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+1 #!/usr/bin/perl -w
+2 <span class="c">#</span>
+3 <span class="c"># $RCSfile: PathLengthFingerprints.pl,v $</span>
+4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
+5 <span class="c"># $Revision: 1.50 $</span>
+6 <span class="c">#</span>
+7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+8 <span class="c">#</span>
+9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+10 <span class="c">#</span>
+11 <span class="c"># This file is part of MayaChemTools.</span>
+12 <span class="c">#</span>
+13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+16 <span class="c"># later version.</span>
+17 <span class="c">#</span>
+18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+21 <span class="c"># details.</span>
+22 <span class="c">#</span>
+23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+27 <span class="c">#</span>
+28
+29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$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::PathLengthFingerprints</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">GeneratePathLengthFingerprints</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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+91
+92 <span class="c">###############################################################################</span>
+93
+94 <span class="c"># Generate fingerprints for a SD file...</span>
+95 <span class="c">#</span>
+<a name="GeneratePathLengthFingerprints-"></a>  96 <span class="k">sub </span><span class="m">GeneratePathLengthFingerprints</span> <span class="s">{</span>
+97   <span class="k">my</span><span class="s">(</span><span class="i">$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">$Molecule</span><span class="cm">,</span> <span class="i">$PathLengthFingerprints</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">$PathLengthFingerprints</span> = <span class="i">GenerateMoleculeFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+124     <span class="k">if</span> <span class="s">(</span>!<span class="i">$PathLengthFingerprints</span><span class="s">)</span> <span class="s">{</span>
+125       <span class="i">$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">$Molecule</span><span class="cm">,</span> <span class="i">$PathLengthFingerprints</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">$NewFPFileIO</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
+216
+217   <span class="c"># Setup common parameters for fingerprints file IO objects...</span>
+218   <span class="c">#</span>
+219   <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+220   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span>
+221     <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Write&#39;</span><span class="cm">,</span> <span class="q">&#39;Overwrite&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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;FingerprintsBitVectorString&#39;</span><span class="cm">,</span> <span class="q">&#39;BitStringFormat&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">BitStringFormat</span>}<span class="cm">,</span> <span class="q">&#39;BitsOrder&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">BitsOrder</span>}<span class="s">)</span><span class="sc">;</span>
+222   <span class="s">}</span>
+223   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span>
+224     <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>
+225   <span class="s">}</span>
+226
+227   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+228     <span class="i">$NewFPSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+229     <span class="k">print</span> <span class="q">&quot;Generating SD file $NewFPSDFile...\n&quot;</span><span class="sc">;</span>
+230     <span class="i">$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>
+231     <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+232   <span class="s">}</span>
+233
+234   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
+235     <span class="i">$NewFPFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+236     <span class="k">print</span> <span class="q">&quot;Generating FP file $NewFPFile...\n&quot;</span><span class="sc">;</span>
+237     <span class="i">$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">$NewFPFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
+238     <span class="i">$NewFPFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+239   <span class="s">}</span>
+240
+241   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
+242     <span class="k">my</span><span class="s">(</span><span class="i">$ColLabelsRef</span><span class="s">)</span><span class="sc">;</span>
+243
+244     <span class="i">$NewFPTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+245     <span class="i">$ColLabelsRef</span> = <span class="i">SetupFPTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+246
+247     <span class="k">print</span> <span class="q">&quot;Generating text file $NewFPTextFile...\n&quot;</span><span class="sc">;</span>
+248     <span class="i">$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>
+249     <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+250   <span class="s">}</span>
+251
+252   <span class="k">return</span> <span class="s">(</span><span class="i">$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>
+253 <span class="s">}</span>
+254
+255 <span class="c"># Write fingerpritns and other data to appropriate output files...</span>
+256 <span class="c">#</span>
+<a name="WriteDataToOutputFiles-"></a> 257 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span>
+258   <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">$Molecule</span><span class="cm">,</span> <span class="i">$PathLengthFingerprints</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">$NewFPFileIO</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+259   <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+260
+261   <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="k">undef</span><span class="sc">;</span>
+262   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span> || <span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
+263     <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+264   <span class="s">}</span>
+265
+266   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
+267     <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
+268
+269     <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+270     <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
+271   <span class="s">}</span>
+272
+273   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
+274     <span class="k">my</span><span class="s">(</span><span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
+275
+276     <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+277     <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="cm">,</span> <span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
+278   <span class="s">}</span>
+279
+280   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
+281     <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
+282
+283     <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>
+284     <span class="i">$NewFPFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="cm">,</span> <span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
+285   <span class="s">}</span>
+286 <span class="s">}</span>
+287
+288 <span class="c"># Generate approriate column labels for FPText output file...</span>
+289 <span class="c">#</span>
+<a name="SetupFPTextFileCoulmnLabels-"></a> 290 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnLabels</span> <span class="s">{</span>
+291   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+292   <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
+293
+294   <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+295   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+296     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
