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+1 #!/usr/bin/perl -w
+2 <span class="c">#</span>
+3 <span class="c"># $RCSfile: TopologicalPharmacophoreAtomPairsFingerprints.pl,v $</span>
+4 <span class="c"># $Date: 2015/02/28 20:46:23 $</span>
+5 <span class="c"># $Revision: 1.36 $</span>
+6 <span class="c">#</span>
+7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+8 <span class="c">#</span>
+9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+10 <span class="c">#</span>
+11 <span class="c"># This file is part of MayaChemTools.</span>
+12 <span class="c">#</span>
+13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+16 <span class="c"># later version.</span>
+17 <span class="c">#</span>
+18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+21 <span class="c"># details.</span>
+22 <span class="c">#</span>
+23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+27 <span class="c">#</span>
+28
+29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$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::FunctionalClassAtomTypes</span><span class="sc">;</span>
+43 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span>
+44
+45 <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>
+46
+47 <span class="c"># Autoflush STDOUT</span>
+48 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+49
+50 <span class="c"># Starting message...</span>
+51 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
+52 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
+53 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+54
+55 <span class="c"># Get the options and setup script...</span>
+56 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+57 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+58   <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>
+59 <span class="s">}</span>
+60
+61 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
+62 <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>
+63
+64 <span class="c"># Process options...</span>
+65 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+66 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+67 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+68
+69 <span class="c"># Setup information about input files...</span>
+70 <span class="k">print</span> <span class="q">&quot;Checking input SD file(s)...\n&quot;</span><span class="sc">;</span>
+71 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
+72 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+73
+74 <span class="c"># Process input files..</span>
+75 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+76 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+77   <span class="k">print</span> <span class="q">&quot;\nProcessing SD files...\n&quot;</span><span class="sc">;</span>
+78 <span class="s">}</span>
+79 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+80   <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+81     <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+82     <span class="i">GenerateTopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+83   <span class="s">}</span>
+84 <span class="s">}</span>
+85 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+86
+87 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+88 <span class="i">$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>
+89 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+90
+91 <span class="c">###############################################################################</span>
+92
+93 <span class="c"># Generate fingerprints for a SD file...</span>
+94 <span class="c">#</span>
+<a name="GenerateTopologicalPharmacophoreAtomPairsFingerprints-"></a>  95 <span class="k">sub </span><span class="m">GenerateTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span>
+96   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+97   <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">$Molecule</span><span class="cm">,</span> <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</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">$NewFPFileIO</span><span class="cm">,</span> <span class="i">$SetupOutputFiles</span><span class="s">)</span><span class="sc">;</span>
+98
+99   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+100
+101   <span class="s">(</span><span class="i">$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>
+102   <span class="i">$SetupOutputFiles</span> = <span class="n">1</span><span class="sc">;</span>
+103
+104   <span class="i">$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">$SDFile</span><span class="s">)</span><span class="sc">;</span>
+105   <span class="i">$MoleculeFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+106
+107   <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+108   <span class="i">$IgnoredCmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+109
+110   <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>
+111     <span class="i">$CmpdCount</span>++<span class="sc">;</span>
+112
+113     <span class="c"># Filter compound data before calculating fingerprints...</span>
+114     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Filter</span>}<span class="s">)</span> <span class="s">{</span>
+115       <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>
+116         <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
+117         <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
+118       <span class="s">}</span>
+119     <span class="s">}</span>
+120
+121     <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span> = <span class="i">GenerateMoleculeFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+122     <span class="k">if</span> <span class="s">(</span>!<span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">)</span> <span class="s">{</span>
+123       <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
+124       <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">&#39;FingerprintsGenerationFailed&#39;</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+125       <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
+126     <span class="s">}</span>
+127
+128     <span class="k">if</span> <span class="s">(</span><span class="i">$SetupOutputFiles</span><span class="s">)</span> <span class="s">{</span>
+129       <span class="i">$SetupOutputFiles</span> = <span class="n">0</span><span class="sc">;</span>
+130       <span class="i">SetupFingerprintsLabelValueIDs</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">)</span><span class="sc">;</span>
+131       <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>
+132     <span class="s">}</span>
+133
+134     <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">$Molecule</span><span class="cm">,</span> <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</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">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
+135   <span class="s">}</span>
+136   <span class="i">$MoleculeFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+137
+138   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
+139     <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+140   <span class="s">}</span>
+141   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
+142     <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+143   <span class="s">}</span>
+144   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
+145     <span class="i">$NewFPFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+146   <span class="s">}</span>
+147
+148   <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>
+149 <span class="s">}</span>
+150
+151 <span class="c"># Process compound being ignored due to problems in fingerprints geneation...</span>
+152 <span class="c">#</span>
+<a name="ProcessIgnoredCompound-"></a> 153 <span class="k">sub </span><span class="m">ProcessIgnoredCompound</span> <span class="s">{</span>
