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+:73ae111cf86f
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+<head>
+<title>MayaChemTools:Code:CalculatePhysicochemicalProperties.pl</title>
+<meta http-equiv="content-type" content="text/html;charset=utf-8">
+<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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+<br/>
+<center>
+<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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+<br/>
+<pre>
+1 #!/usr/bin/perl -w
+2 <span class="c">#</span>
+3 <span class="c"># $RCSfile: CalculatePhysicochemicalProperties.pl,v $</span>
+4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
+5 <span class="c"># $Revision: 1.20 $</span>
+6 <span class="c">#</span>
+7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+8 <span class="c">#</span>
+9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+10 <span class="c">#</span>
+11 <span class="c"># This file is part of MayaChemTools.</span>
+12 <span class="c">#</span>
+13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+16 <span class="c"># later version.</span>
+17 <span class="c">#</span>
+18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+21 <span class="c"># details.</span>
+22 <span class="c">#</span>
+23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+27 <span class="c">#</span>
+28
+29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$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">Molecule</span><span class="sc">;</span>
+40 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span>
+41 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
+42 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptorsGenerator</span><span class="sc">;</span>
+43
+44 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span>
+45
+46 <span class="c"># Autoflush STDOUT</span>
+47 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+48
+49 <span class="c"># Starting message...</span>
+50 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
+51 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
+52 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+53
+54 <span class="c"># Get the options and setup script...</span>
+55 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+56 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+57   <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">&quot;$FindBin::Bin/$ScriptName&quot;</span><span class="s">)</span><span class="sc">;</span>
+58 <span class="s">}</span>
+59
+60 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
+61 <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>
+62
+63 <span class="c"># Process options...</span>
+64 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+65 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+66 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+67
+68 <span class="c"># Setup information about input files...</span>
+69 <span class="k">print</span> <span class="q">&quot;Checking input SD file(s)...\n&quot;</span><span class="sc">;</span>
+70 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
+71 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+72
+73 <span class="c"># Process input files..</span>
+74 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+75 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+76   <span class="k">print</span> <span class="q">&quot;\nProcessing SD files...\n&quot;</span><span class="sc">;</span>
+77 <span class="s">}</span>
+78 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+79   <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+80     <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+81     <span class="i">CalculatePhysicochemicalProperties</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+82   <span class="s">}</span>
+83 <span class="s">}</span>
+84 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+85
+86 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+87 <span class="i">$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>
+88 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+89
+90 <span class="c">###############################################################################</span>
+91
+92 <span class="c"># Calculate physicochemical properties for a SD file...</span>
+93 <span class="c">#</span>
+<a name="CalculatePhysicochemicalProperties-"></a>  94 <span class="k">sub </span><span class="m">CalculatePhysicochemicalProperties</span> <span class="s">{</span>
+95   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+96   <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">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</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">$Molecule</span><span class="cm">,</span> <span class="i">$MolecularDescriptorsGenerator</span><span class="cm">,</span> <span class="i">$PhysicochemicalPropertiesDataRef</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span>
+97
+98   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+99
+100   <span class="c"># Setup output files...</span>
+101   <span class="i">$NewSDFileRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span> <span class="i">$NewTextFileRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+102   <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">SetupAndOpenOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+103
+104   <span class="c"># Setup molecular descriptor generator to calculate property values for specifed</span>
+105   <span class="c"># property names...</span>
+106   <span class="i">$MolecularDescriptorsGenerator</span> = <span class="i">SetupMolecularDescriptorsGenerator</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+107
+108   <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">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</span><span class="s">)</span> = <span class="s">(</span><span class="q">&#39;0&#39;</span><span class="s">)</span> x <span class="n">4</span><span class="sc">;</span>
+109
+110   <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>
+111   <span class="i">$MoleculeFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+112
+113   <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Molecule</span> = <span class="i">$MoleculeFileIO</span><span class="i">-&gt;ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+114     <span class="i">$CmpdCount</span>++<span class="sc">;</span>
+115
+116     <span class="c"># Filter compound data before calculating physiochemical properties...</span>
+117     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Filter</span>}<span class="s">)</span> <span class="s">{</span>
+118       <span class="k">if</span> <span class="s">(</span><span class="i">CheckAndFilterCompound</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+119         <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
+120         <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
+121       <span class="s">}</span>
+122     <span class="s">}</span>
+123
+124     <span class="c"># Calculate properties...</span>
+125     <span class="i">$PhysicochemicalPropertiesDataRef</span> = <span class="i">CalculateMoleculeProperties</span><span class="s">(</span><span class="i">$MolecularDescriptorsGenerator</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+126
+127     <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$PhysicochemicalPropertiesDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+128       <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
+129       <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">&#39;PropertiesCalculationFailed&#39;</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+130       <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
+131     <span class="s">}</span>
+132
+133     <span class="c"># Calculate any rule violations...</span>
+134     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>} &amp;&amp; <span class="i">$PhysicochemicalPropertiesDataRef</span>-&gt;{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
+135       <span class="i">$RuleOf5ViolationsCount</span>++<span class="sc">;</span>
+136     <span class="s">}</span>
+137
+138     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>} &amp;&amp; <span class="i">$PhysicochemicalPropertiesDataRef</span>-&gt;{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
+139       <span class="i">$RuleOf3ViolationsCount</span>++<span class="sc">;</span>
+140     <span class="s">}</span>
+141
+142     <span class="c"># Write out calculate properties...</span>
+143     <span class="i">WriteDataToOutputFiles</span><span class="s">(</span><span class="i">$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">$PhysicochemicalPropertiesDataRef</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span>
+144   <span class="s">}</span>
+145   <span class="i">$MoleculeFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+146
+147   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} &amp;&amp; <span class="i">$NewSDFileRef</span><span class="s">)</span> <span class="s">{</span>
+148     <span class="k">close</span> <span class="i">$NewSDFileRef</span><span class="sc">;</span>
+149   <span class="s">}</span>
+150   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} &amp;&amp; <span class="i">$NewTextFileRef</span><span class="s">)</span> <span class="s">{</span>
+151     <span class="k">close</span> <span class="i">$NewTextFileRef</span><span class="sc">;</span>
+152   <span class="s">}</span>
+153
+154   <span class="i">WriteCalculationSummaryStatistics</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">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</span><span class="s">)</span><span class="sc">;</span>
+155 <span class="s">}</span>
+156
+157 <span class="c"># Process compound being ignored due to problems in physicochemical properties calculation...</span>
+158 <span class="c">#</span>
+<a name="ProcessIgnoredCompound-"></a> 159 <span class="k">sub </span><span class="m">ProcessIgnoredCompound</span> <span class="s">{</span>
+160   <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">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+161   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+162
+163   <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+164   <span class="i">$CmpdID</span> = <span class="i">SetupCmpdIDForTextFiles</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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+165
+166   <span class="j">MODE:</span> <span class="s">{</span>
+167     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNonElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
+168       <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n&quot;</span><span class="sc">;</span>
+169       <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
+170     <span class="s">}</span>
+171
+172     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNoElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
+173       <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n&quot;</span><span class="sc">;</span>
+174       <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
+175     <span class="s">}</span>
+176
+177     <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^PropertiesCalculationFailed$/i</span><span class="s">)</span> <span class="s">{</span>
+178       <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Physicochemical properties calculation didn&#39;t succeed...\n\n&quot;</span><span class="sc">;</span>
+179       <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
+180     <span class="s">}</span>
+181     <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Physicochemical properties calculation didn&#39;t succeed...\n\n&quot;</span><span class="sc">;</span>
+182   <span class="s">}</span>
+183 <span class="s">}</span>
+184
+185 <span class="c"># Check and filter compounds....</span>
+186 <span class="c">#</span>
+<a name="CheckAndFilterCompound-"></a> 187 <span class="k">sub </span><span class="m">CheckAndFilterCompound</span> <span class="s">{</span>
+188   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+189   <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span>
+190
+191   <span class="s">(</span><span class="i">$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>
+192
+193   <span class="k">if</span> <span class="s">(</span><span class="i">$NonElementCount</span><span class="s">)</span> <span class="s">{</span>
+194     <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">&#39;ContainsNonElementalData&#39;</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+195     <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
+196   <span class="s">}</span>
+197
+198   <span class="k">if</span> <span class="s">(</span>!<span class="i">$ElementCount</span><span class="s">)</span> <span class="s">{</span>
+199     <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>
+200     <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
+201   <span class="s">}</span>
+202
+203   <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
+204 <span class="s">}</span>
+205
+206 <span class="c"># Write out compounds physicochemical properties calculation summary statistics...</span>
+207 <span class="c">#</span>
+<a name="WriteCalculationSummaryStatistics-"></a> 208 <span class="k">sub </span><span class="m">WriteCalculationSummaryStatistics</span> <span class="s">{</span>
