&quot;$FingerprintsFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $FingerprintsFile: $! \n&quot;</span><span class="sc">;</span>
+854     <span class="j">FILETYPE:</span> <span class="s">{</span>
+855       <span class="k">if</span> <span class="s">(</span><span class="i">$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">$MaxSimilarMolecules</span> &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+887     <span class="i">$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">&quot;Error: Input fingerprints file, $FingerprintsFile, doesn&#39;t exist.\n&quot;</span><span class="sc">;</span>
+901   <span class="s">}</span>
+902
+903   <span class="i">$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">&quot;Error: Input file, $FingerprintsFile, is not a fingerprints file.\n&quot;</span><span class="sc">;</span>
+906   <span class="s">}</span>
+907
+908   <span class="i">$InDelim</span> = <span class="q">&#39;&#39;</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">$FileDir</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+911     <span class="s">(</span><span class="i">$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">&#39;Tab&#39;</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">&quot;Error: Unknown fingerprints file mode: $FingerprintsFileMode. Supported values: Reference or Database\n&quot;</span><span class="sc">;</span>
+926   <span class="s">}</span>
+927
+928   <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+929
+930   <span class="j">FILETYPE:</span> <span class="s">{</span>
+931     <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span><span class="s">)</span> <span class="s">{</span>
+932       <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Read&#39;</span><span class="cm">,</span> <span class="q">&#39;FingerprintsStringMode&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsMode</span>}<span class="cm">,</span> <span class="q">&#39;ValidateData&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">&#39;DetailLevel&#39;</span> <span class="cm">=&gt;</span>  <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">&#39;FingerprintsFieldLabel&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="q">&quot;${FingerprintsFileMode}FingerprintsField&quot;</span>}<span class="cm">,</span> <span class="q">&#39;CompoundIDMode&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="q">&quot;${FingerprintsFileMode}CompoundIDMode&quot;</span>}<span class="cm">,</span> <span class="q">&#39;CompoundIDFieldLabel&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="q">&quot;${FingerprintsFileMode}CompoundIDField&quot;</span>}<span class="cm">,</span> <span class="q">&#39;CompoundIDPrefix&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="q">&quot;${FingerprintsFileMode}CompoundIDPrefix&quot;</span>}<span class="s">)</span><span class="sc">;</span>
+933       <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
+934     <span class="s">}</span>
+935     <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^FP$/i</span><span class="s">)</span> <span class="s">{</span>
+936       <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Read&#39;</span><span class="cm">,</span> <span class="q">&#39;FingerprintsStringMode&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsMode</span>}<span class="cm">,</span> <span class="q">&#39;ValidateData&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">&#39;DetailLevel&#39;</span> <span class="cm">=&gt;</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$/i</span><span class="s">)</span> <span class="s">{</span>
+940       <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Read&#39;</span><span class="cm">,</span> <span class="q">&#39;FingerprintsStringMode&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsMode</span>}<span class="cm">,</span> <span class="q">&#39;ValidateData&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">&#39;DetailLevel&#39;</span> <span class="cm">=&gt;</span>  <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">&#39;FingerprintsCol&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="q">&quot;${FingerprintsFileMode}FingerprintsCol&quot;</span>}<span class="cm">,</span> <span class="q">&#39;ColMode&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="q">&quot;${FingerprintsFileMode}ColMode&quot;</span>}<span class="cm">,</span> <span class="q">&#39;CompoundIDCol&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="q">&quot;${FingerprintsFileMode}CompoundIDCol&quot;</span>}<span class="cm">,</span> <span class="q">&#39;CompoundIDPrefix&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="q">&quot;${FingerprintsFileMode}CompoundIDPrefix&quot;</span>}<span class="cm">,</span> <span class="q">&#39;InDelim&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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">&quot;Error: Fingerprints file type, $FileType, is not valid. Supported file types: SD, FP or Text\n&quot;</span><span class="sc">;</span>
+944   <span class="s">}</span>
+945
+946   <span class="k">return</span> <span class="i">%FingerprintsFileIOParams</span><span class="sc">;</span>
+947 <span class="s">}</span>
+948
+949 <span class="c"># Make sure fingerprints data file contains valid dta and retrieve fingerprints string mode information...</span>