+154   <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">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+155   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+156
+157   <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+158   <span class="i">$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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+159
+160   <span class="j">MODE:</span> <span class="s">{</span>
+161     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNonElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
+162       <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n&quot;</span><span class="sc">;</span>
+163       <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
+164     <span class="s">}</span>
+165
+166     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNoElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
+167       <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n&quot;</span><span class="sc">;</span>
+168       <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
+169     <span class="s">}</span>
+170
+171     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^FingerprintsGenerationFailed$/i</span><span class="s">)</span> <span class="s">{</span>
+172       <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>
+173       <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
+174     <span class="s">}</span>
+175     <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn&#39;t succeed...\n\n&quot;</span><span class="sc">;</span>
+176   <span class="s">}</span>
+177 <span class="s">}</span>
+178
+179 <span class="c"># Check and filter compounds....</span>
+180 <span class="c">#</span>
+<a name="CheckAndFilterCompound-"></a> 181 <span class="k">sub </span><span class="m">CheckAndFilterCompound</span> <span class="s">{</span>
+182   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+183   <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span>
+184
+185   <span class="s">(</span><span class="i">$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>
+186
+187   <span class="k">if</span> <span class="s">(</span><span class="i">$NonElementCount</span><span class="s">)</span> <span class="s">{</span>
+188     <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">&#39;ContainsNonElementalData&#39;</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+189     <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
+190   <span class="s">}</span>
+191
+192   <span class="k">if</span> <span class="s">(</span>!<span class="i">$ElementCount</span><span class="s">)</span> <span class="s">{</span>
+193     <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>
+194     <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
+195   <span class="s">}</span>
+196
+197   <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
+198 <span class="s">}</span>
+199
+200 <span class="c"># Write out compounds fingerprints generation summary statistics...</span>
+201 <span class="c">#</span>
+<a name="WriteFingerprintsGenerationSummaryStatistics-"></a> 202 <span class="k">sub </span><span class="m">WriteFingerprintsGenerationSummaryStatistics</span> <span class="s">{</span>
+203   <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>
+204   <span class="k">my</span><span class="s">(</span><span class="i">$ProcessedCmpdCount</span><span class="s">)</span><span class="sc">;</span>
+205
+206   <span class="i">$ProcessedCmpdCount</span> = <span class="i">$CmpdCount</span> - <span class="i">$IgnoredCmpdCount</span><span class="sc">;</span>
+207
+208   <span class="k">print</span> <span class="q">&quot;\nNumber of compounds: $CmpdCount\n&quot;</span><span class="sc">;</span>
+209   <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>
+210   <span class="k">print</span> <span class="q">&quot;Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n&quot;</span><span class="sc">;</span>
+211 <span class="s">}</span>
+212
+213 <span class="c"># Append atom pair value IDs to fingerprint label...</span>
+214 <span class="c">#</span>
+<a name="SetupFingerprintsLabelValueIDs-"></a> 215 <span class="k">sub </span><span class="m">SetupFingerprintsLabelValueIDs</span> <span class="s">{</span>
+216   <span class="k">my</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+217
+218   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomPairsSetSizeToUse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> ||
+219       <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabelMode</span>} !~ <span class="q">/^FingerprintsLabelWithIDs$/i</span><span class="s">)</span> <span class="s">{</span>
+220     <span class="k">return</span><span class="sc">;</span>
+221   <span class="s">}</span>
+222
+223   <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>} .= <span class="q">&quot;; Value IDs: &quot;</span> . <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="i">-&gt;GetFingerprintsVector</span><span class="i">-&gt;GetValueIDsString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+224 <span class="s">}</span>
+225
+226 <span class="c"># Open output files...</span>
+227 <span class="c">#</span>
+<a name="SetupAndOpenOutputFiles-"></a> 228 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span>
+229   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+230   <span class="k">my</span><span class="s">(</span><span class="i">$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">$NewFPFileIO</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
+231
+232   <span class="s">(</span><span class="i">$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>
+233
+234   <span class="c"># Setup common parameters for fingerprints file IO objects...</span>
+235   <span class="c">#</span>
+236   <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>
+237
+238   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+239     <span class="i">$NewFPSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+240     <span class="k">print</span> <span class="q">&quot;Generating SD file $NewFPSDFile...\n&quot;</span><span class="sc">;</span>
+241     <span class="i">$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>
+242     <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+243   <span class="s">}</span>
+244
+245   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
+246     <span class="i">$NewFPFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+247     <span class="k">print</span> <span class="q">&quot;Generating FP file $NewFPFile...\n&quot;</span><span class="sc">;</span>
+248     <span class="i">$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">$NewFPFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
+249     <span class="i">$NewFPFileIO</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">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
+253     <span class="k">my</span><span class="s">(</span><span class="i">$ColLabelsRef</span><span class="s">)</span><span class="sc">;</span>
+254
+255     <span class="i">$NewFPTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+256     <span class="i">$ColLabelsRef</span> = <span class="i">SetupFPTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+257
+258     <span class="k">print</span> <span class="q">&quot;Generating text file $NewFPTextFile...\n&quot;</span><span class="sc">;</span>
+259     <span class="i">$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>
+260     <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+261   <span class="s">}</span>
+262
+263   <span class="k">return</span> <span class="s">(</span><span class="i">$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>
+264 <span class="s">}</span>
+265
+266 <span class="c"># Write fingerpritns and other data to appropriate output files...</span>
