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+<title>MayaChemTools:Code:AtomNeighborhoodsFingerprints.pl</title>
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+1 #!/usr/bin/perl -w
+2 <span class="c">#</span>
+3 <span class="c"># $RCSfile: AtomNeighborhoodsFingerprints.pl,v $</span>
+4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
+5 <span class="c"># $Revision: 1.31 $</span>
+6 <span class="c">#</span>
+7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+8 <span class="c">#</span>
+9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+10 <span class="c">#</span>
+11 <span class="c"># This file is part of MayaChemTools.</span>
+12 <span class="c">#</span>
+13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+16 <span class="c"># later version.</span>
+17 <span class="c">#</span>
+18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+21 <span class="c"># details.</span>
+22 <span class="c">#</span>
+23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+27 <span class="c">#</span>
+28
+29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$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">MoleculeFileIO</span><span class="sc">;</span>
+39 <span class="k">use</span> <span class="w">FileIO::FingerprintsSDFileIO</span><span class="sc">;</span>
+40 <span class="k">use</span> <span class="w">FileIO::FingerprintsTextFileIO</span><span class="sc">;</span>
+41 <span class="k">use</span> <span class="w">FileIO::FingerprintsFPFileIO</span><span class="sc">;</span>
+42 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span>
+43 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
+44 <span class="k">use</span> <span class="w">Fingerprints::AtomNeighborhoodsFingerprints</span><span class="sc">;</span>
+45
+46 <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>
+47
+48 <span class="c"># Autoflush STDOUT</span>
+49 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+50
+51 <span class="c"># Starting message...</span>
+52 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
+53 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
+54 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+55
+56 <span class="c"># Get the options and setup script...</span>
+57 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+58 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+59   <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>
+60 <span class="s">}</span>
+61
+62 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
+63 <span class="i">@SDFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">&quot;sdf sd&quot;</span><span class="s">)</span><span class="sc">;</span>
+64
+65 <span class="c"># Process options...</span>
+66 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+67 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+68 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+69
+70 <span class="c"># Setup information about input files...</span>
+71 <span class="k">print</span> <span class="q">&quot;Checking input SD file(s)...\n&quot;</span><span class="sc">;</span>
+72 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
+73 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+74
+75 <span class="c"># Process input files..</span>
+76 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+77 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+78   <span class="k">print</span> <span class="q">&quot;\nProcessing SD files...\n&quot;</span><span class="sc">;</span>
+79 <span class="s">}</span>
+80 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+81   <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+82     <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+83     <span class="i">GenerateAtomNeighborhoodsFingerprints</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+84   <span class="s">}</span>
+85 <span class="s">}</span>
+86 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+87
+88 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+89 <span class="i">$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>
+90 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+91
+92 <span class="c">###############################################################################</span>
+93
+94 <span class="c"># Generate fingerprints for a SD file...</span>
+95 <span class="c">#</span>
+<a name="GenerateAtomNeighborhoodsFingerprints-"></a>  96 <span class="k">sub </span><span class="m">GenerateAtomNeighborhoodsFingerprints</span> <span class="s">{</span>
+97   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+98   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$MoleculeFileIO</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$AtomNeighborhoodsFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
+99
+100   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+101
+102   <span class="c"># Setup output files...</span>
+103   <span class="c">#</span>
+104   <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="i">SetupAndOpenOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+105
+106   <span class="i">$MoleculeFileIO</span> = <span class="w">new</span> <span class="i">MoleculeFileIO</span><span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
+107   <span class="i">$MoleculeFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+108
+109   <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+110   <span class="i">$IgnoredCmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+111
+112   <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Molecule</span> = <span class="i">$MoleculeFileIO</span><span class="i">-&gt;ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+113     <span class="i">$CmpdCount</span>++<span class="sc">;</span>
+114
+115     <span class="c"># Filter compound data before calculating fingerprints...</span>
+116     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Filter</span>}<span class="s">)</span> <span class="s">{</span>
+117       <span class="k">if</span> <span class="s">(</span><span class="i">CheckAndFilterCompound</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+118         <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
+119         <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
+120       <span class="s">}</span>
+121     <span class="s">}</span>
+122
+123     <span class="i">$AtomNeighborhoodsFingerprints</span> = <span class="i">GenerateMoleculeFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+124     <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomNeighborhoodsFingerprints</span><span class="s">)</span> <span class="s">{</span>
+125       <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
+126       <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">&#39;FingerprintsGenerationFailed&#39;</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+127       <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