+950 <span class="c">#</span>
+<a name="RetrieveFingerprintsFileFingerprintsStringInfo-"></a> 951 <span class="k">sub </span><span class="m">RetrieveFingerprintsFileFingerprintsStringInfo</span> <span class="s">{</span>
+952   <span class="k">my</span><span class="s">(</span><span class="i">$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">&quot;Error: Reference fingerprints file, $FingerprintsFile, contains invalid fingerprints data.\n&quot;</span><span class="sc">;</span>
+958   <span class="s">}</span>
+959   <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">-&gt;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">&quot;Error: Reference fingerprints file, $FingerprintsFile, contains invalid fingerprints data.\n&quot;</span><span class="sc">;</span>
+961   <span class="s">}</span>
+962
+963   <span class="i">$FingerprintsStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;GetFingerprintsStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+964   <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;GetFingerprintsBitVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+965   <span class="i">$FingerprintsVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;GetFingerprintsVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+966
+967   <span class="i">$FirstFingerprintsStringType</span> = <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;GetFirstFingerprintsStringType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+968   <span class="i">$FirstFingerprintsStringDescription</span> = <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;GetFirstFingerprintsStringDescription</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+969
+970   <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;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">$OutputFilesInfo</span>{<span class="w">OutFileRoot</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+981   <span class="i">$OutputFilesInfo</span>{<span class="w">SDOutFileName</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+982   <span class="i">$OutputFilesInfo</span>{<span class="w">TextOutFileName</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+983
+984   <span class="i">$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">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">&quot;&quot;</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">$SDOutFileExt</span> = <span class="q">&quot;sdf&quot;</span><span class="sc">;</span>
+990   <span class="i">$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">&quot;tsv&quot;</span> <span class="co">:</span> <span class="q">&quot;csv&quot;</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> &amp;&amp; <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">&quot;${FileName}SimilaritySearching&quot;</span><span class="sc">;</span>
+1004   <span class="s">}</span>
+1005
+1006   <span class="i">$SDOutFileName</span> = <span class="q">&quot;${OutFileRoot}.${SDOutFileExt}&quot;</span><span class="sc">;</span>
+1007   <span class="i">$TextOutFileName</span> = <span class="q">&quot;${OutFileRoot}.${TextOutFileExt}&quot;</span><span class="sc">;</span>
+1008
+1009   <span class="i">$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">&quot;Error: Same output, $SDOutFileName, and reference input file names.\nSpecify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
+1015     <span class="s">}</span>
+1016     <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: Same output, $SDOutFileName, and database input file names.\nSpecify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
+1018     <span class="s">}</span>
+1019   <span class="s">}</span>
+1020
+1021   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: Same output, $TextOutFileName, and reference input file names.\nSpecify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
+1024     <span class="s">}</span>
+1025     <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: Same output, $TextOutFileName, and database input file names.\nSpecify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
+1027     <span class="s">}</span>
+1028   <span class="s">}</span>
+1029
+1030   <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">&quot;Error: The output file $SDOutFileName already exists.\n&quot;</span><span class="sc">;</span>
+1034       <span class="s">}</span>
+1035     <span class="s">}</span>
+1036     <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The output file $TextOutFileName already exists.\n&quot;</span><span class="sc">;</span>
+1039       <span class="s">}</span>
+1040     <span class="s">}</span>
+1041   <span class="s">}</span>
+1042
+1043   <span class="i">$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">$TextOutFileName</span><span class="sc">;</span>
+1046
+1047 <span class="s">}</span>
+1048
+1049 <span class="c"># Process input fingerprints file names...</span>
+1050 <span class="c">#</span>
+<a name="ProcessFingerprintsFileNames-"></a>1051 <span class="k">sub </span><span class="m">ProcessFingerprintsFileNames</span> <span class="s">{</span>
+1052   <span class="i">@FingerprintsFilesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+1053