+267 <span class="c">#</span>
+<a name="WriteDataToOutputFiles-"></a> 268 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span>
+269   <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">$Molecule</span><span class="cm">,</span> <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</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">$NewFPFileIO</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+270   <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+271
+272   <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="k">undef</span><span class="sc">;</span>
+273   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span> || <span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
+274     <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+275   <span class="s">}</span>
+276
+277   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
+278     <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
+279
+280     <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+281     <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
+282   <span class="s">}</span>
+283
+284   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
+285     <span class="k">my</span><span class="s">(</span><span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
+286
+287     <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+288     <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="cm">,</span> <span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
+289   <span class="s">}</span>
+290
+291   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
+292     <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
+293
+294     <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>
+295     <span class="i">$NewFPFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="cm">,</span> <span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
+296   <span class="s">}</span>
+297 <span class="s">}</span>
+298
+299 <span class="c"># Generate approriate column labels for FPText output file...</span>
+300 <span class="c">#</span>
+<a name="SetupFPTextFileCoulmnLabels-"></a> 301 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnLabels</span> <span class="s">{</span>
+302   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+303   <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
+304
+305   <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+306   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+307     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
+308   <span class="s">}</span>
+309   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
+310     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
+311   <span class="s">}</span>
+312   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+313     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
+314   <span class="s">}</span>
+315   <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>
+316     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span>
+317   <span class="s">}</span>
+318   <span class="c"># Add fingerprints label...</span>
+319   <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="sc">;</span>
+320
+321   <span class="k">return</span> \<span class="i">@ColLabels</span><span class="sc">;</span>
+322 <span class="s">}</span>
+323
+324 <span class="c"># Generate column values FPText output file..</span>
+325 <span class="c">#</span>
+<a name="SetupFPTextFileCoulmnValues-"></a> 326 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnValues</span> <span class="s">{</span>
+327   <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>
+328   <span class="k">my</span><span class="s">(</span><span class="i">@ColValues</span><span class="s">)</span><span class="sc">;</span>
+329
+330   <span class="i">@ColValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+331   <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>
+332     <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+333   <span class="s">}</span>
+334   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+335     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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">$FileIndex</span>]}<span class="sc">;</span>
+336   <span class="s">}</span>
+337   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
+338     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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">$FileIndex</span>]}<span class="sc">;</span>
+339   <span class="s">}</span>
+340   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+341     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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>
+342   <span class="s">}</span>
+343
+344   <span class="k">return</span> \<span class="i">@ColValues</span><span class="sc">;</span>
+345 <span class="s">}</span>
+346
+347 <span class="c"># Generate compound ID for FP and FPText output files..</span>
+348 <span class="c">#</span>
+<a name="SetupCmpdIDForOutputFiles-"></a> 349 <span class="k">sub </span><span class="m">SetupCmpdIDForOutputFiles</span> <span class="s">{</span>
+350   <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+351   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span>
+352
+353   <span class="i">$CmpdID</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+354   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolNameOrLabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
+355     <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span>
+356     <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>
+357     <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}${CmpdCount}&quot;</span><span class="sc">;</span>
+358   <span class="s">}</span>
+359   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^LabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
+360     <span class="i">$CmpdID</span> = <span class="q">&quot;$OptionsInfo{CompoundID}${CmpdCount}&quot;</span><span class="sc">;</span>
+361   <span class="s">}</span>
+362   <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>
+363     <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span>
+364     <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
+365     <span class="i">$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>
+366   <span class="s">}</span>
+367   <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>
+368     <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>
+369   <span class="s">}</span>
+370   <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span>
+371 <span class="s">}</span>
+372
+373 <span class="c"># Generate fingerprints for molecule...</span>
+374 <span class="c">#</span>
+<a name="GenerateMoleculeFingerprints-"></a> 375 <span class="k">sub </span><span class="m">GenerateMoleculeFingerprints</span> <span class="s">{</span>
+376   <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+377   <span class="k">my</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">)</span><span class="sc">;</span>
+378
+379   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span>
+380     <span class="i">$Molecule</span><span class="i">-&gt;KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+381   <span class="s">}</span>
+382   <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">-&gt;DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+383     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+384   <span class="s">}</span>
+385   <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>
+386   <span class="i">$Molecule</span><span class="i">-&gt;DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+387
+388   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FuzzifyAtomPairsCount</span>}<span class="s">)</span> <span class="s">{</span>