+128     <span class="s">}</span>
+129
+130     <span class="i">WriteDataToOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$AtomNeighborhoodsFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
+131   <span class="s">}</span>
+132   <span class="i">$MoleculeFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+133
+134   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
+135     <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+136   <span class="s">}</span>
+137   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
+138     <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+139   <span class="s">}</span>
+140   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
+141     <span class="i">$NewFPFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+142   <span class="s">}</span>
+143
+144   <span class="i">WriteFingerprintsGenerationSummaryStatistics</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="s">)</span><span class="sc">;</span>
+145 <span class="s">}</span>
+146
+147 <span class="c"># Process compound being ignored due to problems in fingerprints geneation...</span>
+148 <span class="c">#</span>
+<a name="ProcessIgnoredCompound-"></a> 149 <span class="k">sub </span><span class="m">ProcessIgnoredCompound</span> <span class="s">{</span>
+150   <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+151   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+152
+153   <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+154   <span class="i">$CmpdID</span> = <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+155
+156   <span class="j">MODE:</span> <span class="s">{</span>
+157     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNonElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
+158       <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n&quot;</span><span class="sc">;</span>
+159       <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
+160     <span class="s">}</span>
+161
+162     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNoElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
+163       <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n&quot;</span><span class="sc">;</span>
+164       <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
+165     <span class="s">}</span>
+166
+167     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^FingerprintsGenerationFailed$/i</span><span class="s">)</span> <span class="s">{</span>
+168       <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn&#39;t succeed...\n\n&quot;</span><span class="sc">;</span>
+169       <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
+170     <span class="s">}</span>
+171     <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn&#39;t succeed...\n\n&quot;</span><span class="sc">;</span>
+172   <span class="s">}</span>
+173 <span class="s">}</span>
+174
+175 <span class="c"># Check and filter compounds....</span>
+176 <span class="c">#</span>
+<a name="CheckAndFilterCompound-"></a> 177 <span class="k">sub </span><span class="m">CheckAndFilterCompound</span> <span class="s">{</span>
+178   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+179   <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span>
+180
+181   <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetNumOfElementsAndNonElements</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+182
+183   <span class="k">if</span> <span class="s">(</span><span class="i">$NonElementCount</span><span class="s">)</span> <span class="s">{</span>
+184     <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">&#39;ContainsNonElementalData&#39;</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+185     <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
+186   <span class="s">}</span>
+187
+188   <span class="k">if</span> <span class="s">(</span>!<span class="i">$ElementCount</span><span class="s">)</span> <span class="s">{</span>
+189     <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">&#39;ContainsNoElementalData&#39;</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+190     <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
+191   <span class="s">}</span>
+192
+193   <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
+194 <span class="s">}</span>
+195
+196 <span class="c"># Write out compounds fingerprints generation summary statistics...</span>
+197 <span class="c">#</span>
+<a name="WriteFingerprintsGenerationSummaryStatistics-"></a> 198 <span class="k">sub </span><span class="m">WriteFingerprintsGenerationSummaryStatistics</span> <span class="s">{</span>
+199   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+200   <span class="k">my</span><span class="s">(</span><span class="i">$ProcessedCmpdCount</span><span class="s">)</span><span class="sc">;</span>
+201
+202   <span class="i">$ProcessedCmpdCount</span> = <span class="i">$CmpdCount</span> - <span class="i">$IgnoredCmpdCount</span><span class="sc">;</span>
+203
+204   <span class="k">print</span> <span class="q">&quot;\nNumber of compounds: $CmpdCount\n&quot;</span><span class="sc">;</span>
+205   <span class="k">print</span> <span class="q">&quot;Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n&quot;</span><span class="sc">;</span>
+206   <span class="k">print</span> <span class="q">&quot;Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n&quot;</span><span class="sc">;</span>
+207 <span class="s">}</span>
+208
+209 <span class="c"># Open output files...</span>
+210 <span class="c">#</span>
+<a name="SetupAndOpenOutputFiles-"></a> 211 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span>
+212   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+213   <span class="k">my</span><span class="s">(</span><span class="i">$NewFPSDFile</span><span class="cm">,</span> <span class="i">$NewFPFile</span><span class="cm">,</span> <span class="i">$NewFPTextFile</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
+214
+215   <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
+216
+217   <span class="c"># Setup common parameters for fingerprints file IO objects...</span>
+218   <span class="c">#</span>
+219   <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Write&#39;</span><span class="cm">,</span> <span class="q">&#39;Overwrite&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="cm">,</span> <span class="q">&#39;FingerprintsStringMode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;FingerprintsVectorString&#39;</span><span class="cm">,</span> <span class="q">&#39;VectorStringFormat&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>}<span class="s">)</span><span class="sc">;</span>
+220
+221   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+222     <span class="i">$NewFPSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+223     <span class="k">print</span> <span class="q">&quot;Generating SD file $NewFPSDFile...\n&quot;</span><span class="sc">;</span>