+297   <span class="s">}</span>
+298   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
+299     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
+300   <span class="s">}</span>
+301   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+302     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
+303   <span class="s">}</span>
+304   <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>
+305     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span>
+306   <span class="s">}</span>
+307   <span class="c"># Add fingerprints label...</span>
+308   <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="sc">;</span>
+309
+310   <span class="k">return</span> \<span class="i">@ColLabels</span><span class="sc">;</span>
+311 <span class="s">}</span>
+312
+313 <span class="c"># Generate column values FPText output file..</span>
+314 <span class="c">#</span>
+<a name="SetupFPTextFileCoulmnValues-"></a> 315 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnValues</span> <span class="s">{</span>
+316   <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>
+317   <span class="k">my</span><span class="s">(</span><span class="i">@ColValues</span><span class="s">)</span><span class="sc">;</span>
+318
+319   <span class="i">@ColValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+320   <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>
+321     <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+322   <span class="s">}</span>
+323   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+324     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
+325   <span class="s">}</span>
+326   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
+327     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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">$FileIndex</span>]}<span class="sc">;</span>
+328   <span class="s">}</span>
+329   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+330     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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>
+331   <span class="s">}</span>
+332
+333   <span class="k">return</span> \<span class="i">@ColValues</span><span class="sc">;</span>
+334 <span class="s">}</span>
+335
+336 <span class="c"># Generate compound ID for FP and FPText output files..</span>
+337 <span class="c">#</span>
+<a name="SetupCmpdIDForOutputFiles-"></a> 338 <span class="k">sub </span><span class="m">SetupCmpdIDForOutputFiles</span> <span class="s">{</span>
+339   <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+340   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span>
+341
+342   <span class="i">$CmpdID</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+343   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolNameOrLabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
+344     <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span>
+345     <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>
+346     <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}${CmpdCount}&quot;</span><span class="sc">;</span>
+347   <span class="s">}</span>
+348   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^LabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
+349     <span class="i">$CmpdID</span> = <span class="q">&quot;$OptionsInfo{CompoundID}${CmpdCount}&quot;</span><span class="sc">;</span>
+350   <span class="s">}</span>
+351   <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>
+352     <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span>
+353     <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
+354     <span class="i">$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>
+355   <span class="s">}</span>
+356   <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>
+357     <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>
+358   <span class="s">}</span>
+359   <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span>
+360 <span class="s">}</span>
+361
+362 <span class="c"># Generate fingerprints for molecule...</span>
+363 <span class="c">#</span>
+<a name="GenerateMoleculeFingerprints-"></a> 364 <span class="k">sub </span><span class="m">GenerateMoleculeFingerprints</span> <span class="s">{</span>
+365   <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+366   <span class="k">my</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span><span class="sc">;</span>
+367
+368   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span>
+369     <span class="i">$Molecule</span><span class="i">-&gt;KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+370   <span class="s">}</span>
+371   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreHydrogens</span>}<span class="s">)</span> <span class="s">{</span>
+372     <span class="i">$Molecule</span><span class="i">-&gt;DeleteHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+373   <span class="s">}</span>
+374
+375   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetectAromaticity</span>}<span class="s">)</span> <span class="s">{</span>
+376     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">-&gt;DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+377       <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+378     <span class="s">}</span>
+379     <span class="i">$Molecule</span><span class="i">-&gt;SetAromaticityModel</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>}<span class="s">)</span><span class="sc">;</span>
+380     <span class="i">$Molecule</span><span class="i">-&gt;DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+381   <span class="s">}</span>
+382
+383   <span class="i">$PathLengthFingerprints</span> = <span class="k">undef</span><span class="sc">;</span>
+384   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span>
+385     <span class="i">$PathLengthFingerprints</span> = <span class="i">GeneratePathLengthBitsFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+386   <span class="s">}</span>
+387   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span>
+388     <span class="i">$PathLengthFingerprints</span> = <span class="i">GeneratePathLengthCountFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+389   <span class="s">}</span>
+390   <span class="k">else</span> <span class="s">{</span>
+391     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m, --mode\&quot; is not valid. Allowed values: PathLengthBits or PathLengthCount\n&quot;</span><span class="sc">;</span>
+392   <span class="s">}</span>
+393
+394   <span class="k">return</span> <span class="i">$PathLengthFingerprints</span><span class="sc">;</span>
+395 <span class="s">}</span>
+396
+397 <span class="c"># Generate pathlength bits finerprints for molecule...</span>
+398 <span class="c">#</span>
+<a name="GeneratePathLengthBitsFingerprints-"></a> 399 <span class="k">sub </span><span class="m">GeneratePathLengthBitsFingerprints</span> <span class="s">{</span>
+400   <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+401   <span class="k">my</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span><span class="sc">;</span>
+402
+403   <span class="i">$PathLengthFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::PathLengthFingerprints</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">&#39;Type&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;PathLengthBits&#39;</span><span class="cm">,</span> <span class="q">&#39;AtomIdentifierType&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">&#39;NumOfBitsToSetPerPath&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">NumOfBitsToSetPerPath</span>}<span class="cm">,</span> <span class="q">&#39;Size&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">Size</span>}<span class="cm">,</span> <span class="q">&#39;MinLength&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">MinPathLength</span>}<span class="cm">,</span> <span class="q">&#39;MaxLength&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxPathLength</span>}<span class="cm">,</span> <span class="q">&#39;AllowRings&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">AllowRings</span>}<span class="cm">,</span> <span class="q">&#39;AllowSharedBonds&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">AllowSharedBonds</span>}<span class="cm">,</span> <span class="q">&#39;UseBondSymbols&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">UseBondSymbols</span>}<span class="cm">,</span> <span class="q">&#39;UseUniquePaths&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">UseUniquePaths</span>}<span class="cm">,</span> <span class="q">&#39;UsePerlCoreRandom&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span><span class="sc">;</span>