+209   <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">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+210   <span class="k">my</span><span class="s">(</span><span class="i">$ProcessedCmpdCount</span><span class="s">)</span><span class="sc">;</span>
+211
+212   <span class="i">$ProcessedCmpdCount</span> = <span class="i">$CmpdCount</span> - <span class="i">$IgnoredCmpdCount</span><span class="sc">;</span>
+213
+214   <span class="k">print</span> <span class="q">&quot;\nNumber of compounds: $CmpdCount\n&quot;</span><span class="sc">;</span>
+215   <span class="k">print</span> <span class="q">&quot;Number of compounds processed successfully during physicochemical properties calculation: $ProcessedCmpdCount\n&quot;</span><span class="sc">;</span>
+216   <span class="k">print</span> <span class="q">&quot;Number of compounds ignored during physicochemical properties calculation: $IgnoredCmpdCount\n&quot;</span><span class="sc">;</span>
+217
+218   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
+219     <span class="k">print</span> <span class="q">&quot;Number of compounds with one or more RuleOf5 violations: $RuleOf5ViolationsCount\n&quot;</span><span class="sc">;</span>
+220   <span class="s">}</span>
+221
+222   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
+223     <span class="k">print</span> <span class="q">&quot;Number of compounds with one or more RuleOf3 violations: $RuleOf3ViolationsCount\n&quot;</span><span class="sc">;</span>
+224   <span class="s">}</span>
+225
+226 <span class="s">}</span>
+227
+228 <span class="c"># Open output files...</span>
+229 <span class="c">#</span>
+<a name="SetupAndOpenOutputFiles-"></a> 230 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span>
+231   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+232   <span class="k">my</span><span class="s">(</span><span class="i">$NewSDFile</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span>
+233
+234   <span class="i">$NewSDFileRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+235   <span class="i">$NewTextFileRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+236
+237   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+238     <span class="i">$NewSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+239     <span class="k">print</span> <span class="q">&quot;Generating SD file $NewSDFile...\n&quot;</span><span class="sc">;</span>
+240     <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewSDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $NewSDFile: $! \n&quot;</span><span class="sc">;</span>
+241     <span class="i">$NewSDFileRef</span> = \<span class="i">*NEWSDFILE</span><span class="sc">;</span>
+242   <span class="s">}</span>
+243   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
+244     <span class="i">$NewTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+245     <span class="k">print</span> <span class="q">&quot;Generating text file $NewTextFile...\n&quot;</span><span class="sc">;</span>
+246     <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewTextFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $NewTextFile: $! \n&quot;</span><span class="sc">;</span>
+247     <span class="i">WriteTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> \<span class="i">*NEWTEXTFILE</span><span class="s">)</span><span class="sc">;</span>
+248     <span class="i">$NewTextFileRef</span> = \<span class="i">*NEWTEXTFILE</span><span class="sc">;</span>
+249   <span class="s">}</span>
+250   <span class="k">return</span> <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span>
+251 <span class="s">}</span>
+252
+253 <span class="c"># Write calculated physicochemical properties and other data to appropriate output files...</span>
+254 <span class="c">#</span>
+<a name="WriteDataToOutputFiles-"></a> 255 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span>
+256   <span class="k">my</span><span class="s">(</span><span class="i">$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">$PhysicochemicalPropertiesDataRef</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+257   <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="s">)</span><span class="sc">;</span>
+258
+259   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+260     <span class="c"># Retrieve input compound string used to create molecule and write it out</span>
+261     <span class="c"># without last line containing a delimiter...</span>
+262     <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
+263     <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+264     <span class="i">$CmpdString</span> =~ <span class="q">s/\$\$\$\$$//</span><span class="sc">;</span>
+265     <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">&quot;$CmpdString&quot;</span><span class="sc">;</span>
+266
+267     <span class="c"># Write out calculated physicochemical properties data...</span>
+268     <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
+269       <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>-&gt;{<span class="i">$PropertyName</span>}<span class="sc">;</span>
+270       <span class="k">print</span> <span class="i">$NewSDFileRef</span>  <span class="q">&quot;&gt;  &lt;$PropertyName&gt;\n$PropertyValue\n\n&quot;</span><span class="sc">;</span>
+271     <span class="s">}</span>
+272
+273     <span class="c"># Write out RuleOf5 violations for molecule....</span>
+274     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
+275       <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>-&gt;{<span class="w">RuleOf5Violations</span>}<span class="sc">;</span>
+276       <span class="k">print</span> <span class="i">$NewSDFileRef</span>  <span class="q">&quot;&gt;  &lt;RuleOf5Violations&gt;\n$PropertyValue\n\n&quot;</span><span class="sc">;</span>
+277     <span class="s">}</span>
+278
+279     <span class="c"># Write out RuleOf3 violations for molecule....</span>
+280     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
+281       <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>-&gt;{<span class="w">RuleOf3Violations</span>}<span class="sc">;</span>
+282       <span class="k">print</span> <span class="i">$NewSDFileRef</span>  <span class="q">&quot;&gt;  &lt;RuleOf3Violations&gt;\n$PropertyValue\n\n&quot;</span><span class="sc">;</span>
+283     <span class="s">}</span>
+284
+285     <span class="c"># Write out delimiter...</span>
+286     <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">&quot;\$\$\$\$\n&quot;</span><span class="sc">;</span>
+287   <span class="s">}</span>
+288
+289   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
+290     <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="cm">,</span> <span class="i">$DataFieldLabel</span><span class="cm">,</span> <span class="i">$DataFieldValue</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span><span class="s">)</span><span class="sc">;</span>
+291
+292     <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>
+293     <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+294     <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>
+295       <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">SetupCmpdIDForTextFiles</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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
+296     <span class="s">}</span>
+297     <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+298       <span class="i">@LineWords</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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">$FileIndex</span>]}<span class="sc">;</span>
+299     <span class="s">}</span>
+300     <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
+301       <span class="i">@LineWords</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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">$FileIndex</span>]}<span class="sc">;</span>
+302     <span class="s">}</span>
+303     <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
+304       <span class="i">@LineWords</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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>
+305     <span class="s">}</span>
+306
+307     <span class="c"># Append calculated physicochemical properties data...</span>
+308     <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
+309       <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>-&gt;{<span class="i">$PropertyName</span>}<span class="sc">;</span>
+310       <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span>
+311     <span class="s">}</span>
+312
+313     <span class="c"># Write out RuleOf5 violations for molecule....</span>
+314     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
+315       <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>-&gt;{<span class="w">RuleOf5Violations</span>}<span class="sc">;</span>
+316       <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span>
+317     <span class="s">}</span>
+318
+319     <span class="c"># Write out RuleOf3 violations for molecule....</span>
+320     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
+321       <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>-&gt;{<span class="w">RuleOf3Violations</span>}<span class="sc">;</span>
+322       <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span>
+323     <span class="s">}</span>
+324
+325     <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
+326     <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+327   <span class="s">}</span>
+328 <span class="s">}</span>
+329
+330 <span class="c"># Write out approriate column labels to text file...</span>
+<a name="WriteTextFileCoulmnLabels-"></a> 331 <span class="k">sub </span><span class="m">WriteTextFileCoulmnLabels</span> <span class="s">{</span>
+332   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+333   <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
+334
+335   <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+336   <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>
+337     <span class="k">push</span> <span class="i">@LineWords</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>
+338   <span class="s">}</span>
+339   <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>
+340     <span class="k">push</span> <span class="i">@LineWords</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>
+341   <span class="s">}</span>
+342   <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>
+343     <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
+344   <span class="s">}</span>
+345   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
+346     <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span>
+347   <span class="s">}</span>
+348   <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span><span class="sc">;</span>
+349
+350   <span class="c"># Append physicochemical properties column labels...</span>
+351   <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span>  <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="sc">;</span>
+352
+353   <span class="c"># Write out RuleOf5 violations label...</span>
+354   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
+355     <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">&#39;RuleOf5Violations&#39;</span><span class="sc">;</span>
+356   <span class="s">}</span>
+357
+358   <span class="c"># Write out RuleOf3 violations label...</span>
+359   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
+360     <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">&#39;RuleOf3Violations&#39;</span><span class="sc">;</span>
+361   <span class="s">}</span>
+362
+363   <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
+364   <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+365 <span class="s">}</span>
+366
+367 <span class="c"># Generate compound ID for text files..</span>
+368 <span class="c">#</span>
+<a name="SetupCmpdIDForTextFiles-"></a> 369 <span class="k">sub </span><span class="m">SetupCmpdIDForTextFiles</span> <span class="s">{</span>
+370   <span class="k">my</span><span class="s">(</span><span class="i">$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>
+371   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span>
+372
+373   <span class="i">$CmpdID</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+374   <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>
+375     <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span>
+376     <span class="i">$MolName</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+377     <span class="i">$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>
+378   <span class="s">}</span>
+379   <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>
+380     <span class="i">$CmpdID</span> = <span class="q">&quot;$OptionsInfo{CompoundID}${CmpdCount}&quot;</span><span class="sc">;</span>
+381   <span class="s">}</span>
+382   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
+383     <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span>
+384     <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
+385     <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">$SpecifiedDataField</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
+386   <span class="s">}</span>
+387   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolName$/i</span><span class="s">)</span> <span class="s">{</span>
+388     <span class="i">$CmpdID</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+389   <span class="s">}</span>
+390   <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span>
+391 <span class="s">}</span>
+392
+393 <span class="c"># Calculate physicochemical properties for molecule...</span>
+394 <span class="c">#</span>
