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+<title>MayaChemTools:Code:EStateIndiciesFingerprints.pl</title>
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+<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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+1 #!/usr/bin/perl -w
+2 <span class="c">#</span>
+3 <span class="c"># $RCSfile: EStateIndiciesFingerprints.pl,v $</span>
+4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
+5 <span class="c"># $Revision: 1.23 $</span>
+6 <span class="c">#</span>
+7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+8 <span class="c">#</span>
+9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+10 <span class="c">#</span>
+11 <span class="c"># This file is part of MayaChemTools.</span>
+12 <span class="c">#</span>
+13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+16 <span class="c"># later version.</span>
+17 <span class="c">#</span>
+18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+21 <span class="c"># details.</span>
+22 <span class="c">#</span>
+23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+27 <span class="c">#</span>
+28
+29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$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::EStateAtomTypes</span><span class="sc">;</span>
+43 <span class="k">use</span> <span class="w">Fingerprints::EStateIndiciesFingerprints</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">GenerateEStateIndiciesFingerprints</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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+90
+91 <span class="c">###############################################################################</span>
+92
+93 <span class="c"># Generate fingerprints for a SD file...</span>
+94 <span class="c">#</span>
+<a name="GenerateEStateIndiciesFingerprints-"></a>  95 <span class="k">sub </span><span class="m">GenerateEStateIndiciesFingerprints</span> <span class="s">{</span>
+96   <span class="k">my</span><span class="s">(</span><span class="i">$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">$Molecule</span><span class="cm">,</span> <span class="i">$EStateIndiciesFingerprints</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">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
+98
+99   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+100
+101   <span class="c"># Setup output files...</span>
+102   <span class="c">#</span>
+103   <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>
+104
+105   <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>
+106   <span class="i">$MoleculeFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+107
+108   <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+109   <span class="i">$IgnoredCmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+110
+111   <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Molecule</span> = <span class="i">$MoleculeFileIO</span><span class="i">-&gt;ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+112     <span class="i">$CmpdCount</span>++<span class="sc">;</span>
+113
+114     <span class="c"># Filter compound data before calculating fingerprints...</span>
+115     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Filter</span>}<span class="s">)</span> <span class="s">{</span>
+116       <span class="k">if</span> <span class="s">(</span><span class="i">CheckAndFilterCompound</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+117         <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
+118         <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
+119       <span class="s">}</span>
+120     <span class="s">}</span>
+121
+122     <span class="i">$EStateIndiciesFingerprints</span> = <span class="i">GenerateMoleculeFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+123     <span class="k">if</span> <span class="s">(</span>!<span class="i">$EStateIndiciesFingerprints</span><span class="s">)</span> <span class="s">{</span>
+124       <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
+125       <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>
+126       <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
+127     <span class="s">}</span>
+128
+129     <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">$Molecule</span><span class="cm">,</span> <span class="i">$EStateIndiciesFingerprints</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">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
+130   <span class="s">}</span>
+131   <span class="i">$MoleculeFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+132
+133   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
+134     <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+135   <span class="s">}</span>
+136   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
+137     <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+138   <span class="s">}</span>
+139   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
+140     <span class="i">$NewFPFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+141   <span class="s">}</span>
+142
+143   <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>
+144 <span class="s">}</span>
+145
+146 <span class="c"># Process compound being ignored due to problems in fingerprints geneation...</span>
+147 <span class="c">#</span>
+<a name="ProcessIgnoredCompound-"></a> 148 <span class="k">sub </span><span class="m">ProcessIgnoredCompound</span> <span class="s">{</span>
+149   <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">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+150   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+151
+152   <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+153   <span class="i">$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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+154
+155   <span class="j">MODE:</span> <span class="s">{</span>
+156     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNonElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
+157       <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n&quot;</span><span class="sc">;</span>
+158       <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
+159     <span class="s">}</span>
+160
+161     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNoElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
+162       <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n&quot;</span><span class="sc">;</span>
+163       <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
+164     <span class="s">}</span>
+165
+166     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^FingerprintsGenerationFailed$/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: Fingerprints generation didn&#39;t succeed...\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     <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn&#39;t succeed...\n\n&quot;</span><span class="sc">;</span>
+171   <span class="s">}</span>
+172 <span class="s">}</span>
+173
+174 <span class="c"># Check and filter compounds....</span>
+175 <span class="c">#</span>
+<a name="CheckAndFilterCompound-"></a> 176 <span class="k">sub </span><span class="m">CheckAndFilterCompound</span> <span class="s">{</span>