+224     <span class="i">$NewFPSDFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsSDFileIO</span><span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$NewFPSDFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">&#39;FingerprintsFieldLabel&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="s">)</span><span class="sc">;</span>
+225     <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+226   <span class="s">}</span>
+227
+228   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
+229     <span class="i">$NewFPFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+230     <span class="k">print</span> <span class="q">&quot;Generating FP file $NewFPFile...\n&quot;</span><span class="sc">;</span>
+231     <span class="i">$NewFPFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsFPFileIO</span><span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$NewFPFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
+232     <span class="i">$NewFPFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+233   <span class="s">}</span>
+234
+235   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
+236     <span class="k">my</span><span class="s">(</span><span class="i">$ColLabelsRef</span><span class="s">)</span><span class="sc">;</span>
+237
+238     <span class="i">$NewFPTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+239     <span class="i">$ColLabelsRef</span> = <span class="i">SetupFPTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+240
+241     <span class="k">print</span> <span class="q">&quot;Generating text file $NewFPTextFile...\n&quot;</span><span class="sc">;</span>
+242     <span class="i">$NewFPTextFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsTextFileIO</span><span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$NewFPTextFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">&#39;DataColLabels&#39;</span> <span class="cm">=&gt;</span> <span class="i">$ColLabelsRef</span><span class="cm">,</span> <span class="q">&#39;OutDelim&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="q">&#39;OutQuote&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
+243     <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+244   <span class="s">}</span>
+245
+246   <span class="k">return</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
+247 <span class="s">}</span>
+248
+249 <span class="c"># Write fingerpritns and other data to appropriate output files...</span>
+250 <span class="c">#</span>
+<a name="WriteDataToOutputFiles-"></a> 251 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span>
+252   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$AtomNeighborhoodsFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+253   <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+254
+255   <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="k">undef</span><span class="sc">;</span>
+256   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span> || <span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
+257     <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+258   <span class="s">}</span>
+259
+260   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
+261     <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
+262
+263     <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+264     <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$AtomNeighborhoodsFingerprints</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
+265   <span class="s">}</span>
+266
+267   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
+268     <span class="k">my</span><span class="s">(</span><span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
+269
+270     <span class="i">$ColValuesRef</span> = <span class="i">SetupFPTextFileCoulmnValues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+271     <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$AtomNeighborhoodsFingerprints</span><span class="cm">,</span> <span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
+272   <span class="s">}</span>
+273
+274   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
+275     <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
+276
+277     <span class="i">$CompoundID</span> = <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+278     <span class="i">$NewFPFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$AtomNeighborhoodsFingerprints</span><span class="cm">,</span> <span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
+279   <span class="s">}</span>
+280 <span class="s">}</span>
+281
+282 <span class="c"># Generate approriate column labels for FPText output file...</span>
+283 <span class="c">#</span>
+<a name="SetupFPTextFileCoulmnLabels-"></a> 284 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnLabels</span> <span class="s">{</span>
+285   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+286   <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
+287
+288   <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+289   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+290     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
+291   <span class="s">}</span>
+292   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
+293     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
+294   <span class="s">}</span>
+295   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+296     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
+297   <span class="s">}</span>
+298   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
+299     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span>
+300   <span class="s">}</span>
+301   <span class="c"># Add fingerprints label...</span>
+302   <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="sc">;</span>
+303
+304   <span class="k">return</span> \<span class="i">@ColLabels</span><span class="sc">;</span>
+305 <span class="s">}</span>
+306
+307 <span class="c"># Generate column values FPText output file..</span>
+308 <span class="c">#</span>
+<a name="SetupFPTextFileCoulmnValues-"></a> 309 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnValues</span> <span class="s">{</span>
+310   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+311   <span class="k">my</span><span class="s">(</span><span class="i">@ColValues</span><span class="s">)</span><span class="sc">;</span>
+312
+313   <span class="i">@ColValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+314   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
+315     <span class="k">push</span> <span class="i">@ColValues</span><span class="cm">,</span> <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+316   <span class="s">}</span>