+<a name="CalculateMoleculeProperties-"></a> 395 <span class="k">sub </span><span class="m">CalculateMoleculeProperties</span> <span class="s">{</span>
+396   <span class="k">my</span><span class="s">(</span><span class="i">$MolecularDescriptorsGenerator</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+397   <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="cm">,</span> <span class="i">$MolecularDescriptorsObject</span><span class="cm">,</span> <span class="i">%CalculatedPhysicochemicalProperties</span><span class="s">)</span><span class="sc">;</span>
+398
+399   <span class="i">%CalculatedPhysicochemicalProperties</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+400
+401   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span>
+402     <span class="i">$Molecule</span><span class="i">-&gt;KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+403   <span class="s">}</span>
+404
+405   <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">-&gt;DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+406     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+407   <span class="s">}</span>
+408   <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>
+409   <span class="i">$Molecule</span><span class="i">-&gt;DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+410
+411   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AddHydrogens</span>}<span class="s">)</span> <span class="s">{</span>
+412     <span class="i">$Molecule</span><span class="i">-&gt;AddHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+413   <span class="s">}</span>
+414
+415   <span class="c"># Calculate physicochemical properties...</span>
+416   <span class="i">$MolecularDescriptorsGenerator</span><span class="i">-&gt;SetMolecule</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
+417   <span class="i">$MolecularDescriptorsGenerator</span><span class="i">-&gt;GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+418
+419   <span class="k">if</span> <span class="s">(</span>!<span class="i">$MolecularDescriptorsGenerator</span><span class="i">-&gt;IsDescriptorsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+420     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+421   <span class="s">}</span>
+422
+423   <span class="i">%CalculatedPhysicochemicalProperties</span> = <span class="i">$MolecularDescriptorsGenerator</span><span class="i">-&gt;GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+424
+425   <span class="c"># Count RuleOf3 violations...</span>
+426   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
+427     <span class="i">CalculateRuleViolationsCount</span><span class="s">(</span><span class="q">&#39;RuleOf3Violations&#39;</span><span class="cm">,</span> \<span class="i">%CalculatedPhysicochemicalProperties</span><span class="s">)</span><span class="sc">;</span>
+428   <span class="s">}</span>
+429
+430   <span class="c"># Count RuleOf5 violations...</span>
+431   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
+432     <span class="i">CalculateRuleViolationsCount</span><span class="s">(</span><span class="q">&#39;RuleOf5Violations&#39;</span><span class="cm">,</span> \<span class="i">%CalculatedPhysicochemicalProperties</span><span class="s">)</span><span class="sc">;</span>
+433   <span class="s">}</span>
+434
+435   <span class="k">return</span> \<span class="i">%CalculatedPhysicochemicalProperties</span><span class="sc">;</span>
+436 <span class="s">}</span>
+437
+438 <span class="c"># Setup molecular descriptor generator to calculate property values for specifed</span>
+439 <span class="c"># property names...</span>
+440 <span class="c">#</span>
+<a name="SetupMolecularDescriptorsGenerator-"></a> 441 <span class="k">sub </span><span class="m">SetupMolecularDescriptorsGenerator</span> <span class="s">{</span>
+442   <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$MolecularDescriptorsGenerator</span><span class="s">)</span><span class="sc">;</span>
+443
+444   <span class="i">$MolecularDescriptorsGenerator</span> = <span class="w">new</span> <span class="i">MolecularDescriptors::MolecularDescriptorsGenerator</span><span class="s">(</span><span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Specify&#39;</span><span class="cm">,</span> <span class="q">&#39;DescriptorNames&#39;</span> <span class="cm">=&gt;</span> \<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="s">)</span><span class="sc">;</span>
+445
+446   <span class="c"># Setup molecular desciptor calculation parameters...</span>
+447   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">&#39;MolecularWeight&#39;</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">&#39;ExactMass&#39;</span><span class="s">)</span>}<span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
+448     <span class="i">$MolecularDescriptorsGenerator</span><span class="i">-&gt;SetDescriptorClassParameters</span><span class="s">(</span><span class="q">&#39;DescriptorClassName&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;WeightAndMassDescriptors&#39;</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">PrecisionParametersMap</span>}}<span class="s">)</span><span class="sc">;</span>
+449   <span class="s">}</span>
+450
+451   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">&#39;RotatableBonds&#39;</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+452     <span class="i">$MolecularDescriptorsGenerator</span><span class="i">-&gt;SetDescriptorClassParameters</span><span class="s">(</span><span class="q">&#39;DescriptorClassName&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;RotatableBondsDescriptors&#39;</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RotatableBondsParametersMap</span>}}<span class="s">)</span><span class="sc">;</span>
+453   <span class="s">}</span>
+454
+455   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">&#39;HydrogenBondDonors&#39;</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">&#39;HydrogenBondAcceptors&#39;</span><span class="s">)</span>}<span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
+456     <span class="i">$MolecularDescriptorsGenerator</span><span class="i">-&gt;SetDescriptorClassParameters</span><span class="s">(</span><span class="q">&#39;DescriptorClassName&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;HydrogenBondsDescriptors&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrogenBondsType&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">HydrogenBonds</span>}<span class="s">)</span><span class="sc">;</span>
+457   <span class="s">}</span>
+458
+459   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">&#39;TPSA&#39;</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+460     <span class="i">$MolecularDescriptorsGenerator</span><span class="i">-&gt;SetDescriptorClassParameters</span><span class="s">(</span><span class="q">&#39;DescriptorClassName&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;TPSADescriptors&#39;</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">TPSAParametersMap</span>}}<span class="s">)</span><span class="sc">;</span>
+461   <span class="s">}</span>
+462
+463   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">&#39;MolecularComplexity&#39;</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+464     <span class="i">$MolecularDescriptorsGenerator</span><span class="i">-&gt;SetDescriptorClassParameters</span><span class="s">(</span><span class="q">&#39;DescriptorClassName&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;MolecularComplexityDescriptors&#39;</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}}<span class="s">)</span><span class="sc">;</span>
+465   <span class="s">}</span>
+466
+467   <span class="k">return</span> <span class="i">$MolecularDescriptorsGenerator</span><span class="sc">;</span>
+468 <span class="s">}</span>
+469
+470 <span class="c"># Calculate RuleOf3 or RuleOf5 violations count...</span>
+471 <span class="c">#</span>
+<a name="CalculateRuleViolationsCount-"></a> 472 <span class="k">sub </span><span class="m">CalculateRuleViolationsCount</span> <span class="s">{</span>
+473   <span class="k">my</span><span class="s">(</span><span class="i">$RuleViolationsType</span><span class="cm">,</span> <span class="i">$CalculatedPropertiesMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+474   <span class="k">my</span><span class="s">(</span><span class="i">$RuleViolationsCount</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="s">)</span><span class="sc">;</span>
+475
+476   <span class="i">$RuleViolationsCount</span> = <span class="n">0</span><span class="sc">;</span>
+477
+478   <span class="j">RULEVIOLATIONSTYPE:</span> <span class="s">{</span>
+479     <span class="k">if</span> <span class="s">(</span><span class="i">$RuleViolationsType</span> =~ <span class="q">/^RuleOf3Violations$/i</span><span class="s">)</span> <span class="s">{</span>
+480       <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
+481         <span class="k">if</span> <span class="s">(</span><span class="i">$CalculatedPropertiesMapRef</span>-&gt;{<span class="i">$PropertyName</span>} &gt; <span class="i">$OptionsInfo</span>{<span class="w">RuleOf3MaxPropertyValuesMap</span>}{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span>
+482           <span class="i">$RuleViolationsCount</span>++<span class="sc">;</span>
+483         <span class="s">}</span>
+484       <span class="s">}</span>
+485       <span class="k">last</span> <span class="j">RULEVIOLATIONSTYPE</span><span class="sc">;</span>
+486     <span class="s">}</span>
+487
+488     <span class="k">if</span> <span class="s">(</span><span class="i">$RuleViolationsType</span> =~ <span class="q">/^RuleOf5Violations$/i</span><span class="s">)</span> <span class="s">{</span>
+489       <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
+490         <span class="k">if</span> <span class="s">(</span><span class="i">$CalculatedPropertiesMapRef</span>-&gt;{<span class="i">$PropertyName</span>} &gt; <span class="i">$OptionsInfo</span>{<span class="w">RuleOf5MaxPropertyValuesMap</span>}{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span>
+491           <span class="i">$RuleViolationsCount</span>++<span class="sc">;</span>
+492         <span class="s">}</span>
+493       <span class="s">}</span>
+494       <span class="k">last</span> <span class="j">RULEVIOLATIONSTYPE</span><span class="sc">;</span>
+495     <span class="s">}</span>
+496
+497     <span class="k">die</span> <span class="q">&quot;Warning: Unknown rule violation type: $RuleViolationsType...&quot;</span><span class="sc">;</span>
+498   <span class="s">}</span>
+499
+500   <span class="c"># Set rule violation count...</span>
+501   <span class="i">$CalculatedPropertiesMapRef</span>-&gt;{<span class="i">$RuleViolationsType</span>} = <span class="i">$RuleViolationsCount</span><span class="sc">;</span>
+502
+503 <span class="s">}</span>
+504
+505 <span class="c"># Retrieve information about SD files...</span>
+506 <span class="c">#</span>
+<a name="RetrieveSDFilesInfo-"></a> 507 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
+508   <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">$NewSDFileName</span><span class="cm">,</span> <span class="i">$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>
+509
+510   <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+511   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+512   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+513   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+514   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+515   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+516   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+517
+518   <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>
+519   <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>
+520
+521   <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>
+522     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+523
+524     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+525     <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+526     <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+527     <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+528
+529     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+530     <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>
+531       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+532       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+533     <span class="s">}</span>
+534     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$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>
+535       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
+536       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+537     <span class="s">}</span>
+538
+539     <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span>
+540       <span class="c"># Make sure data field exists in SD file..</span>
+541       <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>
+542
+543       <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+544       <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: $! \n&quot;</span><span class="sc">;</span>
+545       <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
+546       <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+547       <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+548       <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
+549       <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
+550       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span>