+177   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+178   <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span>
+179
+180   <span class="s">(</span><span class="i">$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>
+181
+182   <span class="k">if</span> <span class="s">(</span><span class="i">$NonElementCount</span><span class="s">)</span> <span class="s">{</span>
+183     <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">&#39;ContainsNonElementalData&#39;</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+184     <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
+185   <span class="s">}</span>
+186
+187   <span class="k">if</span> <span class="s">(</span>!<span class="i">$ElementCount</span><span class="s">)</span> <span class="s">{</span>
+188     <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>
+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">return</span> <span class="n">0</span><span class="sc">;</span>
+193 <span class="s">}</span>
+194
+195 <span class="c"># Write out compounds fingerprints generation summary statistics...</span>
+196 <span class="c">#</span>
+<a name="WriteFingerprintsGenerationSummaryStatistics-"></a> 197 <span class="k">sub </span><span class="m">WriteFingerprintsGenerationSummaryStatistics</span> <span class="s">{</span>
+198   <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>
+199   <span class="k">my</span><span class="s">(</span><span class="i">$ProcessedCmpdCount</span><span class="s">)</span><span class="sc">;</span>
+200
+201   <span class="i">$ProcessedCmpdCount</span> = <span class="i">$CmpdCount</span> - <span class="i">$IgnoredCmpdCount</span><span class="sc">;</span>
+202
+203   <span class="k">print</span> <span class="q">&quot;\nNumber of compounds: $CmpdCount\n&quot;</span><span class="sc">;</span>
+204   <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>
+205   <span class="k">print</span> <span class="q">&quot;Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n&quot;</span><span class="sc">;</span>
+206 <span class="s">}</span>
+207
+208 <span class="c"># Open output files...</span>
+209 <span class="c">#</span>
+<a name="SetupAndOpenOutputFiles-"></a> 210 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span>
+211   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+212   <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>
+213
+214   <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">$NewFPFileIO</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
+215
+216   <span class="c"># Setup common parameters for fingerprints file IO objects...</span>
+217   <span class="c">#</span>
+218   <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+219   <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Write&#39;</span><span class="cm">,</span> <span class="q">&#39;Overwrite&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="cm">,</span> <span class="q">&#39;FingerprintsStringMode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;FingerprintsVectorString&#39;</span><span class="cm">,</span> <span class="q">&#39;VectorStringFormat&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>}<span class="s">)</span><span class="sc">;</span>
+220
+221   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+222     <span class="i">$NewFPSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+223     <span class="k">print</span> <span class="q">&quot;Generating SD file $NewFPSDFile...\n&quot;</span><span class="sc">;</span>
+224     <span class="i">$NewFPSDFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsSDFileIO</span><span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$NewFPSDFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">&#39;FingerprintsFieldLabel&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="s">)</span><span class="sc">;</span>
+225     <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+226   <span class="s">}</span>
+227
+228   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
+229     <span class="i">$NewFPFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+230     <span class="k">print</span> <span class="q">&quot;Generating FP file $NewFPFile...\n&quot;</span><span class="sc">;</span>
+231     <span class="i">$NewFPFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsFPFileIO</span><span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$NewFPFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
+232     <span class="i">$NewFPFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+233   <span class="s">}</span>
+234
+235   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
+236     <span class="k">my</span><span class="s">(</span><span class="i">$ColLabelsRef</span><span class="s">)</span><span class="sc">;</span>
+237
+238     <span class="i">$NewFPTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+239     <span class="i">$ColLabelsRef</span> = <span class="i">SetupFPTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+240
+241     <span class="k">print</span> <span class="q">&quot;Generating text file $NewFPTextFile...\n&quot;</span><span class="sc">;</span>
+242     <span class="i">$NewFPTextFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsTextFileIO</span><span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$NewFPTextFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">&#39;DataColLabels&#39;</span> <span class="cm">=&gt;</span> <span class="i">$ColLabelsRef</span><span class="cm">,</span> <span class="q">&#39;OutDelim&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="q">&#39;OutQuote&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
+243     <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+244   <span class="s">}</span>
+245
+246   <span class="k">return</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
+247 <span class="s">}</span>
+248
+249 <span class="c"># Write fingerpritns and other data to appropriate output files...</span>
+250 <span class="c">#</span>
+<a name="WriteDataToOutputFiles-"></a> 251 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span>
+252   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$EStateIndiciesFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+253   <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+254
+255   <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="k">undef</span><span class="sc">;</span>
+256   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span> || <span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
+257     <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+258   <span class="s">}</span>
+259
+260   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
+261     <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
+262
+263     <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+264     <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$EStateIndiciesFingerprints</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
+265   <span class="s">}</span>
+266
+267   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
+268     <span class="k">my</span><span class="s">(</span><span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
+269