+1054   <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+1055     <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">&quot;$FindBin::Bin/$ScriptName&quot;</span><span class="s">)</span><span class="sc">;</span>
+1056   <span class="s">}</span>
+1057
+1058   <span class="c"># Reference fingerprints file name...</span>
+1059   <span class="k">push</span> <span class="i">@FingerprintsFilesList</span><span class="cm">,</span> <span class="i">$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&#39;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">&quot;Error: The value specified, $Options{knn}, for option \&quot;-k, --KNN\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+1097     <span class="s">}</span>
+1098   <span class="s">}</span>
+1099
+1100   <span class="i">ProcessReferenceFingerprintsDataOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+1101   <span class="i">ProcessDatabaseFingerprintsDataOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+1102
+1103   <span class="i">$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">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/tab/i</span> <span class="s">)</span> ? <span class="q">&quot;\t&quot;</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span><span class="s">)</span> ? <span class="q">&quot;\;&quot;</span> <span class="co">:</span> <span class="q">&quot;\,&quot;</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">$SupportedComparisonMeasure</span> <span class="s">(</span><span class="i">Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1133     <span class="c"># Similarity coefficient function/method names contain &quot;Coefficient&quot; in their names.</span>
+1134     <span class="c"># So take &#39;em out and setup a map to original function/method name...</span>
+1135     <span class="i">$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">&#39;&#39;</span><span class="sc">;</span>
+1147   <span class="i">$SpecifiedComparisonMeasureMethod</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+1148
+1149   <span class="i">$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">&quot;Error: The value specified, $SpecifiedMeasure, for option \&quot;-b --BitVectorComparisonMode\&quot; is not valid.\nAllowed values:&quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+1153   <span class="s">}</span>
+1154
+1155   <span class="i">$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">&#39;&#39;</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">$Options</span>{<span class="w">alpha</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1168       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;-a, --alpha\&quot; option in \&quot;TverskySimilarity or WeightedTverskySimilarity\&quot; \&quot;-m --mode\&quot;. \n&quot;</span><span class="sc">;</span>
+1169     <span class="s">}</span>
+1170     <span class="k">my</span><span class="s">(</span><span class="i">$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">$Alpha</span><span class="s">)</span> &amp;&amp; <span class="i">$Alpha</span> &gt;=<span class="n">0</span> &amp;&amp; <span class="i">$Alpha</span> &lt;= <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">&quot;Error: The value specified, $Options{alpha}, for option \&quot;-a, --alpha\&quot; is not valid. Allowed values: &gt;= 0 and &lt;= 1\n&quot;</span><span class="sc">;</span>
+1174     <span class="s">}</span>
+1175     <span class="i">$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">&#39;&#39;</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">$Options</span>{<span class="w">beta</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1183       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;-b, --beta\&quot; option in \&quot;WeightedTverskySimilarity or WeightedTanimotoSimilarity\&quot; \&quot;-m --mode\&quot;. \n&quot;</span><span class="sc">;</span>
+1184     <span class="s">}</span>
+1185     <span class="k">my</span><span class="s">(</span><span class="i">$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">$Beta</span><span class="s">)</span> &amp;&amp; <span class="i">$Beta</span> &gt;=<span class="n">0</span> &amp;&amp; <span class="i">$Beta</span> &lt;= <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">&quot;Error: The value specified, $Options{beta}, for option \&quot;-b, --beta\&quot; is not valid. Allowed values: &gt;= 0 and &lt;= 1\n&quot;</span><span class="sc">;</span>
+1189     <span class="s">}</span>
+1190     <span class="i">$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 &quot;Coefficient&quot; in their names.</span>
+1205     <span class="c"># So take &#39;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">$SpecifiedComparisonMeasureName</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+1219   <span class="i">$SpecifiedComparisonMeasureMethod</span> = <span class="q">&#39;&#39;</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">&quot;Error: The value specified, $SpecifiedMeasure, for option \&quot;-v --VectorComparisonMode\&quot; is not valid.\nAllowed values:&quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+1226   <span class="s">}</span>
+1227
+1228   <span class="i">$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">&quot;Error: The value specified, $SpecifiedFormulism, for option \&quot;--VectorComparisonFormulism\&quot; is not valid. Allowed values: AlgebraicForm, BinaryForm or SetTheoreticForm\n&quot;</span><span class="sc">;</span>