+551         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using  \&quot;--CompoundID\&quot; option in \&quot;DataField\&quot; \&quot;--CompoundIDMode\&quot; doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+552         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+553       <span class="s">}</span>
+554     <span class="s">}</span>
+555
+556     <span class="i">$AllDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+557     <span class="i">$CommonDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+558     <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span>
+559       <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
+560       <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
+561       <span class="s">(</span><span class="i">$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>
+562       <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+563     <span class="s">}</span>
+564
+565     <span class="c"># Setup output file names...</span>
+566     <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">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+567     <span class="s">(</span><span class="i">$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">$SDFile</span><span class="s">)</span><span class="sc">;</span>
+568
+569     <span class="i">$TextOutFileExt</span> = <span class="q">&quot;csv&quot;</span><span class="sc">;</span>
+570     <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>
+571       <span class="i">$TextOutFileExt</span> = <span class="q">&quot;tsv&quot;</span><span class="sc">;</span>
+572     <span class="s">}</span>
+573     <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span>
+574
+575     <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+576       <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>
+577       <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>
+578         <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+579       <span class="s">}</span>
+580       <span class="k">else</span> <span class="s">{</span>
+581         <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
+582       <span class="s">}</span>
+583       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+584     <span class="s">}</span>
+585     <span class="k">else</span> <span class="s">{</span>
+586       <span class="i">$OutFileRoot</span> = <span class="q">&quot;${FileName}PhysicochemicalProperties&quot;</span><span class="sc">;</span>
+587     <span class="s">}</span>
+588
+589     <span class="i">$NewSDFileName</span> = <span class="q">&quot;${OutFileRoot}.${SDOutFileExt}&quot;</span><span class="sc">;</span>
+590     <span class="i">$NewTextFileName</span> = <span class="q">&quot;${OutFileRoot}.${TextOutFileExt}&quot;</span><span class="sc">;</span>
+591
+592     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+593       <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span>
+594         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n&quot;</span><span class="sc">;</span>
+595         <span class="k">print</span> <span class="q">&quot;Specify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
+596         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+597       <span class="s">}</span>
+598     <span class="s">}</span>
+599
+600     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
+601       <span class="c"># Check SD and text outout files...</span>
+602       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
+603         <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span>
+604           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n&quot;</span><span class="sc">;</span>
+605           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+606         <span class="s">}</span>
+607       <span class="s">}</span>
+608       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
+609         <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>
+610           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n&quot;</span><span class="sc">;</span>
+611           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+612         <span class="s">}</span>
+613       <span class="s">}</span>
+614     <span class="s">}</span>
+615
+616     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+617
+618     <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
+619     <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span>
+620     <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span>
+621
+622     <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span>
+623     <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span>
+624   <span class="s">}</span>
+625 <span class="s">}</span>
+626
+627 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 628 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+629   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+630
+631   <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span>
+632
+633   <span class="c"># Process property name related options...</span>
+634   <span class="i">ProcessPropertyNamesOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+635
+636   <span class="c"># Setup RuleOf3 and RuleOf5 violation calculations...</span>
+637   <span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+638   <span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+639
+640   <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span>
+641   <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span>
+642   <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span>
+643
+644   <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span>
+645   <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+646
+647   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+648   <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+649
+650   <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>
+651     <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>
+652       <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span>
+653         <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--CompoundID\&quot; option in \&quot;DataField\&quot; \&quot;--CompoundIDMode\&quot;. \n&quot;</span><span class="sc">;</span>
+654       <span class="s">}</span>
+655       <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span>
+656     <span class="s">}</span>
+657     <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^(LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
+658       <span class="i">$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>
+659     <span class="s">}</span>
+660   <span class="s">}</span>
+661   <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>
+662     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span>
+663       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--DataFields\&quot; option in \&quot;Specify\&quot; \&quot;-d, --DataFieldsMode\&quot;. \n&quot;</span><span class="sc">;</span>
+664     <span class="s">}</span>
+665     <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span>
+666     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span>
+667   <span class="s">}</span>
+668
+669   <span class="c"># Types of hydrogen bonds...</span>
+670   <span class="i">$OptionsInfo</span>{<span class="w">HydrogenBonds</span>} = <span class="i">$Options</span>{<span class="w">hydrogenbonds</span>}<span class="sc">;</span>
+671
+672   <span class="c"># Process precision value parameters...</span>
+673   <span class="i">ProcessPrecisionOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+674
+675   <span class="c"># Process rotatable bonds parameters...</span>
+676   <span class="i">ProcessRotatableBondsOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+677
+678   <span class="c"># Process TPSA parameters...</span>
+679   <span class="i">ProcessTPSAOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+680
+681   <span class="c"># Process molecular complexity parameters...</span>
+682   <span class="i">ProcessMolecularComplexityOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+683
+684   <span class="i">$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>
+685
+686   <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+687
+688   <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
+689   <span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(SD|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+690   <span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(Text|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+691
+692   <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/tab/i</span> <span class="s">)</span> ? <span class="q">&quot;\t&quot;</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span><span class="s">)</span> ? <span class="q">&quot;\;&quot;</span> <span class="co">:</span> <span class="q">&quot;\,&quot;</span><span class="s">)</span><span class="sc">;</span>
+693   <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+694
+695   <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+696   <span class="i">$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>
+697 <span class="s">}</span>
+698
+699 <span class="c"># Process property name related options...</span>
+700 <span class="c">#</span>
+<a name="ProcessPropertyNamesOption-"></a> 701 <span class="k">sub </span><span class="m">ProcessPropertyNamesOption</span> <span class="s">{</span>
+702
+703   <span class="c"># Setup supported physicochemical properties...</span>
+704   <span class="k">my</span><span class="s">(</span><span class="i">$SupportedProperty</span><span class="s">)</span><span class="sc">;</span>
+705
+706   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+707   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+708
+709   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+710   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+711
+712   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+713   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+714
+715   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">DefaultPropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+716
+717   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}} = <span class="q">qw(MolecularWeight ExactMass HeavyAtoms Rings AromaticRings MolecularVolume RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP SMR TPSA Fsp3Carbons Sp3Carbons MolecularComplexity)</span><span class="sc">;</span>
+718
+719   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}} = <span class="q">qw(MolecularWeight HydrogenBondDonors HydrogenBondAcceptors SLogP)</span><span class="sc">;</span>
+720   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="q">&#39;MolecularWeight&#39;</span> <span class="cm">=&gt;</span> <span class="n">500</span><span class="cm">,</span> <span class="q">&#39;HydrogenBondDonors&#39;</span> <span class="cm">=&gt;</span> <span class="n">5</span><span class="cm">,</span> <span class="q">&#39;HydrogenBondAcceptors&#39;</span> <span class="cm">=&gt;</span> <span class="n">10</span><span class="cm">,</span>  <span class="q">&#39;SLogP&#39;</span> <span class="cm">=&gt;</span> <span class="n">5</span><span class="s">)</span><span class="sc">;</span>
+721
+722   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}} = <span class="q">qw(MolecularWeight RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA)</span><span class="sc">;</span>
+723   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="q">&#39;MolecularWeight&#39;</span> <span class="cm">=&gt;</span> <span class="n">300</span><span class="cm">,</span> <span class="q">&#39;RotatableBonds&#39;</span> <span class="cm">=&gt;</span> <span class="n">3</span><span class="cm">,</span> <span class="q">&#39;HydrogenBondDonors&#39;</span> <span class="cm">=&gt;</span> <span class="n">3</span><span class="cm">,</span> <span class="q">&#39;HydrogenBondAcceptors&#39;</span> <span class="cm">=&gt;</span> <span class="n">3</span><span class="cm">,</span> <span class="q">&#39;SLogP&#39;</span> <span class="cm">=&gt;</span> <span class="n">3</span><span class="cm">,</span> <span class="q">&#39;TPSA&#39;</span> <span class="cm">=&gt;</span> <span class="n">60</span><span class="s">)</span><span class="sc">;</span>
+724
+725   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">DefaultPropertyNames</span>}} = <span class="q">qw(MolecularWeight HeavyAtoms MolecularVolume RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA)</span><span class="sc">;</span>
+726
+727   <span class="k">for</span> <span class="i">$SupportedProperty</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
+728     <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$SupportedProperty</span><span class="s">)</span>} = <span class="i">$SupportedProperty</span><span class="sc">;</span>
+729   <span class="s">}</span>
+730
+731   <span class="c"># Process specified properties....</span>
+732   <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="cm">,</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">%SpecifiedPropertyNamesMap</span><span class="s">)</span><span class="sc">;</span>
+733
+734   <span class="i">@SpecifiedPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+735   <span class="i">%SpecifiedPropertyNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+736
+737   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+738   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+739
+740   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+741     <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}}<span class="sc">;</span>