+270     <span class="i">$ColValuesRef</span> = <span class="i">SetupFPTextFileCoulmnValues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+271     <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$EStateIndiciesFingerprints</span><span class="cm">,</span> <span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
+272   <span class="s">}</span>
+273
+274   <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
+275     <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
+276
+277     <span class="i">$CompoundID</span> = <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+278     <span class="i">$NewFPFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$EStateIndiciesFingerprints</span><span class="cm">,</span> <span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
+279   <span class="s">}</span>
+280
+281 <span class="s">}</span>
+282
+283 <span class="c"># Generate approriate column labels for FPText output file...</span>
+284 <span class="c">#</span>
+<a name="SetupFPTextFileCoulmnLabels-"></a> 285 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnLabels</span> <span class="s">{</span>
+286   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+287   <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
+288
+289   <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+290   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+291     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
+292   <span class="s">}</span>
+293   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
+294     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
+295   <span class="s">}</span>
+296   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+297     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
+298   <span class="s">}</span>
+299   <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>
+300     <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span>
+301   <span class="s">}</span>
+302   <span class="c"># Add fingerprints label...</span>
+303   <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="sc">;</span>
+304
+305   <span class="k">return</span> \<span class="i">@ColLabels</span><span class="sc">;</span>
+306 <span class="s">}</span>
+307
+308 <span class="c"># Generate column values FPText output file..</span>
+309 <span class="c">#</span>
+<a name="SetupFPTextFileCoulmnValues-"></a> 310 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnValues</span> <span class="s">{</span>
+311   <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>
+312   <span class="k">my</span><span class="s">(</span><span class="i">@ColValues</span><span class="s">)</span><span class="sc">;</span>
+313
+314   <span class="i">@ColValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+315   <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>
+316     <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+317   <span class="s">}</span>
+318   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+319     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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">$FileIndex</span>]}<span class="sc">;</span>
+320   <span class="s">}</span>
+321   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
+322     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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">$FileIndex</span>]}<span class="sc">;</span>
+323   <span class="s">}</span>
+324   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+325     <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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>
+326   <span class="s">}</span>
+327
+328   <span class="k">return</span> \<span class="i">@ColValues</span><span class="sc">;</span>
+329 <span class="s">}</span>
+330
+331 <span class="c"># Generate compound ID for FP and FPText output files..</span>
+332 <span class="c">#</span>
+<a name="SetupCmpdIDForOutputFiles-"></a> 333 <span class="k">sub </span><span class="m">SetupCmpdIDForOutputFiles</span> <span class="s">{</span>
+334   <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+335   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span>
+336
+337   <span class="i">$CmpdID</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+338   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolNameOrLabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
+339     <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span>
+340     <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>
+341     <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}${CmpdCount}&quot;</span><span class="sc">;</span>
+342   <span class="s">}</span>
+343   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^LabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
+344     <span class="i">$CmpdID</span> = <span class="q">&quot;$OptionsInfo{CompoundID}${CmpdCount}&quot;</span><span class="sc">;</span>
+345   <span class="s">}</span>
+346   <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>
+347     <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span>
+348     <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
+349     <span class="i">$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>
+350   <span class="s">}</span>
+351   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolName$/i</span><span class="s">)</span> <span class="s">{</span>
+352     <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>
+353   <span class="s">}</span>
+354   <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span>
+355 <span class="s">}</span>
+356
+357 <span class="c"># Generate fingerprints for molecule...</span>
+358 <span class="c">#</span>
+<a name="GenerateMoleculeFingerprints-"></a> 359 <span class="k">sub </span><span class="m">GenerateMoleculeFingerprints</span> <span class="s">{</span>
+360   <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+361   <span class="k">my</span><span class="s">(</span><span class="i">$EStateIndiciesFingerprints</span><span class="s">)</span><span class="sc">;</span>
+362
+363   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span>
+364     <span class="i">$Molecule</span><span class="i">-&gt;KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+365   <span class="s">}</span>
+366   <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">-&gt;DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+367     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+368   <span class="s">}</span>
+369   <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>
+370   <span class="i">$Molecule</span><span class="i">-&gt;DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+371
+372   <span class="i">$EStateIndiciesFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::EStateIndiciesFingerprints</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">&#39;EStateAtomTypesSetToUse&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">EStateAtomTypesSetToUse</span>}<span class="cm">,</span> <span class="q">&#39;ValuesPrecision&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">ValuesPrecision</span>}<span class="s">)</span><span class="sc">;</span>
+373
+374   <span class="c"># Generate E-state indicies fingerprints...</span>
+375   <span class="i">$EStateIndiciesFingerprints</span><span class="i">-&gt;GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+376