+317   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+318     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
+319   <span class="s">}</span>
+320   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
+321     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
+322   <span class="s">}</span>
+323   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+324     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
+325   <span class="s">}</span>
+326
+327   <span class="k">return</span> \<span class="i">@ColValues</span><span class="sc">;</span>
+328 <span class="s">}</span>
+329
+330 <span class="c"># Generate compound ID for FP and FPText output files..</span>
+331 <span class="c">#</span>
+<a name="SetupCmpdIDForOutputFiles-"></a> 332 <span class="k">sub </span><span class="m">SetupCmpdIDForOutputFiles</span> <span class="s">{</span>
+333   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+334   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span>
+335
+336   <span class="i">$CmpdID</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+337   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolNameOrLabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
+338     <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span>
+339     <span class="i">$MolName</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+340     <span class="i">$CmpdID</span> = <span class="i">$MolName</span> ? <span class="i">$MolName</span> <span class="co">:</span> <span class="q">&quot;$OptionsInfo{CompoundID}${CmpdCount}&quot;</span><span class="sc">;</span>
+341   <span class="s">}</span>
+342   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^LabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
+343     <span class="i">$CmpdID</span> = <span class="q">&quot;$OptionsInfo{CompoundID}${CmpdCount}&quot;</span><span class="sc">;</span>
+344   <span class="s">}</span>
+345   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
+346     <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span>
+347     <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
+348     <span class="i">$CmpdID</span> = <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$SpecifiedDataField</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$SpecifiedDataField</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
+349   <span class="s">}</span>
+350   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolName$/i</span><span class="s">)</span> <span class="s">{</span>
+351     <span class="i">$CmpdID</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+352   <span class="s">}</span>
+353   <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span>
+354 <span class="s">}</span>
+355
+356 <span class="c"># Generate fingerprints for molecule...</span>
+357 <span class="c">#</span>
+<a name="GenerateMoleculeFingerprints-"></a> 358 <span class="k">sub </span><span class="m">GenerateMoleculeFingerprints</span> <span class="s">{</span>
+359   <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+360   <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighborhoodsFingerprints</span><span class="s">)</span><span class="sc">;</span>
+361
+362   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span>
+363     <span class="i">$Molecule</span><span class="i">-&gt;KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+364   <span class="s">}</span>
+365   <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">-&gt;DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+366     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+367   <span class="s">}</span>
+368   <span class="i">$Molecule</span><span class="i">-&gt;SetAromaticityModel</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>}<span class="s">)</span><span class="sc">;</span>
+369   <span class="i">$Molecule</span><span class="i">-&gt;DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+370
+371   <span class="i">$AtomNeighborhoodsFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::AtomNeighborhoodsFingerprints</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">&#39;MinNeighborhoodRadius&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">MinNeighborhoodRadius</span>}<span class="cm">,</span>  <span class="q">&#39;MaxNeighborhoodRadius&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxNeighborhoodRadius</span>}<span class="cm">,</span> <span class="q">&#39;AtomIdentifierType&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span>
+372   <span class="i">SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$AtomNeighborhoodsFingerprints</span><span class="s">)</span><span class="sc">;</span>
+373
+374   <span class="c"># Generate fingerprints...</span>
+375   <span class="i">$AtomNeighborhoodsFingerprints</span><span class="i">-&gt;GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+376
+377   <span class="c"># Make sure fingerprints generation is successful...</span>
+378   <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomNeighborhoodsFingerprints</span><span class="i">-&gt;IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+379     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+380   <span class="s">}</span>
+381
+382   <span class="k">return</span> <span class="i">$AtomNeighborhoodsFingerprints</span><span class="sc">;</span>
+383 <span class="s">}</span>
+384
+385 <span class="c"># Set atom identifier type to use for generating fingerprints...</span>
+386 <span class="c">#</span>
+<a name="SetAtomIdentifierTypeValuesToUse-"></a> 387 <span class="k">sub </span><span class="m">SetAtomIdentifierTypeValuesToUse</span> <span class="s">{</span>
+388   <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighborhoodsFingerprints</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+389
+390   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+391     <span class="i">$AtomNeighborhoodsFingerprints</span><span class="i">-&gt;SetAtomicInvariantsToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}}<span class="s">)</span><span class="sc">;</span>
+392   <span class="s">}</span>
+393   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+394     <span class="i">$AtomNeighborhoodsFingerprints</span><span class="i">-&gt;SetFunctionalClassesToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span>
+395   <span class="s">}</span>
+396   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
+397     <span class="c"># Nothing to do for now...</span>
+398   <span class="s">}</span>
+399   <span class="k">else</span> <span class="s">{</span>
+400     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{atomidentifiertype}, for option \&quot;-a, --AtomIdentifierType\&quot; is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n&quot;</span><span class="sc">;</span>
+401   <span class="s">}</span>
+402 <span class="s">}</span>
+403
+404 <span class="c"># Retrieve information about SD files...</span>