+404
+405   <span class="c"># Set atom identifier type...</span>
+406   <span class="i">SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span><span class="sc">;</span>
+407
+408   <span class="c"># Generate fingerprints...</span>
+409   <span class="i">$PathLengthFingerprints</span><span class="i">-&gt;GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+410
+411   <span class="c"># Make sure fingerprints generation is successful...</span>
+412   <span class="k">if</span> <span class="s">(</span>!<span class="i">$PathLengthFingerprints</span><span class="i">-&gt;IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+413     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+414   <span class="s">}</span>
+415
+416   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Fold</span>}<span class="s">)</span> <span class="s">{</span>
+417     <span class="k">my</span><span class="s">(</span><span class="i">$CheckSizeValue</span><span class="s">)</span> = <span class="n">0</span><span class="sc">;</span>
+418     <span class="i">$PathLengthFingerprints</span><span class="i">-&gt;FoldFingerprintsBySize</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FoldedSize</span>}<span class="cm">,</span> <span class="i">$CheckSizeValue</span><span class="s">)</span><span class="sc">;</span>
+419   <span class="s">}</span>
+420
+421   <span class="k">return</span> <span class="i">$PathLengthFingerprints</span><span class="sc">;</span>
+422 <span class="s">}</span>
+423
+424 <span class="c"># Generate pathlength count finerprints for molecule...</span>
+425 <span class="c">#</span>
+<a name="GeneratePathLengthCountFingerprints-"></a> 426 <span class="k">sub </span><span class="m">GeneratePathLengthCountFingerprints</span> <span class="s">{</span>
+427   <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+428   <span class="k">my</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span><span class="sc">;</span>
+429
+430   <span class="i">$PathLengthFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::PathLengthFingerprints</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">&#39;Type&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;PathLengthCount&#39;</span><span class="cm">,</span> <span class="q">&#39;AtomIdentifierType&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">&#39;MinLength&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">MinPathLength</span>}<span class="cm">,</span> <span class="q">&#39;MaxLength&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxPathLength</span>}<span class="cm">,</span> <span class="q">&#39;AllowRings&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">AllowRings</span>}<span class="cm">,</span> <span class="q">&#39;AllowSharedBonds&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">AllowSharedBonds</span>}<span class="cm">,</span> <span class="q">&#39;UseBondSymbols&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">UseBondSymbols</span>}<span class="cm">,</span> <span class="q">&#39;UseUniquePaths&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">UseUniquePaths</span>}<span class="s">)</span><span class="sc">;</span>
+431
+432   <span class="c"># Set atom identifier type...</span>
+433   <span class="i">SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span><span class="sc">;</span>
+434
+435   <span class="c"># Generate fingerprints...</span>
+436   <span class="i">$PathLengthFingerprints</span><span class="i">-&gt;GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+437
+438   <span class="c"># Make sure fingerprints generation is successful...</span>
+439   <span class="k">if</span> <span class="s">(</span>!<span class="i">$PathLengthFingerprints</span><span class="i">-&gt;IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+440     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+441   <span class="s">}</span>
+442   <span class="k">return</span> <span class="i">$PathLengthFingerprints</span><span class="sc">;</span>
+443 <span class="s">}</span>
+444
+445 <span class="c"># Set atom identifier type to use for generating path strings...</span>
+446 <span class="c">#</span>
+<a name="SetAtomIdentifierTypeValuesToUse-"></a> 447 <span class="k">sub </span><span class="m">SetAtomIdentifierTypeValuesToUse</span> <span class="s">{</span>
+448   <span class="k">my</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+449
+450   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+451     <span class="i">$PathLengthFingerprints</span><span class="i">-&gt;SetAtomicInvariantsToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}}<span class="s">)</span><span class="sc">;</span>
+452   <span class="s">}</span>
+453   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+454     <span class="i">$PathLengthFingerprints</span><span class="i">-&gt;SetFunctionalClassesToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span>
+455   <span class="s">}</span>
+456   <span class="k">elsif</span> <span class="s">(</span><span class="i">$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>
+457     <span class="c"># Nothing to do for now...</span>
+458   <span class="s">}</span>
+459   <span class="k">else</span> <span class="s">{</span>
+460     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{atomidentifiertype}, for option \&quot;-a, --AtomIdentifierType\&quot; is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n&quot;</span><span class="sc">;</span>
+461   <span class="s">}</span>
+462 <span class="s">}</span>
+463
+464 <span class="c"># Retrieve information about SD files...</span>
+465 <span class="c">#</span>
+<a name="RetrieveSDFilesInfo-"></a> 466 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
+467   <span class="k">my</span><span class="s">(</span><span class="i">$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">$CommonDataFieldsRef</span><span class="s">)</span><span class="sc">;</span>
+468
+469   <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+470   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+471   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+472   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+473   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+474   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+475   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+476   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+477
+478   <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>
+479   <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>
+480
+481   <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>
+482     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+483
+484     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+485     <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+486     <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+487     <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+488     <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+489
+490     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+491     <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>
+492       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+493       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+494     <span class="s">}</span>
+495     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$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>