+389     <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">&#39;AtomPairsSetSizeToUse&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">AtomPairsSetSizeToUse</span>}<span class="cm">,</span> <span class="q">&#39;MinDistance&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">MinDistance</span>}<span class="cm">,</span>  <span class="q">&#39;MaxDistance&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">&#39;AtomTypesToUse&#39;</span> <span class="cm">=&gt;</span> \<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="cm">,</span> <span class="q">&#39;NormalizationMethodology&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">NormalizationMethodology</span>}<span class="cm">,</span> <span class="cm">,</span> <span class="q">&#39;ValuesPrecision&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">ValuesPrecision</span>}<span class="cm">,</span> <span class="q">&#39;FuzzifyAtomPairsCount&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">FuzzifyAtomPairsCount</span>}<span class="cm">,</span> <span class="q">&#39;FuzzificationMode&#39;</span> <span class="cm">=&gt;</span>  <span class="i">$OptionsInfo</span>{<span class="w">FuzzificationMode</span>}<span class="cm">,</span> <span class="q">&#39;FuzzificationMethodology&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">FuzzificationMethodology</span>}<span class="cm">,</span> <span class="q">&#39;FuzzFactor&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">FuzzFactor</span>}<span class="s">)</span><span class="sc">;</span>
+390   <span class="s">}</span>
+391   <span class="k">else</span> <span class="s">{</span>
+392     <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">&#39;AtomPairsSetSizeToUse&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">AtomPairsSetSizeToUse</span>}<span class="cm">,</span> <span class="q">&#39;MinDistance&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">MinDistance</span>}<span class="cm">,</span>  <span class="q">&#39;MaxDistance&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">&#39;AtomTypesToUse&#39;</span> <span class="cm">=&gt;</span> \<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="q">&#39;NormalizationMethodology&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">NormalizationMethodology</span>}<span class="cm">,</span> <span class="q">&#39;ValuesPrecision&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">ValuesPrecision</span>}<span class="s">)</span><span class="sc">;</span>
+393   <span class="s">}</span>
+394
+395   <span class="c"># Set atom types weights...</span>
+396   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseAtomTypesWeight</span>}<span class="s">)</span> <span class="s">{</span>
+397     <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="i">-&gt;SetAtomTypesWeight</span><span class="s">(</span><span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesWeight</span>}}<span class="s">)</span><span class="sc">;</span>
+398   <span class="s">}</span>
+399
+400   <span class="c"># Generate fingerprints...</span>
+401   <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="i">-&gt;GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+402
+403   <span class="c"># Make sure fingerprints generation is successful...</span>
+404   <span class="k">if</span> <span class="s">(</span>!<span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="i">-&gt;IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+405     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+406   <span class="s">}</span>
+407
+408   <span class="k">return</span> <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span>
+409 <span class="s">}</span>
+410
+411 <span class="c"># Retrieve information about SD files...</span>
+412 <span class="c">#</span>
+<a name="RetrieveSDFilesInfo-"></a> 413 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
+414   <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>
+415
+416   <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+417   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+418   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+419   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+420   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+421   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+422   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+423   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+424
+425   <span class="i">$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$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+426   <span class="i">$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)$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+427
+428   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+429     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+430
+431     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+432     <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>
+433     <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>
+434     <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>
+435     <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>
+436
+437     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+438     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+439       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+440       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+441     <span class="s">}</span>
+442     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$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>
+443       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
+444       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+445     <span class="s">}</span>
+446
+447     <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span>
+448       <span class="c"># Make sure data field exists in SD file..</span>
+449       <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>
+450
+451       <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+452       <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: $! \n&quot;</span><span class="sc">;</span>
+453       <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
+454       <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+455       <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+456       <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
+457       <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
+458       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span>
+459         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using  \&quot;--CompoundID\&quot; option in \&quot;DataField\&quot; \&quot;--CompoundIDMode\&quot; doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+460         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+461       <span class="s">}</span>
+462     <span class="s">}</span>
+463
+464     <span class="i">$AllDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+465     <span class="i">$CommonDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+466     <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span>
+467       <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
+468       <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
+469       <span class="s">(</span><span class="i">$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>
+470       <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+471     <span class="s">}</span>
+472
+473     <span class="c"># Setup output file names...</span>
+474     <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">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+475     <span class="s">(</span><span class="i">$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">$SDFile</span><span class="s">)</span><span class="sc">;</span>
+476