+405 <span class="c">#</span>
+<a name="RetrieveSDFilesInfo-"></a> 406 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
+407   <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$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">$OutFileRoot</span><span class="cm">,</span> <span class="i">$TextOutFileExt</span><span class="cm">,</span> <span class="i">$SDOutFileExt</span><span class="cm">,</span> <span class="i">$FPOutFileExt</span><span class="cm">,</span> <span class="i">$NewSDFileName</span><span class="cm">,</span> <span class="i">$NewFPFileName</span><span class="cm">,</span> <span class="i">$NewTextFileName</span><span class="cm">,</span> <span class="i">$CheckDataField</span><span class="cm">,</span> <span class="i">$CollectDataFields</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span><span class="sc">;</span>
+408
+409   <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+410   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+411   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+412   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+413   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+414   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+415   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+416   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+417
+418   <span class="i">$CheckDataField</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} &amp;&amp; <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^DataField$/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>
+419   <span class="i">$CollectDataFields</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} &amp;&amp; <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^(All|Common)$/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>
+420
+421   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+422     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+423
+424     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+425     <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+426     <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+427     <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+428     <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+429
+430     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+431     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+432       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+433       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+434     <span class="s">}</span>
+435     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">&quot;sd sdf&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+436       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
+437       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+438     <span class="s">}</span>
+439
+440     <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span>
+441       <span class="c"># Make sure data field exists in SD file..</span>
+442       <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$SpecifiedDataField</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldValues</span><span class="s">)</span><span class="sc">;</span>
+443
+444       <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+445       <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
+446       <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
+447       <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+448       <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+449       <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
+450       <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
+451       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span>
+452         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using  \&quot;--CompoundID\&quot; option in \&quot;DataField\&quot; \&quot;--CompoundIDMode\&quot; doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+453         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+454       <span class="s">}</span>
+455     <span class="s">}</span>
+456
+457     <span class="i">$AllDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+458     <span class="i">$CommonDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+459     <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span>
+460       <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
+461       <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
+462       <span class="s">(</span><span class="i">$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>
+463       <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+464     <span class="s">}</span>
+465
+466     <span class="c"># Setup output file names...</span>
+467     <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">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+468     <span class="s">(</span><span class="i">$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">$SDFile</span><span class="s">)</span><span class="sc">;</span>
+469
+470     <span class="i">$TextOutFileExt</span> = <span class="q">&quot;csv&quot;</span><span class="sc">;</span>
+471     <span class="k">if</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="s">{</span>
+472       <span class="i">$TextOutFileExt</span> = <span class="q">&quot;tsv&quot;</span><span class="sc">;</span>
+473     <span class="s">}</span>
+474     <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span>
+475     <span class="i">$FPOutFileExt</span> = <span class="q">&quot;fpf&quot;</span><span class="sc">;</span>
+476
+477     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+478       <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
+479       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+480         <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+481       <span class="s">}</span>
+482       <span class="k">else</span> <span class="s">{</span>
+483         <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
+484       <span class="s">}</span>
+485       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+486     <span class="s">}</span>
+487     <span class="k">else</span> <span class="s">{</span>
+488       <span class="i">$OutFileRoot</span> = <span class="q">&quot;${FileName}AtomNeighborhoodsFP&quot;</span><span class="sc">;</span>
+489     <span class="s">}</span>
+490
+491     <span class="i">$NewSDFileName</span> = <span class="q">&quot;${OutFileRoot}.${SDOutFileExt}&quot;</span><span class="sc">;</span>
+492     <span class="i">$NewFPFileName</span> = <span class="q">&quot;${OutFileRoot}.${FPOutFileExt}&quot;</span><span class="sc">;</span>
+493     <span class="i">$NewTextFileName</span> = <span class="q">&quot;${OutFileRoot}.${TextOutFileExt}&quot;</span><span class="sc">;</span>
+494