+496       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
+497       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+498     <span class="s">}</span>
+499
+500     <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span>
+501       <span class="c"># Make sure data field exists in SD file..</span>
+502       <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>
+503
+504       <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+505       <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: $! \n&quot;</span><span class="sc">;</span>
+506       <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
+507       <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+508       <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+509       <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
+510       <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
+511       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span>
+512         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using  \&quot;--CompoundID\&quot; option in \&quot;DataField\&quot; \&quot;--CompoundIDMode\&quot; doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+513         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+514       <span class="s">}</span>
+515     <span class="s">}</span>
+516
+517     <span class="i">$AllDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+518     <span class="i">$CommonDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+519     <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span>
+520       <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
+521       <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
+522       <span class="s">(</span><span class="i">$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>
+523       <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+524     <span class="s">}</span>
+525
+526     <span class="c"># Setup output file names...</span>
+527     <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">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+528     <span class="s">(</span><span class="i">$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">$SDFile</span><span class="s">)</span><span class="sc">;</span>
+529
+530     <span class="i">$TextOutFileExt</span> = <span class="q">&quot;csv&quot;</span><span class="sc">;</span>
+531     <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>
+532       <span class="i">$TextOutFileExt</span> = <span class="q">&quot;tsv&quot;</span><span class="sc">;</span>
+533     <span class="s">}</span>
+534     <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span>
+535     <span class="i">$FPOutFileExt</span> = <span class="q">&quot;fpf&quot;</span><span class="sc">;</span>
+536
+537     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+538       <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
+539       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+540         <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+541       <span class="s">}</span>
+542       <span class="k">else</span> <span class="s">{</span>
+543         <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
+544       <span class="s">}</span>
+545       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+546     <span class="s">}</span>
+547     <span class="k">else</span> <span class="s">{</span>
+548       <span class="i">$OutFileRoot</span> = <span class="q">&quot;${FileName}PathLengthFP&quot;</span><span class="sc">;</span>
+549     <span class="s">}</span>
+550
+551     <span class="i">$NewSDFileName</span> = <span class="q">&quot;${OutFileRoot}.${SDOutFileExt}&quot;</span><span class="sc">;</span>
+552     <span class="i">$NewFPFileName</span> = <span class="q">&quot;${OutFileRoot}.${FPOutFileExt}&quot;</span><span class="sc">;</span>
+553     <span class="i">$NewTextFileName</span> = <span class="q">&quot;${OutFileRoot}.${TextOutFileExt}&quot;</span><span class="sc">;</span>
+554
+555     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+556       <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span>
+557         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n&quot;</span><span class="sc">;</span>
+558         <span class="k">print</span> <span class="q">&quot;Specify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
+559         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+560       <span class="s">}</span>
+561     <span class="s">}</span>
+562
+563     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
+564       <span class="c"># Check SD, FP and text outout files...</span>
+565       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+566         <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span>
+567           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n&quot;</span><span class="sc">;</span>
+568           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+569         <span class="s">}</span>
+570       <span class="s">}</span>
+571       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
+572         <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>
+573           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n&quot;</span><span class="sc">;</span>
+574           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+575         <span class="s">}</span>
+576       <span class="s">}</span>
+577       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
+578         <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>
+579           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n&quot;</span><span class="sc">;</span>
+580           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+581         <span class="s">}</span>
+582       <span class="s">}</span>
+583     <span class="s">}</span>
+584
+585     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+586
+587     <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
+588     <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span>
+589     <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewFPFileName</span><span class="sc">;</span>
+590     <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span>
+591
+592     <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span>
+593     <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span>
+594   <span class="s">}</span>
+595 <span class="s">}</span>
+596
+597 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 598 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+599   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+600
+601   <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+602   <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span>
+603   <span class="i">$OptionsInfo</span>{<span class="w">PathMode</span>} = <span class="i">$Options</span>{<span class="w">pathmode</span>}<span class="sc">;</span>
+604
+605   <span class="i">ProcessAtomIdentifierTypeOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+606
+607   <span class="i">$OptionsInfo</span>{<span class="w">BitsOrder</span>} = <span class="i">$Options</span>{<span class="w">bitsorder</span>}<span class="sc">;</span>
+608   <span class="i">$OptionsInfo</span>{<span class="w">BitStringFormat</span>} = <span class="i">$Options</span>{<span class="w">bitstringformat</span>}<span class="sc">;</span>
+609
+610   <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span>
+611   <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span>
+612   <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span>
+613
+614   <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span>
+615   <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+616
+617   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+618   <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+619
+620   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
+621     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