+1244   <span class="s">}</span>
+1245
+1246   <span class="i">$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">&#39;Cmpd&#39;</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">&quot;Error: Column value, $Options{referencecompoundidcol}, specified using \&quot;--ReferenceCompoundIDCol\&quot; is not valid: Allowed integer values: &gt; 0\n&quot;</span><span class="sc">;</span>
+1266       <span class="s">}</span>
+1267     <span class="s">}</span>
+1268     <span class="i">$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">&#39;AutoDetect&#39;</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">&quot;Error: Column value, $Options{referencefingerprintscol}, specified using \&quot;--ReferenceFingerprintsCol\&quot; is not valid: Allowed integer values: &gt; 0\n&quot;</span><span class="sc">;</span>
+1278       <span class="s">}</span>
+1279     <span class="s">}</span>
+1280     <span class="i">$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">&#39;AutoDetect&#39;</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">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="s">)</span> &amp;&amp; <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$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">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="s">)</span> &amp;&amp; <span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">&quot;Error: Values specified using \&quot;--ReferenceCompoundIDCol\&quot; and \&quot;--ReferenceFingerprintsCol\&quot;, $Options{referencecompoundidcol}, must be different.\n&quot;</span><span class="sc">;</span>
+1290       <span class="s">}</span>
+1291     <span class="s">}</span>
+1292     <span class="k">else</span> <span class="s">{</span>
+1293       <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$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">&quot;Error: Values specified using \&quot;--ReferenceCompoundIDCol\&quot; and \&quot;--ReferenceFingerprintsCol\&quot;, $Options{referencecompoundidcol}, must be different.\n&quot;</span><span class="sc">;</span>
+1295       <span class="s">}</span>
+1296     <span class="s">}</span>
+1297   <span class="s">}</span>
+1298
+1299   <span class="c"># Compound ID and fingerprints field options for SD files...</span>
+1300
+1301   <span class="i">$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">&#39;&#39;</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> &amp;&amp; !<span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>}<span class="s">)</span> <span class="s">{</span>
+1305     <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--ReferenceCompoundIDField\&quot; option in \&quot;DataField\&quot; \&quot;--ReferenceCompoundIDMode\&quot;. \n&quot;</span><span class="sc">;</span>
+1306   <span class="s">}</span>
+1307   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&#39;AutoDetect&#39;</span><span class="sc">;</span>
+1316   <span class="s">}</span>
+1317
+1318   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>} &amp;&amp; <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$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">&quot;Error: Values specified using \&quot;--ReferenceCompoundIDField\&quot; and \&quot;--ReferenceFingerprintsfield\&quot;, $Options{referencecompoundidfield}, must be different.\n&quot;</span><span class="sc">;</span>
+1321     <span class="s">}</span>
+1322   <span class="s">}</span>
+1323
+1324 <span class="s">}</span>
+1325
+1326 <span class="c"># Process options related to data retrieval from database fingerprints SD and CSV/TSV</span>
+1327 <span class="c"># text files...</span>
+1328 <span class="c">#</span>
+<a name="ProcessDatabaseFingerprintsDataOptions-"></a>1329 <span class="k">sub </span><span class="m">ProcessDatabaseFingerprintsDataOptions</span> <span class="s">{</span>
+1330
+1331   <span class="i">$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">&#39;Cmpd&#39;</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">&quot;Error: Column value, $Options{databasecompoundidcol}, specified using \&quot;--DatabaseCompoundIDCol\&quot; is not valid: Allowed integer values: &gt; 0\n&quot;</span><span class="sc">;</span>
+1341       <span class="s">}</span>
+1342     <span class="s">}</span>
+1343     <span class="i">$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">&#39;AutoDetect&#39;</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">&quot;Error: Column value, $Options{databasefingerprintscol}, specified using \&quot;--DatabaseFingerprintsCol\&quot; is not valid: Allowed integer values: &gt; 0\n&quot;</span><span class="sc">;</span>
+1353       <span class="s">}</span>
+1354     <span class="s">}</span>
+1355     <span class="i">$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">&#39;AutoDetect&#39;</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">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="s">)</span> &amp;&amp; <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$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">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="s">)</span> &amp;&amp; <span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">&quot;Error: Values specified using \&quot;--DatabaseCompoundIDCol\&quot; and \&quot;--DatabaseFingerprintsCol\&quot;, $Options{databasecompoundidcol}, must be different.\n&quot;</span><span class="sc">;</span>