+742   <span class="s">}</span>
+743   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf5$/i</span><span class="s">)</span> <span class="s">{</span>
+744     <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}}<span class="sc">;</span>
+745   <span class="s">}</span>
+746   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf3$/i</span><span class="s">)</span> <span class="s">{</span>
+747     <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}}<span class="sc">;</span>
+748   <span class="s">}</span>
+749   <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+750     <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">DefaultPropertyNames</span>}}<span class="sc">;</span>
+751   <span class="s">}</span>
+752   <span class="k">else</span> <span class="s">{</span>
+753     <span class="c"># Comma delimited lisr of specified property names...</span>
+754     <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">@UnsupportedPropertyNames</span><span class="s">)</span><span class="sc">;</span>
+755
+756     <span class="i">$Mode</span> = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+757     <span class="i">$Mode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+758
+759     <span class="i">@PropertyNames</span> = <span class="k">split</span> <span class="q">&quot;,&quot;</span><span class="cm">,</span> <span class="i">$Mode</span><span class="sc">;</span>
+760     <span class="i">@UnsupportedPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+761
+762     <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@PropertyNames</span><span class="s">)</span> <span class="s">{</span>
+763       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+764         <span class="k">push</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span>
+765       <span class="s">}</span>
+766       <span class="k">else</span> <span class="s">{</span>
+767         <span class="k">push</span> <span class="i">@UnsupportedPropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span>
+768       <span class="s">}</span>
+769     <span class="s">}</span>
+770     <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedPropertyNames</span><span class="s">)</span> <span class="s">{</span>
+771       <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedPropertyNames</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+772         <span class="k">warn</span> <span class="q">&quot;Error: The physicochemical property names specified - &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@UnsupportedPropertyNames</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">&quot; - for option \&quot;-m --mode\&quot; are not valid.\n&quot;</span><span class="sc">;</span>
+773       <span class="s">}</span>
+774       <span class="k">else</span> <span class="s">{</span>
+775         <span class="k">warn</span> <span class="q">&quot;Error: The physicochemical property name specified, @UnsupportedPropertyNames , for option \&quot;-m --mode\&quot; is not valid.\n&quot;</span><span class="sc">;</span>
+776       <span class="s">}</span>
+777       <span class="k">die</span> <span class="q">&quot;Allowed values:&quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}}<span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+778     <span class="s">}</span>
+779     <span class="k">if</span> <span class="s">(</span>!<span class="i">@SpecifiedPropertyNames</span><span class="s">)</span> <span class="s">{</span>
+780       <span class="k">die</span> <span class="q">&quot;Error: No valid physicochemical property names specified for option \&quot;-m --mode\&quot;.\n&quot;</span><span class="sc">;</span>
+781     <span class="s">}</span>
+782   <span class="s">}</span>
+783
+784   <span class="c"># Set up specified property names map...</span>
+785   <span class="j">PROPERTY:</span> <span class="k">for</span> <span class="i">$SpecifiedPropertyName</span> <span class="s">(</span><span class="i">@SpecifiedPropertyNames</span><span class="s">)</span> <span class="s">{</span>
+786     <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+787       <span class="k">warn</span> <span class="q">&quot;Warning: The physicochemical property name, $SpecifiedPropertyName, is specified multiple times as value of option \&quot;-m --mode\&quot; .\n&quot;</span><span class="sc">;</span>
+788       <span class="k">next</span> <span class="j">PROPERTY</span><span class="sc">;</span>
+789     <span class="s">}</span>
+790     <span class="c"># Canonical specified property name...</span>
+791     <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>} = <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>}<span class="sc">;</span>
+792   <span class="s">}</span>
+793
+794   <span class="c"># Make sure for calculation of  RuleOf3Violations, all appropriate property names are specified...</span>
+795   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} =~ <span class="q">/^Yes$/i</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf5$/i</span><span class="s">)</span> <span class="s">{</span>
+796     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{ruleof3violations}, for  \&quot;--RuleOf3Violations\&quot; option in \&quot;RuleOf5\&quot; \&quot;-m --Mode\&quot; is not valid. You must specify RuleOf3 value for \&quot;-m --Mode\&quot; to calculate RuleOf3 violations.\n&quot;</span><span class="sc">;</span>
+797   <span class="s">}</span>
+798
+799   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> <span class="s">{</span>
+800     <span class="k">my</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="cm">,</span> <span class="i">@MissingRuleOf3Names</span><span class="s">)</span><span class="sc">;</span>
+801
+802     <span class="i">@MissingRuleOf3Names</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+803     <span class="j">PROPERTY:</span> <span class="k">for</span> <span class="i">$RuleOf3PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
+804       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+805         <span class="k">next</span> <span class="j">PROPERTY</span><span class="sc">;</span>
+806       <span class="s">}</span>
+807       <span class="k">push</span> <span class="i">@MissingRuleOf3Names</span><span class="cm">,</span> <span class="i">$RuleOf3PropertyName</span><span class="sc">;</span>
+808
+809       <span class="c"># Add property name to specified properties names list and map...</span>
+810       <span class="k">push</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">$RuleOf3PropertyName</span><span class="sc">;</span>
+811       <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="s">)</span>} = <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="s">)</span>}<span class="sc">;</span>
+812     <span class="s">}</span>
+813     <span class="k">if</span> <span class="s">(</span><span class="i">@MissingRuleOf3Names</span><span class="s">)</span> <span class="s">{</span>
+814       <span class="k">warn</span> <span class="q">&quot;Warning: The following physicochemical property names not specified in \&quot;-m --Mode\&quot; option are required for calculating RuleOf3Violations and have been added to the list of property names: @MissingRuleOf3Names\n&quot;</span><span class="sc">;</span>
+815     <span class="s">}</span>
+816   <span class="s">}</span>
+817
+818   <span class="c"># Make sure for calculation of  RuleOf5Violations, all appropriate property names are specified...</span>
+819   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} =~ <span class="q">/^Yes$/i</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf3$/i</span><span class="s">)</span> <span class="s">{</span>
+820     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{ruleof5violations}, for  \&quot;--RuleOf5Violations\&quot; option in \&quot;RuleOf3\&quot; \&quot;-m --Mode\&quot; is not valid. You must specify RuleOf5 value for \&quot;-m --Mode\&quot; to calculate RuleOf5 violations.\n&quot;</span><span class="sc">;</span>
+821   <span class="s">}</span>
+822
+823   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> <span class="s">{</span>
+824     <span class="k">my</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="cm">,</span> <span class="i">@MissingRuleOf5Names</span><span class="s">)</span><span class="sc">;</span>
+825
+826     <span class="i">@MissingRuleOf5Names</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+827     <span class="j">PROPERTY:</span> <span class="k">for</span> <span class="i">$RuleOf5PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
+828       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+829         <span class="k">next</span> <span class="j">PROPERTY</span><span class="sc">;</span>
+830       <span class="s">}</span>
+831       <span class="k">push</span> <span class="i">@MissingRuleOf5Names</span><span class="cm">,</span> <span class="i">$RuleOf5PropertyName</span><span class="sc">;</span>
+832
+833       <span class="c"># Add property name to specified properties names list and map...</span>
+834       <span class="k">push</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">$RuleOf5PropertyName</span><span class="sc">;</span>
+835       <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="s">)</span>} = <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="s">)</span>}<span class="sc">;</span>
+836     <span class="s">}</span>
+837     <span class="k">if</span> <span class="s">(</span><span class="i">@MissingRuleOf5Names</span><span class="s">)</span> <span class="s">{</span>
+838       <span class="k">warn</span> <span class="q">&quot;Warning: The following physicochemical property names not specified in \&quot;-m --Mode\&quot; option are required for calculating RuleOf5Violations and have been added to the list of property names: @MissingRuleOf5Names\n&quot;</span><span class="sc">;</span>
+839     <span class="s">}</span>
+840   <span class="s">}</span>
+841   <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+842
+843   <span class="c"># Setup canonical specified property names corresponding to supported names in mixed case...</span>
+844   <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedCanonicalPropertyNames</span><span class="s">)</span><span class="sc">;</span>
+845
+846   <span class="i">@SpecifiedCanonicalPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+847   <span class="k">for</span> <span class="i">$SpecifiedPropertyName</span> <span class="s">(</span><span class="i">@SpecifiedPropertyNames</span><span class="s">)</span> <span class="s">{</span>
+848     <span class="k">push</span> <span class="i">@SpecifiedCanonicalPropertyNames</span><span class="cm">,</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>}<span class="sc">;</span>
+849   <span class="s">}</span>
+850   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}} = <span class="i">@SpecifiedCanonicalPropertyNames</span><span class="sc">;</span>
+851   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}} = <span class="i">%SpecifiedPropertyNamesMap</span><span class="sc">;</span>
+852
+853   <span class="c"># Based on specified property names, figure out whether hydrogens need to be added before</span>
+854   <span class="c"># calculation of properties...</span>
+855   <span class="c">#</span>
+856   <span class="i">$OptionsInfo</span>{<span class="w">AddHydrogens</span>} = <span class="n">0</span><span class="sc">;</span>
+857   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="q">&#39;MolecularVolume&#39;</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="q">&#39;SLogP&#39;</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="q">&#39;SMR&#39;</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+858     <span class="i">$OptionsInfo</span>{<span class="w">AddHydrogens</span>} = <span class="n">1</span><span class="sc">;</span>
+859   <span class="s">}</span>
+860 <span class="s">}</span>
+861
+862 <span class="c"># Process precision option...</span>
+863 <span class="c">#</span>
+<a name="ProcessPrecisionOption-"></a> 864 <span class="k">sub </span><span class="m">ProcessPrecisionOption</span> <span class="s">{</span>
+865   <span class="k">my</span><span class="s">(</span><span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">%PrecisionParametersMap</span><span class="cm">,</span> <span class="i">%PrecisionParameterNamesMap</span><span class="s">)</span><span class="sc">;</span>
+866
+867   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">PrecisionParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+868
+869   <span class="i">%PrecisionParametersMap</span> = <span class="s">(</span><span class="q">&#39;WeightPrecision&#39;</span> <span class="cm">=&gt;</span> <span class="n">2</span><span class="cm">,</span> <span class="q">&#39;MassPrecision&#39;</span> <span class="cm">=&gt;</span> <span class="n">4</span><span class="s">)</span><span class="sc">;</span>
+870   <span class="i">%PrecisionParameterNamesMap</span> = <span class="s">(</span><span class="q">&#39;molecularweight&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;WeightPrecision&#39;</span><span class="cm">,</span> <span class="q">&#39;exactmass&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;MassPrecision&#39;</span><span class="s">)</span><span class="sc">;</span>
+871
+872   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span> <span class="s">{</span>
+873     <span class="c"># Process specified values...</span>
+874     <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedPrecision</span><span class="cm">,</span> <span class="i">@SpecifiedPrecisionValuePairs</span><span class="s">)</span><span class="sc">;</span>