+495     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+496       <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span>
+497         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n&quot;</span><span class="sc">;</span>
+498         <span class="k">print</span> <span class="q">&quot;Specify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
+499         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+500       <span class="s">}</span>
+501     <span class="s">}</span>
+502
+503     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
+504       <span class="c"># Check SD and text outout files...</span>
+505       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+506         <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span>
+507           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n&quot;</span><span class="sc">;</span>
+508           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+509         <span class="s">}</span>
+510       <span class="s">}</span>
+511       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
+512         <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewFPFileName</span><span class="s">)</span> <span class="s">{</span>
+513           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n&quot;</span><span class="sc">;</span>
+514           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+515         <span class="s">}</span>
+516       <span class="s">}</span>
+517       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
+518         <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewTextFileName</span><span class="s">)</span> <span class="s">{</span>
+519           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n&quot;</span><span class="sc">;</span>
+520           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+521         <span class="s">}</span>
+522       <span class="s">}</span>
+523     <span class="s">}</span>
+524
+525     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+526
+527     <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
+528     <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span>
+529     <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewFPFileName</span><span class="sc">;</span>
+530     <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span>
+531
+532     <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span>
+533     <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span>
+534   <span class="s">}</span>
+535 <span class="s">}</span>
+536
+537 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 538 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+539   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+540
+541   <span class="i">ProcessAtomIdentifierTypeOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+542
+543   <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span>
+544
+545   <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span>
+546   <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span>
+547   <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span>
+548
+549   <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span>
+550   <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+551
+552   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+553   <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+554
+555   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
+556     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
+557       <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span>
+558         <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--CompoundID\&quot; option in \&quot;DataField\&quot; \&quot;--CompoundIDMode\&quot;. \n&quot;</span><span class="sc">;</span>
+559       <span class="s">}</span>
+560       <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span>
+561     <span class="s">}</span>
+562     <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^(LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
+563       <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>} ? <span class="i">$Options</span>{<span class="w">compoundid</span>} <span class="co">:</span> <span class="q">&#39;Cmpd&#39;</span><span class="sc">;</span>
+564     <span class="s">}</span>
+565   <span class="s">}</span>
+566   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+567     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span>
+568       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--DataFields\&quot; option in \&quot;Specify\&quot; \&quot;-d, --DataFieldsMode\&quot;. \n&quot;</span><span class="sc">;</span>
+569     <span class="s">}</span>
+570     <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span>
+571     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span>
+572   <span class="s">}</span>
+573
+574   <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>} = <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} ? <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} <span class="co">:</span> <span class="q">&#39;AtomNeighborhoodsFingerprints&#39;</span><span class="sc">;</span>
+575
+576   <span class="i">$OptionsInfo</span>{<span class="w">Filter</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+577
+578   <span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+579
+580   <span class="i">$OptionsInfo</span>{<span class="w">MinNeighborhoodRadius</span>} = <span class="i">$Options</span>{<span class="w">minneighborhoodradius</span>}<span class="sc">;</span>
+581   <span class="i">$OptionsInfo</span>{<span class="w">MaxNeighborhoodRadius</span>} = <span class="i">$Options</span>{<span class="w">maxneighborhoodradius</span>}<span class="sc">;</span>
+582
+583   <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
+584   <span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(SD|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+585   <span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(FP|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+586   <span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(Text|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+587
+588   <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="i">$Options</span>{<span class="w">outdelim</span>}<span class="sc">;</span>
+589   <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+590
+591   <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+592   <span class="i">$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>
+593
+594   <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>} = <span class="q">&#39;ValuesString&#39;</span><span class="sc">;</span>
+595 <span class="s">}</span>
+596
+597 <span class="c"># Process atom identifier type and related options...</span>
+598 <span class="c">#</span>
+<a name="ProcessAtomIdentifierTypeOptions-"></a> 599 <span class="k">sub </span><span class="m">ProcessAtomIdentifierTypeOptions</span> <span class="s">{</span>