+477     <span class="i">$TextOutFileExt</span> = <span class="q">&quot;csv&quot;</span><span class="sc">;</span>
+478     <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>
+479       <span class="i">$TextOutFileExt</span> = <span class="q">&quot;tsv&quot;</span><span class="sc">;</span>
+480     <span class="s">}</span>
+481     <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span>
+482     <span class="i">$FPOutFileExt</span> = <span class="q">&quot;fpf&quot;</span><span class="sc">;</span>
+483
+484     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+485       <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
+486       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+487         <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+488       <span class="s">}</span>
+489       <span class="k">else</span> <span class="s">{</span>
+490         <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
+491       <span class="s">}</span>
+492       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+493     <span class="s">}</span>
+494     <span class="k">else</span> <span class="s">{</span>
+495       <span class="i">$OutFileRoot</span> = <span class="q">&quot;${FileName}TopologicalPharmacophoreAtomPairsFP&quot;</span><span class="sc">;</span>
+496     <span class="s">}</span>
+497
+498     <span class="i">$NewSDFileName</span> = <span class="q">&quot;${OutFileRoot}.${SDOutFileExt}&quot;</span><span class="sc">;</span>
+499     <span class="i">$NewFPFileName</span> = <span class="q">&quot;${OutFileRoot}.${FPOutFileExt}&quot;</span><span class="sc">;</span>
+500     <span class="i">$NewTextFileName</span> = <span class="q">&quot;${OutFileRoot}.${TextOutFileExt}&quot;</span><span class="sc">;</span>
+501
+502     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+503       <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span>
+504         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n&quot;</span><span class="sc">;</span>
+505         <span class="k">print</span> <span class="q">&quot;Specify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
+506         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+507       <span class="s">}</span>
+508     <span class="s">}</span>
+509
+510     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
+511       <span class="c"># Check SD and text outout files...</span>
+512       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+513         <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span>
+514           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n&quot;</span><span class="sc">;</span>
+515           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+516         <span class="s">}</span>
+517       <span class="s">}</span>
+518       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
+519         <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>
+520           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n&quot;</span><span class="sc">;</span>
+521           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+522         <span class="s">}</span>
+523       <span class="s">}</span>
+524       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
+525         <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>
+526           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n&quot;</span><span class="sc">;</span>
+527           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+528         <span class="s">}</span>
+529       <span class="s">}</span>
+530     <span class="s">}</span>
+531
+532     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+533
+534     <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
+535     <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span>
+536     <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewFPFileName</span><span class="sc">;</span>
+537     <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span>
+538
+539     <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span>
+540     <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span>
+541   <span class="s">}</span>
+542 <span class="s">}</span>
+543
+544 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 545 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+546   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+547
+548   <span class="i">ProcessAtomTypesToUseOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+549   <span class="i">ProcessAtomTypesWeightOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+550
+551   <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span>
+552
+553   <span class="i">$OptionsInfo</span>{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="i">$Options</span>{<span class="w">atompairssetsizetouse</span>}<span class="sc">;</span>
+554
+555   <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span>
+556   <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span>
+557   <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span>
+558
+559   <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span>
+560   <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+561
+562   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+563   <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+564
+565   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
+566     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
+567       <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span>
+568         <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>
+569       <span class="s">}</span>
+570       <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span>
+571     <span class="s">}</span>
+572     <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>
+573       <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>} ? <span class="i">$Options</span>{<span class="w">compoundid</span>} <span class="co">:</span> <span class="q">&#39;Cmpd&#39;</span><span class="sc">;</span>
+574     <span class="s">}</span>
+575   <span class="s">}</span>
+576   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+577     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span>
+578       <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>
+579     <span class="s">}</span>
+580     <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span>
+581     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span>
+582   <span class="s">}</span>
+583
+584   <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+585
+586   <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabelMode</span>} = <span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>}<span class="sc">;</span>
+587   <span class="i">$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;TopologicalPharmacophoreAtomPairsFingerprints&#39;</span><span class="sc">;</span>
+588
+589   <span class="i">$OptionsInfo</span>{<span class="w">FuzzifyAtomPairsCount</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzifyatompairscount</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+590   <span class="i">$OptionsInfo</span>{<span class="w">FuzzificationMode</span>} = <span class="i">$Options</span>{<span class="w">fuzzificationmode</span>}<span class="sc">;</span>
+591   <span class="i">$OptionsInfo</span>{<span class="w">FuzzificationMethodology</span>} = <span class="i">$Options</span>{<span class="w">fuzzificationmethodology</span>}<span class="sc">;</span>
+592   <span class="i">$OptionsInfo</span>{<span class="w">FuzzFactor</span>} = <span class="i">$Options</span>{<span class="w">fuzzfactor</span>}<span class="sc">;</span>
+593
+594   <span class="i">$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>
+595
+596   <span class="i">$OptionsInfo</span>{<span class="w">MinDistance</span>} = <span class="i">$Options</span>{<span class="w">mindistance</span>}<span class="sc">;</span>