+1365       <span class="s">}</span>
+1366     <span class="s">}</span>
+1367     <span class="k">else</span> <span class="s">{</span>
+1368       <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$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">&quot;Error: Values specified using \&quot;--DatabaseCompoundIDCol\&quot; and \&quot;--DatabaseFingerprintsCol\&quot;, $Options{databasecompoundidcol}, must be different.\n&quot;</span><span class="sc">;</span>
+1370       <span class="s">}</span>
+1371     <span class="s">}</span>
+1372   <span class="s">}</span>
+1373
+1374   <span class="c"># Database data column options for text files...</span>
+1375
+1376   <span class="i">$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">&#39;&#39;</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">&quot;Error: You must specify a value for \&quot;--DatabaseDataCols\&quot; option in \&quot;Specify\&quot; \&quot;--DatabaseDataColsMode\&quot;. \n&quot;</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">&quot;Error: Column value, $DatabaseColNum, specified using \&quot;--DatabaseDataCols\&quot; is not valid: Allowed integer values: &gt; 0\n&quot;</span><span class="sc">;</span>
+1394         <span class="s">}</span>
+1395       <span class="s">}</span>
+1396     <span class="s">}</span>
+1397     <span class="k">else</span> <span class="s">{</span>
+1398       <span class="i">@SpecifiedDataCols</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$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">&#39;All&#39;</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> &amp;&amp; !<span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataCols</span>}<span class="s">)</span> <span class="s">{</span>
+1408     <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--DatabaseDataCols\&quot; option in \&quot;Specify\&quot; \&quot;--DatabaseDataColsMode\&quot;. \n&quot;</span><span class="sc">;</span>
+1409   <span class="s">}</span>
+1410
+1411   <span class="c"># Compound ID and fingerprints field options for SD files...</span>
+1412
+1413   <span class="i">$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">&#39;&#39;</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">$Options</span>{<span class="w">databasecompoundidfield</span>}<span class="s">)</span> <span class="s">{</span>
+1418       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--DatabaseCompoundIDField\&quot; option in \&quot;DataField\&quot; \&quot;--DatabaseCompoundIDMode\&quot;. \n&quot;</span><span class="sc">;</span>
+1419     <span class="s">}</span>
+1420     <span class="i">$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">$OptionsInfo</span>{<span class="w">DatabaseFingerprintsField</span>} = <span class="q">&#39;AutoDetect&#39;</span><span class="sc">;</span>
+1429   <span class="s">}</span>
+1430
+1431   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>} &amp;&amp; <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">&quot;Error: Values specified using \&quot;--DatabaseCompoundIDField\&quot; and \&quot;--DatabaseFingerprintsfield\&quot;, $Options{databasecompoundidfield}, must be different.\n&quot;</span><span class="sc">;</span>
+1434     <span class="s">}</span>
+1435   <span class="s">}</span>
+1436
+1437   <span class="c"># Database data field options for SD files...</span>
+1438
+1439   <span class="i">$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">&#39;&#39;</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$/i</span> &amp;&amp; !<span class="i">$Options</span>{<span class="w">databasedatafields</span>}<span class="s">)</span> <span class="s">{</span>
+1444     <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--DatabaseDataFields\&quot; option in \&quot;Specify\&quot; \&quot;--DatabaseDataFieldsMode\&quot;. \n&quot;</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">&quot;TanimotoSimilarity&quot;</span><span class="sc">;</span>
+1465
+1466   <span class="i">$Options</span>{<span class="w">databasecolmode</span>} = <span class="q">&#39;colnum&#39;</span><span class="sc">;</span>
+1467
+1468   <span class="i">$Options</span>{<span class="w">databasecompoundidprefix</span>} = <span class="q">&#39;Cmpd&#39;</span><span class="sc">;</span>
+1469   <span class="i">$Options</span>{<span class="w">databasecompoundidmode</span>} = <span class="q">&#39;LabelPrefix&#39;</span><span class="sc">;</span>
+1470
+1471   <span class="i">$Options</span>{<span class="w">databasedatacolsmode</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+1472   <span class="i">$Options</span>{<span class="w">databasedatafieldsmode</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+1473
+1474   <span class="i">$Options</span>{<span class="w">distancecutoff</span>} = <span class="n">10</span><span class="sc">;</span>
+1475
+1476   <span class="i">$Options</span>{<span class="w">referencecolmode</span>} = <span class="q">&#39;colnum&#39;</span><span class="sc">;</span>
+1477
+1478   <span class="i">$Options</span>{<span class="w">referencecompoundidprefix</span>} = <span class="q">&#39;Cmpd&#39;</span><span class="sc">;</span>