+600
+601   <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} = <span class="i">$Options</span>{<span class="w">atomidentifiertype</span>}<span class="sc">;</span>
+602
+603   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+604     <span class="i">ProcessAtomicInvariantsToUseOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+605   <span class="s">}</span>
+606   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+607     <span class="i">ProcessFunctionalClassesToUse</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+608   <span class="s">}</span>
+609   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
+610     <span class="c"># Nothing to do for now...</span>
+611   <span class="s">}</span>
+612   <span class="k">else</span> <span class="s">{</span>
+613     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{atomidentifiertype}, for option \&quot;-a, --AtomIdentifierType\&quot; is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n&quot;</span><span class="sc">;</span>
+614   <span class="s">}</span>
+615 <span class="s">}</span>
+616
+617 <span class="c"># Process specified atomic invariants to use...</span>
+618 <span class="c">#</span>
+<a name="ProcessAtomicInvariantsToUseOption-"></a> 619 <span class="k">sub </span><span class="m">ProcessAtomicInvariantsToUseOption</span> <span class="s">{</span>
+620   <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomSymbolSpecified</span><span class="cm">,</span> <span class="i">@AtomicInvariantsWords</span><span class="s">)</span><span class="sc">;</span>
+621
+622   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+623   <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+624     <span class="k">die</span> <span class="q">&quot;Error: Atomic invariants value specified using \&quot;--AtomicInvariantsToUse\&quot; option is empty\n&quot;</span><span class="sc">;</span>
+625   <span class="s">}</span>
+626   <span class="i">$AtomSymbolSpecified</span> = <span class="n">0</span><span class="sc">;</span>
+627   <span class="i">@AtomicInvariantsWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>}<span class="sc">;</span>
+628   <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsWords</span><span class="s">)</span> <span class="s">{</span>
+629     <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+630       <span class="k">die</span> <span class="q">&quot;Error: Atomic invariant specified, $AtomicInvariant, using \&quot;--AtomicInvariantsToUse\&quot; option is not valid...\n &quot;</span><span class="sc">;</span>
+631     <span class="s">}</span>
+632     <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AS|AtomSymbol)$/i</span><span class="s">)</span> <span class="s">{</span>
+633       <span class="i">$AtomSymbolSpecified</span> = <span class="n">1</span><span class="sc">;</span>
+634     <span class="s">}</span>
+635     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
+636   <span class="s">}</span>
+637   <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSymbolSpecified</span><span class="s">)</span> <span class="s">{</span>
+638     <span class="k">die</span> <span class="q">&quot;Error: Atomic invariant, AS or AtomSymbol, must be specified as using \&quot;--AtomicInvariantsToUse\&quot; option...\n &quot;</span><span class="sc">;</span>
+639   <span class="s">}</span>
+640 <span class="s">}</span>
+641
+642 <span class="c"># Process specified functional classes invariants to use...</span>
+643 <span class="c">#</span>
+<a name="ProcessFunctionalClassesToUse-"></a> 644 <span class="k">sub </span><span class="m">ProcessFunctionalClassesToUse</span> <span class="s">{</span>
+645   <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUseWords</span><span class="s">)</span><span class="sc">;</span>
+646
+647   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+648   <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">functionalclassestouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+649     <span class="k">die</span> <span class="q">&quot;Error: Functional classes value specified using \&quot;--FunctionalClassesToUse\&quot; option is empty\n&quot;</span><span class="sc">;</span>
+650   <span class="s">}</span>
+651   <span class="i">@FunctionalClassesToUseWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">functionalclassestouse</span>}<span class="sc">;</span>
+652   <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesToUseWords</span><span class="s">)</span> <span class="s">{</span>
+653     <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+654       <span class="k">die</span> <span class="q">&quot;Error: Functional class specified, $FunctionalClass, using \&quot;--FunctionalClassesToUse\&quot; option is not valid...\n &quot;</span><span class="sc">;</span>
+655     <span class="s">}</span>
+656     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="sc">;</span>
+657   <span class="s">}</span>
+658 <span class="s">}</span>
+659
+660 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 661 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+662
+663   <span class="c"># Retrieve all the options...</span>
+664   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+665
+666   <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">&#39;MayaChemToolsAromaticityModel&#39;</span><span class="sc">;</span>
+667
+668   <span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} = <span class="q">&#39;AtomicInvariantsAtomTypes&#39;</span><span class="sc">;</span>
+669   <span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>} = <span class="q">&#39;AS,X,BO,H,FC&#39;</span><span class="sc">;</span>
+670   <span class="i">$Options</span>{<span class="w">functionalclassestouse</span>} = <span class="q">&#39;HBD,HBA,PI,NI,Ar,Hal&#39;</span><span class="sc">;</span>
+671
+672   <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">&#39;LabelPrefix&#39;</span><span class="sc">;</span>
+673   <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+674   <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+675
+676   <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+677
+678   <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+679
+680   <span class="i">$Options</span>{<span class="w">minneighborhoodradius</span>} = <span class="n">0</span><span class="sc">;</span>
+681   <span class="i">$Options</span>{<span class="w">maxneighborhoodradius</span>} = <span class="n">2</span><span class="sc">;</span>
+682
+683   <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">&#39;text&#39;</span><span class="sc">;</span>
+684   <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&#39;comma&#39;</span><span class="sc">;</span>
+685   <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+686