+622       <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span>
+623         <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>
+624       <span class="s">}</span>
+625       <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span>
+626     <span class="s">}</span>
+627     <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>
+628       <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>} ? <span class="i">$Options</span>{<span class="w">compoundid</span>} <span class="co">:</span> <span class="q">&#39;Cmpd&#39;</span><span class="sc">;</span>
+629     <span class="s">}</span>
+630   <span class="s">}</span>
+631   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+632     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span>
+633       <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>
+634     <span class="s">}</span>
+635     <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span>
+636     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span>
+637   <span class="s">}</span>
+638
+639   <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>
+640     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">detectaromaticity</span>} =~ <span class="q">/^No$/i</span><span class="s">)</span> <span class="s">{</span>
+641       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{detectaromaticity}, for option \&quot;--DetectAromaticity\&quot; is not valid. No value is only allowed during AtomicInvariantsAtomTypes value for \&quot;-a, --AtomIdentifierType\&quot; \n&quot;</span><span class="sc">;</span>
+642     <span class="s">}</span>
+643   <span class="s">}</span>
+644   <span class="i">$OptionsInfo</span>{<span class="w">DetectAromaticity</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">detectaromaticity</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+645
+646   <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+647
+648   <span class="i">$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;PathLengthFingerprints&#39;</span><span class="sc">;</span>
+649
+650   <span class="k">my</span><span class="s">(</span><span class="i">$Size</span><span class="cm">,</span> <span class="i">$MinSize</span><span class="cm">,</span> <span class="i">$MaxSize</span><span class="s">)</span><span class="sc">;</span>
+651   <span class="i">$MinSize</span> = <span class="n">32</span><span class="sc">;</span>
+652   <span class="i">$MaxSize</span> = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span>
+653   <span class="i">$Size</span> = <span class="i">$Options</span>{<span class="w">size</span>}<span class="sc">;</span>
+654   <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span> &amp;&amp; <span class="i">$Size</span> &gt;= <span class="i">$MinSize</span> &amp;&amp; <span class="i">$Size</span> &lt;= <span class="i">$MaxSize</span> &amp;&amp; <span class="i">IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$Size</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+655     <span class="k">die</span> <span class="q">&quot;Error: Invalid size value, $Size, for \&quot;-s, --size\&quot; option. Allowed values: power of 2, &gt;= minimum size of $MinSize, and &lt;= maximum size of $MaxSize.\n&quot;</span><span class="sc">;</span>
+656   <span class="s">}</span>
+657   <span class="i">$OptionsInfo</span>{<span class="w">Size</span>} = <span class="i">$Size</span><span class="sc">;</span>
+658
+659   <span class="i">$OptionsInfo</span>{<span class="w">Fold</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">fold</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+660   <span class="k">my</span><span class="s">(</span><span class="i">$FoldedSize</span><span class="s">)</span><span class="sc">;</span>
+661   <span class="i">$FoldedSize</span> = <span class="i">$Options</span>{<span class="w">foldedsize</span>}<span class="sc">;</span>
+662   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fold</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> <span class="s">{</span>
+663     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$FoldedSize</span><span class="s">)</span> &amp;&amp; <span class="i">$FoldedSize</span> &lt; <span class="i">$Size</span> &amp;&amp; <span class="i">IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$FoldedSize</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+664       <span class="k">die</span> <span class="q">&quot;Error: Invalid folded size value, $FoldedSize, for \&quot;--FoldedSize\&quot; option. Allowed values: power of 2, &gt;= minimum size of $MinSize, and &lt; size value of $Size.\n&quot;</span><span class="sc">;</span>
+665     <span class="s">}</span>
+666   <span class="s">}</span>
+667   <span class="i">$OptionsInfo</span>{<span class="w">FoldedSize</span>} = <span class="i">$FoldedSize</span><span class="sc">;</span>
+668
+669   <span class="i">$OptionsInfo</span>{<span class="w">IgnoreHydrogens</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignorehydrogens</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+670   <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+671
+672   <span class="k">my</span><span class="s">(</span><span class="i">$MinPathLength</span><span class="cm">,</span> <span class="i">$MaxPathLength</span><span class="s">)</span><span class="sc">;</span>
+673   <span class="i">$MinPathLength</span> = <span class="i">$Options</span>{<span class="w">minpathlength</span>}<span class="sc">;</span>
+674   <span class="i">$MaxPathLength</span> = <span class="i">$Options</span>{<span class="w">maxpathlength</span>}<span class="sc">;</span>
+675   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$MinPathLength</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+676     <span class="k">die</span> <span class="q">&quot;Error: Invalid path length value, $MinPathLength, for \&quot;--MinPathLength\&quot; option. Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
+677   <span class="s">}</span>
+678   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$MaxPathLength</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+679     <span class="k">die</span> <span class="q">&quot;Error: Invalid path length value, $MaxPathLength, for \&quot;--MinPathLength\&quot; option. Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
+680   <span class="s">}</span>
+681   <span class="k">if</span> <span class="s">(</span><span class="i">$MinPathLength</span> &gt;= <span class="i">$MaxPathLength</span><span class="s">)</span> <span class="s">{</span>
+682     <span class="k">die</span> <span class="q">&quot;Error: Invalid minimum and maximum path length values, $MinPathLength and $MaxPathLength, for \&quot;--MinPathLength\&quot;  and \&quot;--MaxPathLength\&quot;options. Allowed values: minimum path length value must be smaller than maximum path length value.\n&quot;</span><span class="sc">;</span>
+683   <span class="s">}</span>
+684   <span class="i">$OptionsInfo</span>{<span class="w">MinPathLength</span>} = <span class="i">$MinPathLength</span><span class="sc">;</span>
+685   <span class="i">$OptionsInfo</span>{<span class="w">MaxPathLength</span>} = <span class="i">$MaxPathLength</span><span class="sc">;</span>
+686
+687   <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBitsToSetPerPath</span><span class="s">)</span><span class="sc">;</span>
+688   <span class="i">$NumOfBitsToSetPerPath</span> = <span class="i">$Options</span>{<span class="w">numofbitstosetperpath</span>}<span class="sc">;</span>
+689   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$MaxPathLength</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+690     <span class="k">die</span> <span class="q">&quot;Error: Invalid  value, $NumOfBitsToSetPerPath, for \&quot;-n, --NumOfBitsToSetPerPath\&quot; option. Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
+691   <span class="s">}</span>
+692   <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfBitsToSetPerPath</span> &gt;= <span class="i">$Size</span><span class="s">)</span> <span class="s">{</span>