+377   <span class="c"># Make sure E-state indicies fingerprints generation is successful...</span>
+378   <span class="k">if</span> <span class="s">(</span>!<span class="i">$EStateIndiciesFingerprints</span><span class="i">-&gt;IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+379     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+380   <span class="s">}</span>
+381
+382   <span class="k">return</span> <span class="i">$EStateIndiciesFingerprints</span><span class="sc">;</span>
+383 <span class="s">}</span>
+384
+385 <span class="c"># Retrieve information about SD files...</span>
+386 <span class="c">#</span>
+<a name="RetrieveSDFilesInfo-"></a> 387 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
+388   <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>
+389
+390   <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+391   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+392   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+393   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+394   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+395   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+396   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+397   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+398
+399   <span class="i">$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$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+400   <span class="i">$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)$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+401
+402   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+403     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+404
+405     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+406     <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>
+407     <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>
+408     <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>
+409     <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>
+410
+411     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+412     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+413       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+414       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+415     <span class="s">}</span>
+416     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$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>
+417       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
+418       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+419     <span class="s">}</span>
+420
+421     <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span>
+422       <span class="c"># Make sure data field exists in SD file..</span>
+423       <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>
+424
+425       <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+426       <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: $! \n&quot;</span><span class="sc">;</span>
+427       <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
+428       <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+429       <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+430       <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
+431       <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
+432       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span>
+433         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using  \&quot;--CompoundID\&quot; option in \&quot;DataField\&quot; \&quot;--CompoundIDMode\&quot; doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+434         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+435       <span class="s">}</span>
+436     <span class="s">}</span>
+437
+438     <span class="i">$AllDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+439     <span class="i">$CommonDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+440     <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span>
+441       <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
+442       <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
+443       <span class="s">(</span><span class="i">$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>
+444       <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+445     <span class="s">}</span>
+446
+447     <span class="c"># Setup output file names...</span>
+448     <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">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+449     <span class="s">(</span><span class="i">$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">$SDFile</span><span class="s">)</span><span class="sc">;</span>
+450
+451     <span class="i">$TextOutFileExt</span> = <span class="q">&quot;csv&quot;</span><span class="sc">;</span>
+452     <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>
+453       <span class="i">$TextOutFileExt</span> = <span class="q">&quot;tsv&quot;</span><span class="sc">;</span>
+454     <span class="s">}</span>
+455     <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span>
+456     <span class="i">$FPOutFileExt</span> = <span class="q">&quot;fpf&quot;</span><span class="sc">;</span>
+457
+458     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+459       <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
+460       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+461         <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+462       <span class="s">}</span>
+463       <span class="k">else</span> <span class="s">{</span>
+464         <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
+465       <span class="s">}</span>
+466       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+467     <span class="s">}</span>
+468     <span class="k">else</span> <span class="s">{</span>
+469       <span class="i">$OutFileRoot</span> = <span class="q">&quot;${FileName}EStateIndiciesFP&quot;</span><span class="sc">;</span>
+470     <span class="s">}</span>
+471
+472     <span class="i">$NewSDFileName</span> = <span class="q">&quot;${OutFileRoot}.${SDOutFileExt}&quot;</span><span class="sc">;</span>
+473     <span class="i">$NewFPFileName</span> = <span class="q">&quot;${OutFileRoot}.${FPOutFileExt}&quot;</span><span class="sc">;</span>
+474     <span class="i">$NewTextFileName</span> = <span class="q">&quot;${OutFileRoot}.${TextOutFileExt}&quot;</span><span class="sc">;</span>
+475
+476     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+477       <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span>
+478         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n&quot;</span><span class="sc">;</span>
+479         <span class="k">print</span> <span class="q">&quot;Specify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
+480         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+481       <span class="s">}</span>
+482     <span class="s">}</span>
+483
+484     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
+485       <span class="c"># Check SD and text outout files...</span>
+486       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+487         <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span>