+1479   <span class="i">$Options</span>{<span class="w">referencecompoundidmode</span>} = <span class="q">&#39;LabelPrefix&#39;</span><span class="sc">;</span>
+1480
+1481   <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
+1482
+1483   <span class="i">$Options</span>{<span class="w">fingerprintsmode</span>} = <span class="q">&#39;AutoDetect&#39;</span><span class="sc">;</span>
+1484   <span class="i">$Options</span>{<span class="w">groupfusionrule</span>} = <span class="q">&#39;Max&#39;</span><span class="sc">;</span>
+1485   <span class="i">$Options</span>{<span class="w">groupfusionapplycutoff</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+1486
+1487   <span class="i">$Options</span>{<span class="w">knn</span>} = <span class="q">&#39;All&#39;</span><span class="sc">;</span>
+1488
+1489   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;MultipleReferences&#39;</span><span class="sc">;</span>
+1490
+1491   <span class="i">$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">&#39;comma&#39;</span><span class="sc">;</span>
+1495   <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&#39;comma&#39;</span><span class="sc">;</span>
+1496   <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+1497
+1498   <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">&#39;text&#39;</span><span class="sc">;</span>
+1499
+1500   <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span>
+1501
+1502   <span class="i">$Options</span>{<span class="w">searchmode</span>} = <span class="q">&#39;SimilaritySearch&#39;</span><span class="sc">;</span>
+1503
+1504   <span class="i">$Options</span>{<span class="w">similarcountmode</span>} = <span class="q">&#39;NumOfSimilar&#39;</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">&#39;TanimotoSimilarity&#39;</span><span class="sc">;</span>
+1509   <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>} = <span class="q">&#39;AlgebraicForm&#39;</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">&quot;alpha=f&quot;</span><span class="cm">,</span> <span class="q">&quot;beta=f&quot;</span><span class="cm">,</span> <span class="q">&quot;bitvectorcomparisonmode|b=s&quot;</span><span class="cm">,</span> <span class="q">&quot;databasecolmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;databasecompoundidcol=s&quot;</span><span class="cm">,</span> <span class="q">&quot;databasecompoundidprefix=s&quot;</span><span class="cm">,</span> <span class="q">&quot;databasecompoundidfield=s&quot;</span><span class="cm">,</span> <span class="q">&quot;databasecompoundidmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;databasedatacols=s&quot;</span><span class="cm">,</span> <span class="q">&quot;databasedatacolsmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;databasedatafields=s&quot;</span><span class="cm">,</span> <span class="q">&quot;databasedatafieldsmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;databasefingerprintscol=s&quot;</span><span class="cm">,</span> <span class="q">&quot;databasefingerprintsfield=s&quot;</span><span class="cm">,</span> <span class="q">&quot;distancecutoff=f&quot;</span><span class="cm">,</span> <span class="q">&quot;detail|d=i&quot;</span><span class="cm">,</span> <span class="q">&quot;fast|f&quot;</span><span class="cm">,</span> <span class="q">&quot;fingerprintsmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;groupfusionrule|g=s&quot;</span><span class="cm">,</span> <span class="cm">,</span> <span class="q">&quot;groupfusionapplycutoff=s&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;indelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;knn|k=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;numofsimilarmolecules|n=i&quot;</span><span class="cm">,</span> <span class="q">&quot;outdelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;output=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;percentsimilarmolecules|p=f&quot;</span><span class="cm">,</span> <span class="q">&quot;precision=s&quot;</span><span class="cm">,</span> <span class="q">&quot;quote|q=s&quot;</span><span class="cm">,</span> <span class="q">&quot;referencecolmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;referencecompoundidcol=s&quot;</span><span class="cm">,</span> <span class="q">&quot;referencecompoundidprefix=s&quot;</span><span class="cm">,</span> <span class="q">&quot;referencecompoundidfield=s&quot;</span><span class="cm">,</span> <span class="q">&quot;referencecompoundidmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;referencefingerprintscol=s&quot;</span><span class="cm">,</span> <span class="q">&quot;referencefingerprintsfield=s&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;searchmode|s=s&quot;</span><span class="cm">,</span> <span class="q">&quot;similarcountmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;similaritycutoff=f&quot;</span><span class="cm">,</span> <span class="q">&quot;vectorcomparisonmode|v=s&quot;</span><span class="cm">,</span> <span class="q">&quot;vectorcomparisonformulism=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1512     <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+1513   <span class="s">}</span>
+1514   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+1517     <span class="s">}</span>