+875
+876     <span class="i">$SpecifiedPrecision</span> = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
+877     <span class="i">$SpecifiedPrecision</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+878     <span class="i">@SpecifiedPrecisionValuePairs</span> = <span class="k">split</span> <span class="q">&quot;,&quot;</span><span class="cm">,</span> <span class="i">$SpecifiedPrecision</span><span class="sc">;</span>
+879     <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedPrecisionValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+880       <span class="k">die</span> <span class="q">&quot;Error: Invalid number of values specified using \&quot;--Precision\&quot; option: It must contain even number of values.\n&quot;</span><span class="sc">;</span>
+881     <span class="s">}</span>
+882     <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> &lt; <span class="i">@SpecifiedPrecisionValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
+883       <span class="i">$ParameterName</span> = <span class="i">$SpecifiedPrecisionValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+884       <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedPrecisionValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
+885       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$PrecisionParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+886         <span class="k">die</span> <span class="q">&quot;Error: The precision parameter name specified, $ParameterName, for option \&quot;--Precision\&quot; is not valid.\n&quot;</span><span class="sc">;</span>
+887       <span class="s">}</span>
+888       <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+889         <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \&quot;--Precision\&quot; is not valid. Allowed values: positive integer. \n&quot;</span><span class="sc">;</span>
+890       <span class="s">}</span>
+891       <span class="i">$ParameterName</span> = <span class="i">$PrecisionParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span>
+892       <span class="i">$PrecisionParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span>
+893     <span class="s">}</span>
+894   <span class="s">}</span>
+895   <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
+896   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">PrecisionParametersMap</span>}} = <span class="i">%PrecisionParametersMap</span><span class="sc">;</span>
+897 <span class="s">}</span>
+898
+899 <span class="c"># Process rotatable bonds option...</span>
+<a name="ProcessRotatableBondsOption-"></a> 900 <span class="k">sub </span><span class="m">ProcessRotatableBondsOption</span> <span class="s">{</span>
+901   <span class="k">my</span><span class="s">(</span><span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">%RotatableBondsParametersMap</span><span class="cm">,</span> <span class="i">%RotatableBondsParameterNamesMap</span><span class="s">)</span><span class="sc">;</span>
+902
+903   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RotatableBondsParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+904   <span class="i">%RotatableBondsParametersMap</span> = <span class="s">(</span><span class="q">&#39;IgnoreTerminalBonds&#39;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="cm">,</span> <span class="q">&#39;IgnoreBondsToTripleBonds&#39;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="cm">,</span> <span class="q">&#39;IgnoreAmideBonds&#39;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="cm">,</span> <span class="q">&#39;IgnoreThioamideBonds&#39;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="cm">,</span> <span class="q">&#39;IgnoreSulfonamideBonds&#39;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
+905
+906   <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%RotatableBondsParametersMap</span><span class="s">)</span> <span class="s">{</span>
+907     <span class="i">$RotatableBondsParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>} = <span class="i">$ParameterName</span><span class="sc">;</span>
+908   <span class="s">}</span>
+909
+910   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">rotatablebonds</span>}<span class="s">)</span> <span class="s">{</span>
+911     <span class="c"># Process specified values...</span>
+912     <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedRotatableBonds</span><span class="cm">,</span> <span class="i">@SpecifiedRotatableBondsValuePairs</span><span class="s">)</span><span class="sc">;</span>
+913
+914     <span class="i">$SpecifiedRotatableBonds</span> = <span class="i">$Options</span>{<span class="w">rotatablebonds</span>}<span class="sc">;</span>
+915     <span class="i">$SpecifiedRotatableBonds</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+916     <span class="i">@SpecifiedRotatableBondsValuePairs</span> = <span class="k">split</span> <span class="q">&quot;,&quot;</span><span class="cm">,</span> <span class="i">$SpecifiedRotatableBonds</span><span class="sc">;</span>
+917     <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedRotatableBondsValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+918       <span class="k">die</span> <span class="q">&quot;Error: Invalid number of values specified using \&quot;--RotatableBonds\&quot; option: It must contain even number of values.\n&quot;</span><span class="sc">;</span>
+919     <span class="s">}</span>
+920     <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> &lt; <span class="i">@SpecifiedRotatableBondsValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
+921       <span class="i">$ParameterName</span> = <span class="i">$SpecifiedRotatableBondsValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+922       <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedRotatableBondsValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
+923       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$RotatableBondsParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+924         <span class="k">die</span> <span class="q">&quot;Error: The rotatable bonds parameter name specified, $ParameterName, for option \&quot;--RotatableBonds\&quot; is not valid.\n&quot;</span><span class="sc">;</span>
+925       <span class="s">}</span>
+926       <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+927         <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \&quot;--RotatableBonds\&quot; is not valid. Allowed values: Yes or No. \n&quot;</span><span class="sc">;</span>
+928       <span class="s">}</span>
+929       <span class="i">$ParameterName</span> = <span class="i">$RotatableBondsParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span>
+930       <span class="i">$ParameterValue</span> = <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+931       <span class="i">$RotatableBondsParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span>
+932     <span class="s">}</span>
+933   <span class="s">}</span>
+934   <span class="i">$OptionsInfo</span>{<span class="w">RotatableBonds</span>} = <span class="i">$Options</span>{<span class="w">rotatablebonds</span>}<span class="sc">;</span>
+935   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RotatableBondsParametersMap</span>}} = <span class="i">%RotatableBondsParametersMap</span><span class="sc">;</span>
+936 <span class="s">}</span>
+937
+938 <span class="c"># Process TPSA option...</span>
+939 <span class="c">#</span>
+<a name="ProcessTPSAOption-"></a> 940 <span class="k">sub </span><span class="m">ProcessTPSAOption</span> <span class="s">{</span>
+941   <span class="k">my</span><span class="s">(</span><span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">%TPSAParametersMap</span><span class="cm">,</span> <span class="i">%TPSAParameterNamesMap</span><span class="s">)</span><span class="sc">;</span>
+942
+943   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">TPSAParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+944
+945   <span class="i">%TPSAParametersMap</span> = <span class="s">(</span><span class="q">&#39;IgnorePhosphorus&#39;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="cm">,</span> <span class="q">&#39;IgnoreSulfur&#39;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
+946   <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%TPSAParametersMap</span><span class="s">)</span> <span class="s">{</span>
+947     <span class="i">$TPSAParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>} = <span class="i">$ParameterName</span><span class="sc">;</span>
+948   <span class="s">}</span>
+949
+950   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">tpsa</span>}<span class="s">)</span> <span class="s">{</span>
+951     <span class="c"># Process specified values...</span>
+952     <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedTPSA</span><span class="cm">,</span> <span class="i">@SpecifiedTPSAValuePairs</span><span class="s">)</span><span class="sc">;</span>
+953
+954     <span class="i">$SpecifiedTPSA</span> = <span class="i">$Options</span>{<span class="w">tpsa</span>}<span class="sc">;</span>
+955     <span class="i">$SpecifiedTPSA</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+956     <span class="i">@SpecifiedTPSAValuePairs</span> = <span class="k">split</span> <span class="q">&quot;,&quot;</span><span class="cm">,</span> <span class="i">$SpecifiedTPSA</span><span class="sc">;</span>
+957     <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedTPSAValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+958       <span class="k">die</span> <span class="q">&quot;Error: Invalid number of values specified using \&quot;--TPSA\&quot; option: It must contain even number of values.\n&quot;</span><span class="sc">;</span>
+959     <span class="s">}</span>
+960     <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> &lt; <span class="i">@SpecifiedTPSAValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
+961       <span class="i">$ParameterName</span> = <span class="i">$SpecifiedTPSAValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+962       <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedTPSAValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
+963       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$TPSAParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+964         <span class="k">die</span> <span class="q">&quot;Error: The TPSA parameter name specified, $ParameterName, for option \&quot;--TPSA\&quot; is not valid.\n&quot;</span><span class="sc">;</span>
+965       <span class="s">}</span>
+966       <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+967         <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \&quot;--TPSA\&quot; is not valid. Allowed values: Yes or No. \n&quot;</span><span class="sc">;</span>
+968       <span class="s">}</span>
+969       <span class="i">$ParameterName</span> = <span class="i">$TPSAParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span>
+970       <span class="i">$ParameterValue</span> = <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+971       <span class="i">$TPSAParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span>
+972     <span class="s">}</span>
+973   <span class="s">}</span>
+974   <span class="i">$OptionsInfo</span>{<span class="w">TPSA</span>} = <span class="i">$Options</span>{<span class="w">tpsa</span>}<span class="sc">;</span>
+975   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">TPSAParametersMap</span>}} = <span class="i">%TPSAParametersMap</span><span class="sc">;</span>
+976 <span class="s">}</span>
+977
+978 <span class="c"># Process molecular complexity parameters...</span>
+979 <span class="c">#</span>
+<a name="ProcessMolecularComplexityOption-"></a> 980 <span class="k">sub </span><span class="m">ProcessMolecularComplexityOption</span> <span class="s">{</span>
+981   <span class="k">my</span><span class="s">(</span><span class="i">$MolecularComplexityType</span><span class="cm">,</span> <span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@ParameterValues</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="i">%ComplexityParametersMap</span><span class="cm">,</span> <span class="i">%ComplexityParameterNamesMap</span><span class="s">)</span><span class="sc">;</span>
+982
+983   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+984
+985   <span class="i">%ComplexityParametersMap</span> = <span class="s">(</span><span class="q">&#39;MolecularComplexityType&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;&#39;</span><span class="cm">,</span> <span class="q">&#39;AtomIdentifierType&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;&#39;</span><span class="cm">,</span>
+986                               <span class="q">&#39;AtomicInvariantsToUse&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;&#39;</span><span class="cm">,</span> <span class="q">&#39;FunctionalClassesToUse&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;&#39;</span><span class="cm">,</span>
+987                               <span class="q">&#39;MACCSKeysSize&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;166&#39;</span><span class="cm">,</span> <span class="q">&#39;NeighborhoodRadius&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;2&#39;</span><span class="cm">,</span>
+988                               <span class="q">&#39;MinPathLength&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;1&#39;</span><span class="cm">,</span> <span class="q">&#39;MaxPathLength&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;8&#39;</span><span class="cm">,</span> <span class="q">&#39;UseBondSymbols&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;1&#39;</span><span class="cm">,</span>