+488           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n&quot;</span><span class="sc">;</span>
+489           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+490         <span class="s">}</span>
+491       <span class="s">}</span>
+492       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
+493         <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>
+494           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n&quot;</span><span class="sc">;</span>
+495           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+496         <span class="s">}</span>
+497       <span class="s">}</span>
+498       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
+499         <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>
+500           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n&quot;</span><span class="sc">;</span>
+501           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+502         <span class="s">}</span>
+503       <span class="s">}</span>
+504     <span class="s">}</span>
+505
+506     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+507
+508     <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
+509     <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span>
+510     <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewFPFileName</span><span class="sc">;</span>
+511     <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span>
+512
+513     <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span>
+514     <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span>
+515   <span class="s">}</span>
+516 <span class="s">}</span>
+517
+518 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 519 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+520   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+521
+522   <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span>
+523
+524   <span class="i">$OptionsInfo</span>{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="i">$Options</span>{<span class="w">estateatomtypessettouse</span>} ? <span class="i">$Options</span>{<span class="w">estateatomtypessettouse</span>} <span class="co">:</span> <span class="q">&#39;ArbitrarySize&#39;</span><span class="sc">;</span>
+525
+526   <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span>
+527   <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span>
+528   <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span>
+529
+530   <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span>
+531   <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+532
+533   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+534   <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+535
+536   <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>
+537     <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>
+538       <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span>
+539         <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--CompoundID\&quot; option in \&quot;DataField\&quot; \&quot;--CompoundIDMode\&quot;. \n&quot;</span><span class="sc">;</span>
+540       <span class="s">}</span>
+541       <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span>
+542     <span class="s">}</span>
+543     <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^(LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
+544       <span class="i">$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>
+545     <span class="s">}</span>
+546   <span class="s">}</span>
+547   <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>
+548     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span>
+549       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--DataFields\&quot; option in \&quot;Specify\&quot; \&quot;-d, --DataFieldsMode\&quot;. \n&quot;</span><span class="sc">;</span>
+550     <span class="s">}</span>
+551     <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span>
+552     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span>
+553   <span class="s">}</span>
+554
+555   <span class="i">$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;EStateIndiciesFingerprints&#39;</span><span class="sc">;</span>
+556
+557   <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+558
+559   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>} =~ <span class="q">/^FingerprintsLabelWithIDs$/</span><span class="s">)</span> <span class="s">{</span>
+560     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">estateatomtypessettouse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span>
+561       <span class="c"># Append E-state atom types for non-hydrogen atoms to the fingerprints label...</span>
+562       <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span>
+563       <span class="i">@IDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+564       <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">AtomTypes::EStateAtomTypes::GetAllPossibleEStateNonHydrogenAtomTypes</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+565         <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="q">&quot;S${AtomType}&quot;</span><span class="sc">;</span>
+566       <span class="s">}</span>
+567       <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>} .= <span class="q">&quot;; EStateAtomTypes: &quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@IDs</span><span class="cm">,</span> <span class="q">&quot; &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
+568     <span class="s">}</span>
+569   <span class="s">}</span>
+570   <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabelMode</span>} = <span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>}<span class="sc">;</span>
+571
+572   <span class="i">$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>
+573
+574   <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
+575   <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+576   <span class="i">$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>
+577   <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+578
+579   <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="i">$Options</span>{<span class="w">outdelim</span>}<span class="sc">;</span>
+580   <span class="i">$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>
+581
+582   <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>
+583   <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+584
+585   <span class="c"># Precision for E-state indicies...</span>
+586   <span class="i">$OptionsInfo</span>{<span class="w">ValuesPrecision</span>} = <span class="i">$Options</span>{<span class="w">valuesprecision</span>}<span class="sc">;</span>
+587
+588   <span class="c"># Setup default vector string format...</span>
+589   <span class="k">my</span><span class="s">(</span><span class="i">$VectorStringFormat</span><span class="s">)</span><span class="sc">;</span>
+590   <span class="i">$VectorStringFormat</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+591   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="s">)</span> <span class="s">{</span>
+592     <span class="i">$VectorStringFormat</span> = <span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="sc">;</span>
+593   <span class="s">}</span>
+594   <span class="k">else</span> <span class="s">{</span>