+597   <span class="i">$OptionsInfo</span>{<span class="w">MaxDistance</span>} = <span class="i">$Options</span>{<span class="w">maxdistance</span>}<span class="sc">;</span>
+598
+599   <span class="i">$OptionsInfo</span>{<span class="w">NormalizationMethodology</span>} = <span class="i">$Options</span>{<span class="w">normalizationmethodology</span>}<span class="sc">;</span>
+600
+601   <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
+602   <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+603   <span class="i">$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>
+604   <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+605
+606   <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="i">$Options</span>{<span class="w">outdelim</span>}<span class="sc">;</span>
+607   <span class="i">$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>
+608
+609   <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>
+610   <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+611
+612   <span class="i">$OptionsInfo</span>{<span class="w">ValuesPrecision</span>} = <span class="i">$Options</span>{<span class="w">valuesprecision</span>}<span class="sc">;</span>
+613
+614   <span class="c"># Setup default vector string format...</span>
+615   <span class="k">my</span><span class="s">(</span><span class="i">$VectorStringFormat</span><span class="s">)</span><span class="sc">;</span>
+616   <span class="i">$VectorStringFormat</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+617
+618   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="s">)</span> <span class="s">{</span>
+619     <span class="i">$VectorStringFormat</span> = <span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="sc">;</span>
+620
+621     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atompairssetsizetouse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> &amp;&amp; <span class="i">$VectorStringFormat</span> =~ <span class="q">/^ValuesString$/i</span><span class="s">)</span> <span class="s">{</span>
+622       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{vectorstringformat}, for option \&quot;-v, --VectorStringFormat\&quot; is not valid for $Options{atompairssetsizetouse} value of \&quot;--AtomPairsSetSizeToUse\&quot; option. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n&quot;</span><span class="sc">;</span>
+623     <span class="s">}</span>
+624   <span class="s">}</span>
+625   <span class="k">else</span> <span class="s">{</span>
+626     <span class="i">$VectorStringFormat</span> = <span class="s">(</span><span class="i">$Options</span>{<span class="w">atompairssetsizetouse</span>} =~ <span class="q">/^FixedSize$/</span><span class="s">)</span> ? <span class="q">&quot;ValuesString&quot;</span> <span class="co">:</span> <span class="q">&quot;IDsAndValuesString&quot;</span><span class="sc">;</span>
+627   <span class="s">}</span>
+628   <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>} = <span class="i">$VectorStringFormat</span><span class="sc">;</span>
+629 <span class="s">}</span>
+630
+631 <span class="c"># Process atom type to use option...</span>
+632 <span class="c">#</span>
+<a name="ProcessAtomTypesToUseOption-"></a> 633 <span class="k">sub </span><span class="m">ProcessAtomTypesToUseOption</span> <span class="s">{</span>
+634   <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypesToUse</span><span class="cm">,</span> <span class="i">@AtomTypesWords</span><span class="s">)</span><span class="sc">;</span>
+635
+636   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+637   <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomtypestouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+638     <span class="k">die</span> <span class="q">&quot;Error: Atom types value specified using \&quot;-a, --AtomTypesToUse\&quot; option is empty\n&quot;</span><span class="sc">;</span>
+639   <span class="s">}</span>
+640
+641   <span class="i">$SpecifiedAtomTypesToUse</span> = <span class="i">$Options</span>{<span class="w">atomtypestouse</span>}<span class="sc">;</span>
+642   <span class="i">$SpecifiedAtomTypesToUse</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+643   <span class="i">@AtomTypesWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypesToUse</span><span class="sc">;</span>
+644
+645   <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypesWords</span><span class="s">)</span> <span class="s">{</span>
+646     <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$AtomType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+647       <span class="k">die</span> <span class="q">&quot;Error: Atomic type specified, $AtomType, using \&quot;-a, --AtomTypesToUse\&quot; option is not valid...\n &quot;</span><span class="sc">;</span>
+648     <span class="s">}</span>
+649     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span>
+650   <span class="s">}</span>
+651 <span class="s">}</span>
+652
+653 <span class="c"># Process atom types weight option...</span>
+654 <span class="c">#</span>
+<a name="ProcessAtomTypesWeightOption-"></a> 655 <span class="k">sub </span><span class="m">ProcessAtomTypesWeightOption</span> <span class="s">{</span>
+656   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$AtomTypeWeight</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypesWeight</span><span class="cm">,</span> <span class="i">@AtomTypesWeightsPairs</span><span class="s">)</span><span class="sc">;</span>
+657
+658   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesWeight</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+659
+660   <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomtypesweight</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+661     <span class="k">die</span> <span class="q">&quot;Error: Atom types weight value specified using \&quot;--AtomTypesWeight\&quot; option is empty\n&quot;</span><span class="sc">;</span>
+662   <span class="s">}</span>
+663   <span class="i">$OptionsInfo</span>{<span class="w">UseAtomTypesWeight</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomtypesweight</span>} =~ <span class="q">/^None$/i</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
+664   <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">UseAtomTypesWeight</span>}<span class="s">)</span> <span class="s">{</span>
+665     <span class="k">return</span><span class="sc">;</span>
+666   <span class="s">}</span>
+667
+668   <span class="c"># Process specified atom type/weight pairs...</span>
+669   <span class="i">$SpecifiedAtomTypesWeight</span> = <span class="i">$Options</span>{<span class="w">atomtypesweight</span>}<span class="sc">;</span>
+670   <span class="i">$SpecifiedAtomTypesWeight</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+671   <span class="i">@AtomTypesWeightsPairs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypesWeight</span><span class="sc">;</span>
+672
+673   <span class="k">if</span> <span class="s">(</span><span class="i">@AtomTypesWeightsPairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+674     <span class="k">die</span> <span class="q">&quot;Error: Invalid number of values specified using \&quot;--AtomTypesWeight\&quot; option: It must contain even number of values.\n&quot;</span><span class="sc">;</span>
+675   <span class="s">}</span>
+676
+677   <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> &lt; <span class="i">@AtomTypesWeightsPairs</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+678     <span class="i">$AtomType</span> = <span class="i">$AtomTypesWeightsPairs</span>[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$AtomTypeWeight</span> = <span class="i">$AtomTypesWeightsPairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