+989                               <span class="q">&#39;MinDistance&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;1&#39;</span><span class="cm">,</span> <span class="q">&#39;MaxDistance&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;10&#39;</span><span class="cm">,</span> <span class="q">&#39;UseTriangleInequality&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;&#39;</span><span class="cm">,</span>
+990                               <span class="q">&#39;DistanceBinSize&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;2&#39;</span><span class="cm">,</span> <span class="q">&#39;NormalizationMethodology&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;None&#39;</span><span class="s">)</span><span class="sc">;</span>
+991
+992   <span class="i">%ComplexityParameterNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+993   <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%ComplexityParametersMap</span><span class="s">)</span> <span class="s">{</span>
+994     <span class="i">$ComplexityParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>} = <span class="i">$ParameterName</span><span class="sc">;</span>
+995   <span class="s">}</span>
+996
+997   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">molecularcomplexity</span>}<span class="s">)</span> <span class="s">{</span>
+998     <span class="c"># Process specified values...</span>
+999     <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedComplexity</span><span class="cm">,</span> <span class="i">@SpecifiedComplexityValuePairs</span><span class="s">)</span><span class="sc">;</span>
+1000
+1001     <span class="i">$SpecifiedComplexity</span> = <span class="i">$Options</span>{<span class="w">molecularcomplexity</span>}<span class="sc">;</span>
+1002
+1003     <span class="i">@SpecifiedComplexityValuePairs</span> = <span class="k">split</span> <span class="q">&quot;,&quot;</span><span class="cm">,</span> <span class="i">$SpecifiedComplexity</span><span class="sc">;</span>
+1004     <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedComplexityValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+1005       <span class="k">die</span> <span class="q">&quot;Error: Invalid number of values specified using \&quot;--MolecularComplexity\&quot; option: It must contain even number of values.\n&quot;</span><span class="sc">;</span>
+1006     <span class="s">}</span>
+1007
+1008     <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> &lt; <span class="i">@SpecifiedComplexityValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
+1009       <span class="i">$ParameterName</span> = <span class="i">$SpecifiedComplexityValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+1010       <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedComplexityValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
+1011
+1012       <span class="i">$ParameterName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span><span class="sc">;</span>
+1013       <span class="i">$ParameterValue</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="sc">;</span>
+1014
+1015       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ComplexityParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+1016         <span class="k">die</span> <span class="q">&quot;Error: The molecular complexity parameter name specified, $ParameterName, for option \&quot;--MolecularComplexity\&quot; is not valid.\n&quot;</span><span class="sc">;</span>
+1017       <span class="s">}</span>
+1018       <span class="i">$ParameterName</span> = <span class="i">$ComplexityParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span>
+1019
+1020       <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^AtomicInvariantsToUse$/i</span><span class="s">)</span> <span class="s">{</span>
+1021         <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbolFound</span><span class="s">)</span><span class="sc">;</span>
+1022
+1023         <span class="i">$AtomSymbolFound</span> = <span class="n">0</span><span class="sc">;</span>
+1024         <span class="i">@ParameterValues</span> = <span class="k">split</span><span class="s">(</span><span class="q">&#39; &#39;</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="s">)</span><span class="sc">;</span>
+1025         <span class="k">for</span> <span class="i">$ParameterValue</span> <span class="s">(</span><span class="i">@ParameterValues</span><span class="s">)</span> <span class="s">{</span>
+1026           <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1027             <span class="k">die</span> <span class="q">&quot;Error: The atomic invariant specified, $ParameterValue, for  AtomicInvariantsToUse in option \&quot;--MolecularComplexity\&quot; is not valid.\n&quot;</span><span class="sc">;</span>
+1028           <span class="s">}</span>
+1029           <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^(AS|AtomSymbol)$/i</span><span class="s">)</span> <span class="s">{</span>
+1030             <span class="i">$AtomSymbolFound</span> = <span class="n">1</span><span class="sc">;</span>
+1031           <span class="s">}</span>
+1032         <span class="s">}</span>
+1033         <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSymbolFound</span><span class="s">)</span> <span class="s">{</span>
+1034           <span class="k">die</span> <span class="q">&quot;Error: The atomic invariants specified using AtomicInvariantsToUse in option \&quot;--MolecularComplexity\&quot; is not valid: AtomicInvariant atom symbol, AS or AtomSymbol, must be specified.\n&quot;</span><span class="sc">;</span>
+1035         <span class="s">}</span>
+1036         <span class="i">$ParameterValue</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ParameterValues</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>
+1037       <span class="s">}</span>
+1038       <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^FunctionalClassesToUse$/i</span><span class="s">)</span> <span class="s">{</span>
+1039         <span class="i">@ParameterValues</span> = <span class="k">split</span><span class="s">(</span><span class="q">&#39; &#39;</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="s">)</span><span class="sc">;</span>
+1040         <span class="k">for</span> <span class="i">$ParameterValue</span> <span class="s">(</span><span class="i">@ParameterValues</span><span class="s">)</span> <span class="s">{</span>
+1041           <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1042             <span class="k">die</span> <span class="q">&quot;Error: The functional class specified, $ParameterValue, for  FunctionalClassesToUse in option \&quot;--MolecularComplexity\&quot; is not valid.\n&quot;</span><span class="sc">;</span>
+1043           <span class="s">}</span>
+1044         <span class="s">}</span>
+1045         <span class="i">$ParameterValue</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ParameterValues</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>
+1046       <span class="s">}</span>
+1047       <span class="k">else</span> <span class="s">{</span>
+1048         <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/ /</span><span class="s">)</span> <span class="s">{</span>
+1049           <span class="i">$ParameterValue</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+1050         <span class="s">}</span>
+1051         <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+1052           <span class="i">$ParameterValue</span> = <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+1053         <span class="s">}</span>
+1054       <span class="s">}</span>
+1055
+1056       <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^MolecularComplexityType$/i</span><span class="s">)</span> <span class="s">{</span>
+1057         <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|MACCSKeys|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
+1058           <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \&quot;--MolecularComplexity\&quot; is not valid. Allowed values: AtomTypesFingerprints, ExtendedConnectivityFingerprints, MACCSKeys, PathLengthFingerprints, TopologicalAtomPairsFingerprints, TopologicalAtomTripletsFingerprints, TopologicalAtomTorsionsFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints..\n&quot;</span><span class="sc">;</span>
+1059         <span class="s">}</span>
+1060       <span class="s">}</span>
+1061       <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^AtomIdentifierType$/i</span><span class="s">)</span> <span class="s">{</span>
+1062         <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
+1063           <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \&quot;--MolecularComplexity\&quot; is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes.\n&quot;</span><span class="sc">;</span>
+1064         <span class="s">}</span>
+1065       <span class="s">}</span>
+1066       <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^(MACCSKeysSize|MinPathLength|MaxPathLength|MinDistance|MaxDistance|DistanceBinSize)$/i</span><span class="s">)</span> <span class="s">{</span>
+1067         <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1068           <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \&quot;--MolecularComplexity\&quot; is not valid. Allowed values: positive integer. \n&quot;</span><span class="sc">;</span>
+1069         <span class="s">}</span>
+1070       <span class="s">}</span>
+1071       <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^NeighborhoodRadius$/i</span><span class="s">)</span> <span class="s">{</span>
+1072         <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsInteger</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span> &amp;&amp; <span class="i">$ParameterValue</span> &gt;=<span class="n">0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1073           <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \&quot;--MolecularComplexity\&quot; is not valid. Allowed values: 0 or positive integer. \n&quot;</span><span class="sc">;</span>
+1074         <span class="s">}</span>
+1075       <span class="s">}</span>
+1076       <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^NormalizationMethodology$/i</span><span class="s">)</span> <span class="s">{</span>
+1077         <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(None|ByHeavyAtomsCount|ByPossibleKeysCount)$/i</span><span class="s">)</span> <span class="s">{</span>
+1078           <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \&quot;--MolecularComplexity\&quot; is not valid. Allowed values: None, ByHeavyAtomsCount, or ByPossibleKeysCount\n&quot;</span><span class="sc">;</span>
+1079         <span class="s">}</span>
+1080       <span class="s">}</span>
+1081       <span class="i">$ComplexityParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span>
+1082     <span class="s">}</span>
+1083
+1084     <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MACCSKeysSize</span>} !~ <span class="q">/^(166|322)$/i</span><span class="s">)</span> <span class="s">{</span>
+1085       <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified, $ComplexityParametersMap{MACCSKeysSize}, for parameter name, MACCSKeysSize in option \&quot;--MolecularComplexity\&quot; is not valid. Allowed values: 166 or 322\n&quot;</span><span class="sc">;</span>
+1086     <span class="s">}</span>
+1087     <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MinPathLength</span>} &gt; <span class="i">$ComplexityParametersMap</span>{<span class="w">MaxPathLength</span>}<span class="s">)</span> <span class="s">{</span>
+1088       <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified for MinPathLength, $ComplexityParametersMap{MinPathLength}, must be &lt;= MaxPathLength, $ComplexityParametersMap{MaxPathLength} ...\n&quot;</span><span class="sc">;</span>
+1089     <span class="s">}</span>
+1090     <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MinDistance</span>} &gt; <span class="i">$ComplexityParametersMap</span>{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
+1091       <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified for MinDistance, $ComplexityParametersMap{MinDistance}, must be &lt;= MaxDistance, $ComplexityParametersMap{MaxDistance} ...\n&quot;</span><span class="sc">;</span>
+1092     <span class="s">}</span>
+1093   <span class="s">}</span>
+1094
+1095   <span class="c"># Set default parameter values...</span>
+1096
+1097   <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MolecularComplexityType</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1098     <span class="i">$ComplexityParametersMap</span>{<span class="w">MolecularComplexityType</span>} = <span class="q">&#39;MACCSKeys&#39;</span><span class="sc">;</span>
+1099   <span class="s">}</span>
+1100   <span class="i">$MolecularComplexityType</span> = <span class="i">$ComplexityParametersMap</span>{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span>
+1101
+1102
+1103   <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1104     <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} = <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> ? <span class="q">&quot;FunctionalClassAtomTypes&quot;</span> <span class="co">:</span> <span class="q">&quot;AtomicInvariantsAtomTypes&quot;</span><span class="sc">;</span>
+1105   <span class="s">}</span>
+1106