+687   <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;aromaticitymodel=s&quot;</span><span class="cm">,</span> <span class="q">&quot;atomidentifiertype|a=s&quot;</span><span class="cm">,</span> <span class="q">&quot;atomicinvariantstouse=s&quot;</span><span class="cm">,</span> <span class="q">&quot;functionalclassestouse=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundid=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundidlabel=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundidmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;datafields=s&quot;</span><span class="cm">,</span> <span class="q">&quot;datafieldsmode|d=s&quot;</span><span class="cm">,</span> <span class="q">&quot;filter|f=s&quot;</span><span class="cm">,</span> <span class="q">&quot;fingerprintslabel=s&quot;</span><span class="cm">,</span>  <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;keeplargestcomponent|k=s&quot;</span><span class="cm">,</span>  <span class="q">&quot;minneighborhoodradius=s&quot;</span><span class="cm">,</span> <span class="q">&quot;maxneighborhoodradius=s&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;quote|q=s&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=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>
+688     <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 $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+689   <span class="s">}</span>
+690   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+691     <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>
+692       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+693     <span class="s">}</span>
+694     <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
+695   <span class="s">}</span>
+696   <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+697     <span class="k">my</span><span class="s">(</span><span class="i">@SupportedModels</span><span class="s">)</span> = <span class="i">Molecule::GetSupportedAromaticityModels</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+698     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{aromaticitymodel}, for option \&quot;--AromaticityModel\&quot; is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n&quot;</span><span class="sc">;</span>
+699   <span class="s">}</span>
+700   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} !~ <span class="q">/^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
+701     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{atomidentifiertype}, for option \&quot;-a, --AtomIdentifierType\&quot; is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n&quot;</span><span class="sc">;</span>
+702   <span class="s">}</span>
+703   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
+704     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{compoundidmode}, for option \&quot;--CompoundIDMode\&quot; is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n&quot;</span><span class="sc">;</span>
+705   <span class="s">}</span>
+706   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span>
+707     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{datafieldsmode}, for option \&quot;-d, --DataFieldsMode\&quot; is not valid. Allowed values: All, Common, Specify or CompoundID\n&quot;</span><span class="sc">;</span>
+708   <span class="s">}</span>
+709   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+710     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{filter}, for option \&quot;-f, --Filter\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+711   <span class="s">}</span>
+712   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+713     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{keeplargestcomponent}, for option \&quot;-k, --KeepLargestComponent\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+714   <span class="s">}</span>
+715   <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">minneighborhoodradius</span>}<span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$Options</span>{<span class="w">minneighborhoodradius</span>} &gt;= <span class="n">0</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+716     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{minneighborhoodradius}, for option \&quot;--MinNeighborhoodRadius\&quot; is not valid. Allowed values: &gt;= 0 \n&quot;</span><span class="sc">;</span>
+717   <span class="s">}</span>
+718   <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">maxneighborhoodradius</span>}<span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$Options</span>{<span class="w">maxneighborhoodradius</span>} &gt;= <span class="n">0</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+719     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{maxneighborhoodradius}, for option \&quot;--MaxNeighborhoodRadius\&quot; is not valid. Allowed values: &gt;= 0 \n&quot;</span><span class="sc">;</span>
+720   <span class="s">}</span>
+721   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">minneighborhoodradius</span>} &gt; <span class="i">$Options</span>{<span class="w">maxneighborhoodradius</span>}<span class="s">)</span> <span class="s">{</span>
+722     <span class="k">die</span> <span class="q">&quot;Error: The value specified, specified, $Options{minneighborhoodradius}, for option \&quot;--MinNeighborhoodRadius\&quot; must be less than the value specified, $Options{maxneighborhoodradius}, for option \&quot;--MaxNeighborhoodRadius\&quot; \n&quot;</span><span class="sc">;</span>
+723   <span class="s">}</span>
+724   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|FP|text|all)$/i</span><span class="s">)</span> <span class="s">{</span>
+725     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{output}, for option \&quot;--output\&quot; is not valid. Allowed values: SD, FP, text, or all\n&quot;</span><span class="sc">;</span>
+726   <span class="s">}</span>
+727   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
+728     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--outdelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
+729   <span class="s">}</span>
+730   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+731     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+732   <span class="s">}</span>
+733   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^No$/i</span><span class="s">)</span> <span class="s">{</span>
+734     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not allowed with, semicolon value of \&quot;--outdelim\&quot; option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n&quot;</span><span class="sc">;</span>
+735   <span class="s">}</span>
+736 <span class="s">}</span>
+737
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
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Mercurial > repos > deepakjadmin > mayatool3_test2

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