+693     <span class="k">die</span> <span class="q">&quot;Error: Invalid  value, $NumOfBitsToSetPerPath, for \&quot;-n, --NumOfBitsToSetPerPath\&quot; option. Allowed values: It must be less than the size, $Size, of the fingerprint bit-string.\n&quot;</span><span class="sc">;</span>
+694   <span class="s">}</span>
+695   <span class="i">$OptionsInfo</span>{<span class="w">NumOfBitsToSetPerPath</span>} = <span class="i">$NumOfBitsToSetPerPath</span><span class="sc">;</span>
+696
+697   <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
+698   <span class="i">$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>
+699   <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+700   <span class="i">$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>
+701
+702   <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="i">$Options</span>{<span class="w">outdelim</span>}<span class="sc">;</span>
+703   <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+704
+705   <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+706   <span class="i">$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>
+707
+708   <span class="i">$OptionsInfo</span>{<span class="w">UseBondSymbols</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">usebondsymbols</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+709
+710   <span class="i">$OptionsInfo</span>{<span class="w">UsePerlCoreRandom</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">useperlcorerandom</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+711
+712   <span class="i">$OptionsInfo</span>{<span class="w">UseUniquePaths</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">useuniquepaths</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+713
+714   <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>} = <span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="sc">;</span>
+715
+716   <span class="c"># Setup parameters used during generation of fingerprints by PathLengthFingerprints class...</span>
+717   <span class="k">my</span><span class="s">(</span><span class="i">$AllowRings</span><span class="cm">,</span> <span class="i">$AllowSharedBonds</span><span class="s">)</span><span class="sc">;</span>
+718   <span class="i">$AllowRings</span> = <span class="n">1</span><span class="sc">;</span>
+719   <span class="i">$AllowSharedBonds</span> = <span class="n">1</span><span class="sc">;</span>
+720   <span class="j">MODE:</span> <span class="s">{</span>
+721     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">pathmode</span>} =~ <span class="q">/^AtomPathsWithoutRings$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$AllowSharedBonds</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$AllowRings</span> = <span class="n">0</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
+722     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">pathmode</span>} =~ <span class="q">/^AtomPathsWithRings$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$AllowSharedBonds</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$AllowRings</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
+723     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">pathmode</span>} =~ <span class="q">/^AllAtomPathsWithoutRings$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$AllowSharedBonds</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$AllowRings</span> = <span class="n">0</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
+724     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">pathmode</span>} =~ <span class="q">/^AllAtomPathsWithRings$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$AllowSharedBonds</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$AllowRings</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
+725     <span class="k">die</span> <span class="q">&quot;Error: ProcessOptions: mode value, $Options{pathmode}, is not supported.\n&quot;</span><span class="sc">;</span>
+726   <span class="s">}</span>
+727   <span class="i">$OptionsInfo</span>{<span class="w">AllowRings</span>} = <span class="i">$AllowRings</span><span class="sc">;</span>
+728   <span class="i">$OptionsInfo</span>{<span class="w">AllowSharedBonds</span>} = <span class="i">$AllowSharedBonds</span><span class="sc">;</span>
+729 <span class="s">}</span>
+730
+731 <span class="c"># Process atom identifier type and related options...</span>
+732 <span class="c">#</span>
+<a name="ProcessAtomIdentifierTypeOptions-"></a> 733 <span class="k">sub </span><span class="m">ProcessAtomIdentifierTypeOptions</span> <span class="s">{</span>
+734
+735   <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} = <span class="i">$Options</span>{<span class="w">atomidentifiertype</span>}<span class="sc">;</span>
+736
+737   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+738     <span class="i">ProcessAtomicInvariantsToUseOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+739   <span class="s">}</span>
+740   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+741     <span class="i">ProcessFunctionalClassesToUse</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+742   <span class="s">}</span>
+743   <span class="k">elsif</span> <span class="s">(</span><span class="i">$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>
+744     <span class="c"># Nothing to do for now...</span>
+745   <span class="s">}</span>
+746   <span class="k">else</span> <span class="s">{</span>
+747     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{atomidentifiertype}, for option \&quot;-a, --AtomIdentifierType\&quot; is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n&quot;</span><span class="sc">;</span>
+748   <span class="s">}</span>
+749 <span class="s">}</span>
+750
+751 <span class="c"># Process specified atomic invariants to use...</span>
+752 <span class="c">#</span>
+<a name="ProcessAtomicInvariantsToUseOption-"></a> 753 <span class="k">sub </span><span class="m">ProcessAtomicInvariantsToUseOption</span> <span class="s">{</span>
+754   <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomSymbolSpecified</span><span class="cm">,</span> <span class="i">@AtomicInvariantsWords</span><span class="s">)</span><span class="sc">;</span>
+755
+756   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+757   <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+758     <span class="k">die</span> <span class="q">&quot;Error: Atomic invariants value specified using \&quot;--AtomicInvariantsToUse\&quot; option is empty\n&quot;</span><span class="sc">;</span>
+759   <span class="s">}</span>
+760   <span class="i">$AtomSymbolSpecified</span> = <span class="n">0</span><span class="sc">;</span>
+761   <span class="i">@AtomicInvariantsWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>}<span class="sc">;</span>
+762   <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsWords</span><span class="s">)</span> <span class="s">{</span>
+763     <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>
+764       <span class="k">die</span> <span class="q">&quot;Error: Atomic invariant specified, $AtomicInvariant, using \&quot;--AtomicInvariantsToUse\&quot; option is not valid...\n &quot;</span><span class="sc">;</span>
+765     <span class="s">}</span>
+766     <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AS|AtomSymbol)$/i</span><span class="s">)</span> <span class="s">{</span>
+767       <span class="i">$AtomSymbolSpecified</span> = <span class="n">1</span><span class="sc">;</span>
+768     <span class="s">}</span>
+769     <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>
+770   <span class="s">}</span>
+771   <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSymbolSpecified</span><span class="s">)</span> <span class="s">{</span>
+772     <span class="k">die</span> <span class="q">&quot;Error: Atomic invariant, AS or AtomSymbol, must be specified as using \&quot;--AtomicInvariantsToUse\&quot; option...\n &quot;</span><span class="sc">;</span>
+773   <span class="s">}</span>