+679     <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$AtomType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+680       <span class="k">die</span> <span class="q">&quot;Error: Atom type specified, $AtomType, using \&quot;--AtomTypesWeight\&quot; option is not valid\n &quot;</span><span class="sc">;</span>
+681     <span class="s">}</span>
+682     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$AtomTypeWeight</span><span class="s">)</span> &amp;&amp; <span class="i">$AtomTypeWeight</span> &gt;= <span class="n">0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+683       <span class="k">die</span> <span class="q">&quot;Error: Atom type weight specified, $AtomTypeWeight, using option \&quot;--AtomTypesWeight\&quot; is not valid. Allowed values: real numbers &gt;= 0 \n&quot;</span><span class="sc">;</span>
+684     <span class="s">}</span>
+685     <span class="i">$OptionsInfo</span>{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>} = <span class="i">$AtomTypeWeight</span><span class="sc">;</span>
+686   <span class="s">}</span>
+687 <span class="s">}</span>
+688
+689 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 690 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+691
+692   <span class="c"># Retrieve all the options...</span>
+693   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+694
+695   <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">&#39;MayaChemToolsAromaticityModel&#39;</span><span class="sc">;</span>
+696
+697   <span class="i">$Options</span>{<span class="w">atompairssetsizetouse</span>} = <span class="q">&#39;ArbitrarySize&#39;</span><span class="sc">;</span>
+698
+699   <span class="i">$Options</span>{<span class="w">atomtypestouse</span>} = <span class="q">&#39;HBD,HBA,PI,NI,H&#39;</span><span class="sc">;</span>
+700   <span class="i">$Options</span>{<span class="w">atomtypesweight</span>} = <span class="q">&#39;None&#39;</span><span class="sc">;</span>
+701
+702   <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">&#39;LabelPrefix&#39;</span><span class="sc">;</span>
+703   <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+704   <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+705
+706   <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+707
+708   <span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>} = <span class="q">&#39;FingerprintsLabelOnly&#39;</span><span class="sc">;</span>
+709
+710   <span class="i">$Options</span>{<span class="w">fuzzifyatompairscount</span>} = <span class="q">&#39;No&#39;</span><span class="sc">;</span>
+711   <span class="i">$Options</span>{<span class="w">fuzzificationmode</span>} = <span class="q">&#39;AfterNormalization&#39;</span><span class="sc">;</span>
+712   <span class="i">$Options</span>{<span class="w">fuzzificationmethodology</span>} = <span class="q">&#39;FuzzyBinning&#39;</span><span class="sc">;</span>
+713   <span class="i">$Options</span>{<span class="w">fuzzfactor</span>} = <span class="n">0.15</span><span class="sc">;</span>
+714
+715   <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+716
+717   <span class="i">$Options</span>{<span class="w">mindistance</span>} = <span class="n">1</span><span class="sc">;</span>
+718   <span class="i">$Options</span>{<span class="w">maxdistance</span>} = <span class="n">10</span><span class="sc">;</span>
+719
+720   <span class="i">$Options</span>{<span class="w">normalizationmethodology</span>} = <span class="q">&#39;None&#39;</span><span class="sc">;</span>
+721
+722   <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">&#39;text&#39;</span><span class="sc">;</span>
+723   <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&#39;comma&#39;</span><span class="sc">;</span>
+724   <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+725
+726   <span class="i">$Options</span>{<span class="w">valuesprecision</span>} = <span class="n">2</span><span class="sc">;</span>
+727
+728   <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+729
+730   <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;atompairssetsizetouse=s&quot;</span><span class="cm">,</span> <span class="q">&quot;atomtypestouse|a=s&quot;</span><span class="cm">,</span> <span class="q">&quot;atomtypesweight=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundid=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundidlabel=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundidmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;datafields=s&quot;</span><span class="cm">,</span> <span class="q">&quot;datafieldsmode|d=s&quot;</span><span class="cm">,</span> <span class="q">&quot;filter|f=s&quot;</span><span class="cm">,</span> <span class="q">&quot;fingerprintslabelmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;fingerprintslabel=s&quot;</span><span class="cm">,</span> <span class="q">&quot;fuzzifyatompairscount=s&quot;</span><span class="cm">,</span> <span class="q">&quot;fuzzificationmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;fuzzificationmethodology=s&quot;</span><span class="cm">,</span> <span class="q">&quot;fuzzfactor=s&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;keeplargestcomponent|k=s&quot;</span><span class="cm">,</span>  <span class="q">&quot;mindistance=s&quot;</span><span class="cm">,</span> <span class="q">&quot;maxdistance=s&quot;</span><span class="cm">,</span> <span class="q">&quot;normalizationmethodology|n=s&quot;</span><span class="cm">,</span> <span class="q">&quot;outdelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;output=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;quote|q=s&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;valuesprecision=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>
+731     <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 $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+732   <span class="s">}</span>
+733   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+734     <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>
+735       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+736     <span class="s">}</span>
+737     <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
+738   <span class="s">}</span>
+739   <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+740     <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>
+741     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{aromaticitymodel}, for option \&quot;--AromaticityModel\&quot; is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n&quot;</span><span class="sc">;</span>
+742   <span class="s">}</span>
+743   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atompairssetsizetouse</span>} !~ <span class="q">/^(ArbitrarySize|FixedSize)$/i</span><span class="s">)</span> <span class="s">{</span>
+744     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{atompairssetsizetouse}, for option \&quot;--AtomPairsSetSizeToUse\&quot; is not valid. Allowed values: ArbitrarySize or FixedSize\n&quot;</span><span class="sc">;</span>
+745   <span class="s">}</span>
+746   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
+747     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{compoundidmode}, for option \&quot;--CompoundIDMode\&quot; is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n&quot;</span><span class="sc">;</span>
+748   <span class="s">}</span>
+749   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span>
+750     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{datafieldsmode}, for option \&quot;-d, --DataFieldsMode\&quot; is not valid. Allowed values: All, Common, Specify or CompoundID\n&quot;</span><span class="sc">;</span>
+751   <span class="s">}</span>
+752   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+753     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{filter}, for option \&quot;-f, --Filter\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+754   <span class="s">}</span>