+595     <span class="i">$VectorStringFormat</span> = <span class="s">(</span><span class="i">$Options</span>{<span class="w">estateatomtypessettouse</span>} =~ <span class="q">/^FixedSize$/</span><span class="s">)</span> ? <span class="q">&quot;ValuesString&quot;</span> <span class="co">:</span> <span class="q">&quot;IDsAndValuesString&quot;</span><span class="sc">;</span>
+596   <span class="s">}</span>
+597   <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>} = <span class="i">$VectorStringFormat</span><span class="sc">;</span>
+598 <span class="s">}</span>
+599
+600 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 601 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+602
+603   <span class="c"># Retrieve all the options...</span>
+604   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+605
+606   <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">&#39;MayaChemToolsAromaticityModel&#39;</span><span class="sc">;</span>
+607
+608   <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">&#39;LabelPrefix&#39;</span><span class="sc">;</span>
+609   <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+610   <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+611
+612   <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+613
+614   <span class="i">$Options</span>{<span class="w">estateatomtypessettouse</span>} = <span class="q">&#39;ArbitrarySize&#39;</span><span class="sc">;</span>
+615
+616   <span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>} = <span class="q">&#39;FingerprintsLabelOnly&#39;</span><span class="sc">;</span>
+617   <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+618
+619   <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">&#39;text&#39;</span><span class="sc">;</span>
+620   <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&#39;comma&#39;</span><span class="sc">;</span>
+621   <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+622
+623   <span class="i">$Options</span>{<span class="w">valuesprecision</span>} = <span class="n">3</span><span class="sc">;</span>
+624
+625   <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+626
+627   <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;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;estateatomtypessettouse|e=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;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;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>
+628     <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 $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+629   <span class="s">}</span>
+630   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+631     <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>
+632       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+633     <span class="s">}</span>
+634     <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
+635   <span class="s">}</span>
+636   <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+637     <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>
+638     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{aromaticitymodel}, for option \&quot;--AromaticityModel\&quot; is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n&quot;</span><span class="sc">;</span>
+639   <span class="s">}</span>
+640   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
+641     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{compoundidmode}, for option \&quot;--CompoundIDMode\&quot; is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n&quot;</span><span class="sc">;</span>
+642   <span class="s">}</span>
+643   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span>
+644     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{datafieldsmode}, for option \&quot;-d, --DataFieldsMode\&quot; is not valid. Allowed values: All, Common, Specify or CompoundID\n&quot;</span><span class="sc">;</span>
+645   <span class="s">}</span>
+646   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">estateatomtypessettouse</span>} &amp;&amp; <span class="i">$Options</span>{<span class="w">estateatomtypessettouse</span>} !~ <span class="q">/^(ArbitrarySize|FixedSize)$/</span><span class="s">)</span> <span class="s">{</span>
+647     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{estateatomtypessettouse}, for option \&quot;-e, --EStateAtomTypesSetToUse\&quot; is not valid. Allowed values: ArbitrarySize or FixedSize\n&quot;</span><span class="sc">;</span>
+648   <span class="s">}</span>
+649   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+650     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{filter}, for option \&quot;-f, --Filter\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+651   <span class="s">}</span>
+652   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>} !~ <span class="q">/^(FingerprintsLabelOnly|FingerprintsLabelWithIDs)$/i</span><span class="s">)</span> <span class="s">{</span>
+653     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{fingerprintslabelmode}, for option \&quot;--FingerprintsLabelMode\&quot; is not valid. Allowed values: FingerprintsLabelOnly or FingerprintsLabelWithIDs\n&quot;</span><span class="sc">;</span>
+654   <span class="s">}</span>
+655   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+656     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{keeplargestcomponent}, for option \&quot;-k, --KeepLargestComponent\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+657   <span class="s">}</span>
+658   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|FP|text|all)$/i</span><span class="s">)</span> <span class="s">{</span>
+659     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{output}, for option \&quot;--output\&quot; is not valid. Allowed values: SD, FP, text, or all\n&quot;</span><span class="sc">;</span>
+660   <span class="s">}</span>
+661   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
+662     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--outdelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
+663   <span class="s">}</span>
+664   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+665     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+666   <span class="s">}</span>
+667   <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+668     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not allowed with, semicolon value of \&quot;--outdelim\&quot; option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n&quot;</span><span class="sc">;</span>
+669   <span class="s">}</span>
+670   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">valuesprecision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+671     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{valuesprecision}, for option \&quot;--ValuesPrecision\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+672   <span class="s">}</span>
+673   <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+674     <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>
+675   <span class="s">}</span>
+676 <span class="s">}</span>
+677
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>

Mercurial > repos > deepakjadmin > mayatool3_test2

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