+774 <span class="s">}</span>
+775
+776 <span class="c"># Process specified functional classes invariants to use...</span>
+777 <span class="c">#</span>
+<a name="ProcessFunctionalClassesToUse-"></a> 778 <span class="k">sub </span><span class="m">ProcessFunctionalClassesToUse</span> <span class="s">{</span>
+779   <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUseWords</span><span class="s">)</span><span class="sc">;</span>
+780
+781   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+782   <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">functionalclassestouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+783     <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>
+784   <span class="s">}</span>
+785   <span class="i">@FunctionalClassesToUseWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">functionalclassestouse</span>}<span class="sc">;</span>
+786   <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesToUseWords</span><span class="s">)</span> <span class="s">{</span>
+787     <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>
+788       <span class="k">die</span> <span class="q">&quot;Error: Functional class specified, $FunctionalClass, using \&quot;--FunctionalClassesToUse\&quot; option is not valid...\n &quot;</span><span class="sc">;</span>
+789     <span class="s">}</span>
+790     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="sc">;</span>
+791   <span class="s">}</span>
+792 <span class="s">}</span>
+793
+794 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 795 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+796
+797   <span class="c"># Retrieve all the options...</span>
+798   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+799
+800   <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">&#39;MayaChemToolsAromaticityModel&#39;</span><span class="sc">;</span>
+801
+802   <span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} = <span class="q">&#39;AtomicInvariantsAtomTypes&#39;</span><span class="sc">;</span>
+803   <span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>} = <span class="q">&#39;AS&#39;</span><span class="sc">;</span>
+804
+805   <span class="i">$Options</span>{<span class="w">functionalclassestouse</span>} = <span class="q">&#39;HBD,HBA,PI,NI,Ar,Hal&#39;</span><span class="sc">;</span>
+806
+807   <span class="i">$Options</span>{<span class="w">bitsorder</span>} = <span class="q">&#39;Ascending&#39;</span><span class="sc">;</span>
+808   <span class="i">$Options</span>{<span class="w">bitstringformat</span>} = <span class="q">&#39;HexadecimalString&#39;</span><span class="sc">;</span>
+809
+810   <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">&#39;LabelPrefix&#39;</span><span class="sc">;</span>
+811   <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+812   <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+813   <span class="i">$Options</span>{<span class="w">detectaromaticity</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+814
+815   <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+816
+817   <span class="i">$Options</span>{<span class="w">fold</span>} = <span class="q">&#39;No&#39;</span><span class="sc">;</span>
+818   <span class="i">$Options</span>{<span class="w">foldedsize</span>} = <span class="n">256</span><span class="sc">;</span>
+819
+820   <span class="i">$Options</span>{<span class="w">ignorehydrogens</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+821   <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+822
+823   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;PathLengthBits&#39;</span><span class="sc">;</span>
+824   <span class="i">$Options</span>{<span class="w">pathmode</span>} = <span class="q">&#39;AllAtomPathsWithRings&#39;</span><span class="sc">;</span>
+825
+826   <span class="i">$Options</span>{<span class="w">minpathlength</span>} = <span class="n">1</span><span class="sc">;</span>
+827   <span class="i">$Options</span>{<span class="w">maxpathlength</span>} = <span class="n">8</span><span class="sc">;</span>
+828
+829   <span class="i">$Options</span>{<span class="w">numofbitstosetperpath</span>} = <span class="n">1</span><span class="sc">;</span>
+830
+831   <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">&#39;text&#39;</span><span class="sc">;</span>
+832   <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&#39;comma&#39;</span><span class="sc">;</span>
+833   <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+834
+835   <span class="i">$Options</span>{<span class="w">size</span>} = <span class="n">1024</span><span class="sc">;</span>
+836
+837   <span class="i">$Options</span>{<span class="w">usebondsymbols</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+838   <span class="i">$Options</span>{<span class="w">useperlcorerandom</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+839   <span class="i">$Options</span>{<span class="w">useuniquepaths</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+840
+841   <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} = <span class="q">&#39;IDsAndValuesString&#39;</span><span class="sc">;</span>
+842
+843   <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;bitsorder=s&quot;</span><span class="cm">,</span> <span class="q">&quot;bitstringformat|b=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;detectaromaticity=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;fold=s&quot;</span><span class="cm">,</span> <span class="q">&quot;foldedsize=i&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;ignorehydrogens|i=s&quot;</span><span class="cm">,</span> <span class="q">&quot;keeplargestcomponent|k=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;minpathlength=i&quot;</span><span class="cm">,</span> <span class="q">&quot;maxpathlength=i&quot;</span><span class="cm">,</span> <span class="q">&quot;numofbitstosetperpath|n=i&quot;</span><span class="cm">,</span> <span class="q">&quot;outdelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;output=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;pathmode|p=s&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;size|s=i&quot;</span><span class="cm">,</span> <span class="q">&quot;usebondsymbols|u=s&quot;</span><span class="cm">,</span> <span class="q">&quot;useperlcorerandom=s&quot;</span><span class="cm">,</span> <span class="q">&quot;useuniquepaths=s&quot;</span><span class="cm">,</span> <span class="q">&quot;vectorstringformat|v=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>
+844     <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 $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+845   <span class="s">}</span>
+846   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+847     <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>
+848       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+849     <span class="s">}</span>
+850     <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
+851   <span class="s">}</span>
+852   <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+853     <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>
+854     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{aromaticitymodel}, for option \&quot;--AromaticityModel\&quot; is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n&quot;</span><span class="sc">;</span>
+855   <span class="s">}</span>
+856   <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+857     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{atomidentifiertype}, for option \&quot;-a, --AtomIdentifierType\&quot; is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n&quot;</span><span class="sc">;</span>
+858   <span class="s">}</span>
+859   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">bitsorder</span>} !~ <span class="q">/^(Ascending|Descending)$/i</span><span class="s">)</span> <span class="s">{</span>
+860     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{bitsorder}, for option \&quot;--BitsOrder\&quot; is not valid. Allowed values: Ascending or Descending\n&quot;</span><span class="sc">;</span>