+755   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>} !~ <span class="q">/^(FingerprintsLabelOnly|FingerprintsLabelWithIDs)$/i</span><span class="s">)</span> <span class="s">{</span>
+756     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{fingerprintslabelmode}, for option \&quot;--FingerprintsLabelMode\&quot; is not valid. Allowed values: FingerprintsLabelOnly or FingerprintsLabelWithIDs\n&quot;</span><span class="sc">;</span>
+757   <span class="s">}</span>
+758   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzifyatompairscount</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+759     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{fuzzifyatompairscount}, for option \&quot;--FuzzifyAtomPairsCount\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+760   <span class="s">}</span>
+761   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzificationmode</span>} !~ <span class="q">/^(BeforeNormalization|AfterNormalization)$/i</span><span class="s">)</span> <span class="s">{</span>
+762     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{fuzzificationmode}, for option \&quot;--FuzzificationMode\&quot; is not valid. Allowed values: BeforeNormalization or AfterNormalization\n&quot;</span><span class="sc">;</span>
+763   <span class="s">}</span>
+764   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzificationmethodology</span>} !~ <span class="q">/^(FuzzyBinning|FuzzyBinSmoothing)$/i</span><span class="s">)</span> <span class="s">{</span>
+765     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{fuzzificationmethodology}, for option \&quot;--FuzzificationMethodology\&quot; is not valid. Allowed values: FuzzyBinning or FuzzyBinSmoothing\n&quot;</span><span class="sc">;</span>
+766   <span class="s">}</span>
+767   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsFloat</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzfactor</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+768     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{fuzzfactor}, for option \&quot;--FuzzFactor\&quot; is not valid. Allowed values: real numbers &gt;= 0 \n&quot;</span><span class="sc">;</span>
+769   <span class="s">}</span>
+770   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzificationmethodology</span>} !~ <span class="q">/^FuzzyBinning$/i</span><span class="s">)</span> <span class="s">{</span>
+771     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzfactor</span>} &gt;=<span class="n">0</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">fuzzfactor</span>} &lt;= <span class="n">1.0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+772       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{fuzzfactor}, for option \&quot;--FuzzFactor\&quot; during FuzzyBinning \&quot;--FuzzificationMethodology\&quot; is not valid. Allowed values: &gt;= 0 and &lt;= 1 \n&quot;</span><span class="sc">;</span>
+773     <span class="s">}</span>
+774   <span class="s">}</span>
+775   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzificationmethodology</span>} !~ <span class="q">/^FuzzyBinSmoothing$/i</span><span class="s">)</span> <span class="s">{</span>
+776     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzfactor</span>} &gt;=<span class="n">0</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">fuzzfactor</span>} &lt;= <span class="n">0.5</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+777       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{fuzzfactor}, for option \&quot;--FuzzFactor\&quot; during FuzzyBinSmoothing \&quot;--FuzzificationMethodology\&quot; is not valid. Allowed values: &gt;= 0 and &lt;= 0.5 \n&quot;</span><span class="sc">;</span>
+778     <span class="s">}</span>
+779   <span class="s">}</span>
+780   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+781     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{keeplargestcomponent}, for option \&quot;-k, --KeepLargestComponent\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+782   <span class="s">}</span>
+783   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">mindistance</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+784     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mindistance}, for option \&quot;--MinDistance\&quot; is not valid. Allowed values: &gt;= 0 \n&quot;</span><span class="sc">;</span>
+785   <span class="s">}</span>
+786   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">maxdistance</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+787     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{maxdistance}, for option \&quot;--MaxDistance\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+788   <span class="s">}</span>
+789   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mindistance</span>} &gt; <span class="i">$Options</span>{<span class="w">maxdistance</span>}<span class="s">)</span> <span class="s">{</span>
+790     <span class="k">die</span> <span class="q">&quot;Error: The value specified, specified, $Options{mindistance}, for option \&quot;--MinDistance\&quot; must be less than the value specified, $Options{maxdistance}, for option \&quot;--MaxDistance\&quot; \n&quot;</span><span class="sc">;</span>
+791   <span class="s">}</span>
+792   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">normalizationmethodology</span>} !~ <span class="q">/^(None|ByHeavyAtomsCount|ByAtomTypesCount)$/i</span><span class="s">)</span> <span class="s">{</span>
+793     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{normalizationmethodology}, for option \&quot;--NormalizationMethodology\&quot; is not valid. Allowed values: None, ByHeavyAtomsCount, or ByAtomTypesCount\n&quot;</span><span class="sc">;</span>
+794   <span class="s">}</span>
+795   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|FP|text|all)$/i</span><span class="s">)</span> <span class="s">{</span>
+796     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{output}, for option \&quot;--output\&quot; is not valid. Allowed values: SD, FP, text, or all\n&quot;</span><span class="sc">;</span>
+797   <span class="s">}</span>
+798   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
+799     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--outdelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
+800   <span class="s">}</span>
+801   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+802     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+803   <span class="s">}</span>
+804   <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+805     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not allowed with, semicolon value of \&quot;--outdelim\&quot; option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n&quot;</span><span class="sc">;</span>
+806   <span class="s">}</span>
+807   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">valuesprecision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+808     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{valuesprecision}, for option \&quot;--ValuesPrecision\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+809   <span class="s">}</span>
+810   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>} &amp;&amp; <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} !~ <span class="q">/^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i</span><span class="s">)</span> <span class="s">{</span>
+811     <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: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n&quot;</span><span class="sc">;</span>
+812   <span class="s">}</span>
+813 <span class="s">}</span>
+814
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>

Mercurial > repos > deepakjadmin > mayatool3_test1

comparison docs/scripts/html/code/TopologicalPharmacophoreAtomPairsFingerprints.html @ 1:2abf0d43254d draft