+1518     <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
+1519   <span class="s">}</span>
+1520   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{databasecolmode}, for option \&quot;--DatabaseColMode\&quot; is not valid. Allowed values: ColNum, or ColLabel\n&quot;</span><span class="sc">;</span>
+1522   <span class="s">}</span>
+1523   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{databasecompoundidmode}, for option \&quot;--DatabaseCompoundIDMode\&quot; is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n&quot;</span><span class="sc">;</span>
+1525   <span class="s">}</span>
+1526   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{databasedatacolsmode}, for option \&quot;--DatabaseDataColsMode\&quot; is not valid. Allowed values: All, Specify, or CompoundID\n&quot;</span><span class="sc">;</span>
+1528   <span class="s">}</span>
+1529   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{databasedatafieldsmode}, for option \&quot;--DatabaseDataFieldsMode\&quot; is not valid. Allowed values: All, Common, Specify, or CompoundID\n&quot;</span><span class="sc">;</span>
+1531   <span class="s">}</span>
+1532   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{detail}, for option \&quot;-d, --detail\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+1534   <span class="s">}</span>
+1535   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{fingerprintsmode}, for option \&quot;--FingerprintsMode\&quot; is not valid. Allowed values: AutoDetect, FingerprintsBitVectorString or FingerprintsVectorString \n&quot;</span><span class="sc">;</span>
+1537   <span class="s">}</span>
+1538   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{groupfusionrule}, for option \&quot;-g, --GroupFusionRule\&quot; is not valid. Allowed values: Max, Min, Mean, Median, Sum, Euclidean\n&quot;</span><span class="sc">;</span>
+1540   <span class="s">}</span>
+1541   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{quote}, for option \&quot;--GroupFusionApplyCutoff\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+1543   <span class="s">}</span>
+1544   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{indelim}, for option \&quot;--InDelim\&quot; is not valid. Allowed values: comma, or semicolon\n&quot;</span><span class="sc">;</span>
+1546   <span class="s">}</span>
+1547   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m, --mode\&quot; is not valid. Allowed values: IndividualReference, MultipleReferences\n&quot;</span><span class="sc">;</span>
+1549   <span class="s">}</span>
+1550   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{numofsimilarmolecules}, for option \&quot;-n, --NumOfSimilarMolecules\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+1552   <span class="s">}</span>
+1553   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--OutDelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
+1555   <span class="s">}</span>
+1556   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{output}, for option \&quot;--output\&quot; is not valid. Allowed values: SD, text, or both\n&quot;</span><span class="sc">;</span>
+1558   <span class="s">}</span>
+1559   <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>}<span class="s">)</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>} &gt; <span class="n">0</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>} &lt;= <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">&quot;Error: The value specified, $Options{percentsimilarmolecules}, for option \&quot;-p, --PercentSimilarMolecules\&quot; is not valid. Allowed values: &gt; 0 and &lt;= 100 \n&quot;</span><span class="sc">;</span>
+1561   <span class="s">}</span>
+1562   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+1564   <span class="s">}</span>
+1565   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{precision}, for option \&quot;--precision\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+1567   <span class="s">}</span>
+1568   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{referencecolmode}, for option \&quot;--ReferenceColMode\&quot; is not valid. Allowed values: ColNum, or ColLabel\n&quot;</span><span class="sc">;</span>
+1570   <span class="s">}</span>
+1571   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{referencecompoundidmode}, for option \&quot;--ReferenceCompoundIDMode\&quot; is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n&quot;</span><span class="sc">;</span>
+1573   <span class="s">}</span>
+1574   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{searchmode}, for option \&quot;-s, --SearchMode\&quot; is not valid. Allowed values: SimilaritySearch, DissimilaritySearch \n&quot;</span><span class="sc">;</span>
+1576   <span class="s">}</span>
+1577   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{similarcountmode}, for option \&quot;--SimilarCountMode\&quot; is not valid. Allowed values: NumOfSimilar, PercentSimilar \n&quot;</span><span class="sc">;</span>
+1579   <span class="s">}</span>
+1580 <span class="s">}</span>
+1581
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>

Mercurial > repos > deepakjadmin > mayatool3_test2

comparison docs/scripts/html/code/SimilaritySearchingFingerprints.html @ 0:4816e4a8ae95 draft default tip