+861   <span class="s">}</span>
+862   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">bitstringformat</span>} !~ <span class="q">/^(BinaryString|HexadecimalString)$/i</span><span class="s">)</span> <span class="s">{</span>
+863     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{bitstringformat}, for option \&quot;-b, --bitstringformat\&quot; is not valid. Allowed values: BinaryString or HexadecimalString\n&quot;</span><span class="sc">;</span>
+864   <span class="s">}</span>
+865   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
+866     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{compoundidmode}, for option \&quot;--CompoundIDMode\&quot; is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n&quot;</span><span class="sc">;</span>
+867   <span class="s">}</span>
+868   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span>
+869     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{datafieldsmode}, for option \&quot;-d, --DataFieldsMode\&quot; is not valid. Allowed values: All, Common, Specify or CompoundID\n&quot;</span><span class="sc">;</span>
+870   <span class="s">}</span>
+871   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">detectaromaticity</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+872     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{detectaromaticity}, for option \&quot;--DetectAromaticity\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+873   <span class="s">}</span>
+874   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+875     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{filter}, for option \&quot;-f, --Filter\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+876   <span class="s">}</span>
+877   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fold</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+878     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{fold}, for option \&quot;--fold\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+879   <span class="s">}</span>
+880   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">foldedsize</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+881     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{foldedsize}, for option \&quot;--FoldedSize\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+882   <span class="s">}</span>
+883   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignorehydrogens</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+884     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{ignorehydrogens}, for option \&quot;-i, --IgnoreHydrogens\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+885   <span class="s">}</span>
+886   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+887     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{keeplargestcomponent}, for option \&quot;-k, --KeepLargestComponent\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+888   <span class="s">}</span>
+889   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(PathLengthBits|PathLengthCount)$/i</span><span class="s">)</span> <span class="s">{</span>
+890     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m, --mode\&quot; is not valid. Allowed values: PathLengthBits or PathLengthCount\n&quot;</span><span class="sc">;</span>
+891   <span class="s">}</span>
+892   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">minpathlength</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+893     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{minpathlength}, for option \&quot;--MinPathLength\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+894   <span class="s">}</span>
+895   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">numofbitstosetperpath</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+896     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{NumOfBitsToSetPerPath}, for option \&quot;--NumOfBitsToSetPerPath\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+897   <span class="s">}</span>
+898   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">maxpathlength</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+899     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{maxpathlength}, for option \&quot;--MaxPathLength\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+900   <span class="s">}</span>
+901   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|FP|text|all)$/i</span><span class="s">)</span> <span class="s">{</span>
+902     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{output}, for option \&quot;--output\&quot; is not valid. Allowed values: SD, FP, text, or all\n&quot;</span><span class="sc">;</span>
+903   <span class="s">}</span>
+904   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
+905     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--outdelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
+906   <span class="s">}</span>
+907   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">pathmode</span>} !~ <span class="q">/^(AtomPathsWithoutRings|AtomPathsWithRings|AllAtomPathsWithoutRings|AllAtomPathsWithRings)$/i</span><span class="s">)</span> <span class="s">{</span>
+908     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{pathmode}, for option \&quot;-m, --PathMode\&quot; is not valid. Allowed values: AtomPathsWithoutRings, AtomPathsWithRings, AllAtomPathsWithoutRings or AllAtomPathsWithRings\n&quot;</span><span class="sc">;</span>
+909   <span class="s">}</span>
+910   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+911     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+912   <span class="s">}</span>
+913   <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+914     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not allowed with, semicolon value of \&quot;--outdelim\&quot; option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n&quot;</span><span class="sc">;</span>
+915   <span class="s">}</span>
+916
+917   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">size</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+918     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{size}, for option \&quot;-s, --size\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+919   <span class="s">}</span>
+920   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">usebondsymbols</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+921     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{usebondsymbols}, for option \&quot;-u, --UseBondSymbols\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+922   <span class="s">}</span>
+923   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">useperlcorerandom</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+924     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{useperlcorerandom}, for option \&quot;--UsePerlCoreRandom\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+925   <span class="s">}</span>
+926   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">useuniquepaths</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+927     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{useuniquepaths}, for option \&quot;--UseUniquePaths\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+928   <span class="s">}</span>
+929   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>} !~ <span class="q">/^(IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i</span><span class="s">)</span> <span class="s">{</span>
+930     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{vectorstringformat}, for option \&quot;-v, --VectorStringFormat\&quot; is not valid. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n&quot;</span><span class="sc">;</span>
+931   <span class="s">}</span>
+932 <span class="s">}</span>
+933
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>

Mercurial > repos > deepakjadmin > mayatool3_test1

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