+1107   <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1108     <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span>
+1109
+1110     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^(AtomTypesFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
+1111       <span class="i">$AtomicInvariantsToUse</span> = <span class="q">&quot;AS,X,BO,H,FC&quot;</span><span class="sc">;</span>
+1112     <span class="s">}</span>
+1113     <span class="k">elsif</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1114       <span class="i">$AtomicInvariantsToUse</span> = <span class="q">&quot;AS,X,BO,H,FC,MN&quot;</span><span class="sc">;</span>
+1115     <span class="s">}</span>
+1116     <span class="k">else</span> <span class="s">{</span>
+1117       <span class="i">$AtomicInvariantsToUse</span> = <span class="q">&quot;AS&quot;</span><span class="sc">;</span>
+1118     <span class="s">}</span>
+1119     <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>} = <span class="i">$AtomicInvariantsToUse</span><span class="sc">;</span>
+1120   <span class="s">}</span>
+1121
+1122   <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1123     <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span>
+1124
+1125     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1126       <span class="i">$FunctionalClassesToUse</span> = <span class="q">&quot;HBD,HBA,PI,NI,H&quot;</span><span class="sc">;</span>
+1127     <span class="s">}</span>
+1128     <span class="k">elsif</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1129       <span class="i">$FunctionalClassesToUse</span> = <span class="q">&quot;HBD,HBA,PI,NI,H,Ar&quot;</span><span class="sc">;</span>
+1130     <span class="s">}</span>
+1131     <span class="k">else</span> <span class="s">{</span>
+1132       <span class="i">$FunctionalClassesToUse</span> = <span class="q">&quot;HBD,HBA,PI,NI,H,Ar,Hal&quot;</span><span class="sc">;</span>
+1133     <span class="s">}</span>
+1134     <span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>} = <span class="i">$FunctionalClassesToUse</span><span class="sc">;</span>
+1135   <span class="s">}</span>
+1136
+1137   <span class="k">my</span><span class="s">(</span><span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span>
+1138   <span class="i">@AtomicInvariantsToUse</span> = <span class="k">split</span> <span class="q">&#39;,&#39;</span><span class="cm">,</span> <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>}<span class="sc">;</span>
+1139   <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>} = \<span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span>
+1140
+1141   <span class="k">my</span><span class="s">(</span><span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span>
+1142   <span class="i">@FunctionalClassesToUse</span> = <span class="k">split</span> <span class="q">&#39;,&#39;</span><span class="cm">,</span> <span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>}<span class="sc">;</span>
+1143   <span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>} = \<span class="i">@FunctionalClassesToUse</span><span class="sc">;</span>
+1144
+1145   <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">UseTriangleInequality</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1146     <span class="i">$ComplexityParametersMap</span>{<span class="w">UseTriangleInequality</span>} = <span class="n">0</span><span class="sc">;</span>
+1147     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1148       <span class="i">$ComplexityParametersMap</span>{<span class="w">UseTriangleInequality</span>} = <span class="n">1</span><span class="sc">;</span>
+1149     <span class="s">}</span>
+1150   <span class="s">}</span>
+1151
+1152   <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
+1153     <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+1154       <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified for AtomIdentifierType, $ComplexityParametersMap{AtomIdentifierType}, in option \&quot;--MolecularComplexity\&quot; is not valid for MolecularComplexityType, $MolecularComplexityType: Allowed value: FunctionalClassAtomTypes...\n&quot;</span><span class="sc">;</span>
+1155     <span class="s">}</span>
+1156   <span class="s">}</span>
+1157
+1158   <span class="c"># Set up approprate paremeter names for specified molecular complexity...</span>
+1159
+1160   <span class="i">@ParameterNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+1161   <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="q">&#39;MolecularComplexityType&#39;</span><span class="sc">;</span>
+1162
+1163   <span class="i">@AtomIdentifierTypeParameters</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+1164   <span class="k">push</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="q">&#39;AtomIdentifierType&#39;</span><span class="sc">;</span>
+1165   <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+1166     <span class="k">push</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="q">&#39;AtomicInvariantsToUse&#39;</span><span class="sc">;</span>
+1167   <span class="s">}</span>
+1168   <span class="k">elsif</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+1169     <span class="k">push</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="q">&#39;FunctionalClassesToUse&#39;</span><span class="sc">;</span>
+1170   <span class="s">}</span>
+1171
+1172   <span class="j">COMPLEXITYTYPE:</span> <span class="s">{</span>
+1173     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^AtomTypesFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1174       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
+1175       <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
+1176     <span class="s">}</span>
+1177     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1178       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
+1179       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">&#39;NeighborhoodRadius&#39;</span><span class="cm">,</span> <span class="q">&#39;NormalizationMethodology&#39;</span><span class="s">)</span><span class="sc">;</span>
+1180       <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
+1181     <span class="s">}</span>
+1182     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span>
+1183       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="q">&#39;MACCSKeysSize&#39;</span><span class="sc">;</span>
+1184       <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
+1185     <span class="s">}</span>
+1186     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1187       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
+1188       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">&#39;MinPathLength&#39;</span><span class="cm">,</span> <span class="q">&#39;MaxPathLength&#39;</span><span class="cm">,</span> <span class="q">&#39;UseBondSymbols&#39;</span><span class="s">)</span><span class="sc">;</span>
+1189       <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
+1190     <span class="s">}</span>
+1191     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1192       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
+1193       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">&#39;MinDistance&#39;</span><span class="cm">,</span> <span class="q">&#39;MaxDistance&#39;</span><span class="s">)</span><span class="sc">;</span>
+1194       <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
+1195     <span class="s">}</span>
+1196     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1197       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
+1198       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">&#39;MinDistance&#39;</span><span class="cm">,</span> <span class="q">&#39;MaxDistance&#39;</span><span class="cm">,</span> <span class="q">&#39;UseTriangleInequality&#39;</span><span class="s">)</span><span class="sc">;</span>
+1199       <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
+1200     <span class="s">}</span>
+1201     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalAtomTorsionsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1202       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
+1203       <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
+1204     <span class="s">}</span>
+1205     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1206       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">&#39;AtomIdentifierType&#39;</span><span class="cm">,</span> <span class="q">&#39;FunctionalClassesToUse&#39;</span><span class="cm">,</span> <span class="q">&#39;MinDistance&#39;</span><span class="cm">,</span> <span class="q">&#39;MaxDistance&#39;</span><span class="cm">,</span> <span class="q">&#39;NormalizationMethodology&#39;</span><span class="s">)</span><span class="sc">;</span>
+1207       <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
+1208     <span class="s">}</span>
+1209     <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
+1210       <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">&#39;AtomIdentifierType&#39;</span><span class="cm">,</span> <span class="q">&#39;FunctionalClassesToUse&#39;</span><span class="cm">,</span> <span class="q">&#39;MinDistance&#39;</span><span class="cm">,</span> <span class="q">&#39;MaxDistance&#39;</span><span class="cm">,</span> <span class="q">&#39;UseTriangleInequality&#39;</span><span class="cm">,</span> <span class="q">&#39;NormalizationMethodology&#39;</span><span class="cm">,</span> <span class="q">&#39;DistanceBinSize&#39;</span><span class="s">)</span><span class="sc">;</span>
+1211       <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
+1212     <span class="s">}</span>
+1213     <span class="k">die</span> <span class="q">&quot;Error: The parameter value specified, $ParameterValue, for parameter name MolecularComplexityType using \&quot;--MolecularComplexity\&quot; is not valid.\n&quot;</span><span class="sc">;</span>
+1214   <span class="s">}</span>
+1215
+1216   <span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexity</span>} = <span class="i">$Options</span>{<span class="w">molecularcomplexity</span>}<span class="sc">;</span>
+1217
+1218   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+1219   <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="i">@ParameterNames</span><span class="s">)</span> <span class="s">{</span>
+1220     <span class="i">$ParameterValue</span> = <span class="i">$ComplexityParametersMap</span>{<span class="i">$ParameterName</span>}<span class="sc">;</span>
+1221     <span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span>
+1222   <span class="s">}</span>
+1223 <span class="s">}</span>
+1224
+1225 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a>1226 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+1227
+1228   <span class="c"># Retrieve all the options...</span>
+1229   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+1230
+1231   <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">&#39;MayaChemToolsAromaticityModel&#39;</span><span class="sc">;</span>
+1232
+1233   <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">&#39;LabelPrefix&#39;</span><span class="sc">;</span>
+1234   <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+1235   <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
+1236
+1237   <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+1238
+1239   <span class="i">$Options</span>{<span class="w">hydrogenbonds</span>} = <span class="q">&#39;HBondsType2&#39;</span><span class="sc">;</span>
+1240
+1241   <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+1242
+1243   <span class="c"># Default mode values are set later...</span>
+1244   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+1245
+1246   <span class="c"># Default moelcular complexity values are set later...</span>
+1247   <span class="i">$Options</span>{<span class="w">molecularcomplexity</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+1248
+1249   <span class="c"># Default precision values are set later...</span>
+1250   <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+1251
+1252   <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">&#39;text&#39;</span><span class="sc">;</span>
+1253   <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&#39;comma&#39;</span><span class="sc">;</span>
+1254   <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+1255
+1256   <span class="c"># Default rotatable bond parameter values are set later...</span>
+1257   <span class="i">$Options</span>{<span class="w">rotatablebonds</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+1258
+1259   <span class="i">$Options</span>{<span class="w">ruleof3violations</span>} = <span class="q">&#39;No&#39;</span><span class="sc">;</span>
+1260   <span class="i">$Options</span>{<span class="w">ruleof5violations</span>} = <span class="q">&#39;No&#39;</span><span class="sc">;</span>
+1261
+1262   <span class="c"># Default TPSA paramater values are set later...</span>
+1263   <span class="i">$Options</span>{<span class="w">tpsa</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+1264
+1265   <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;filter|f=s&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;hydrogenbonds=s&quot;</span><span class="cm">,</span> <span class="q">&quot;keeplargestcomponent|k=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;molecularcomplexity=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;precision=s&quot;</span><span class="cm">,</span> <span class="q">&quot;rotatablebonds=s&quot;</span><span class="cm">,</span> <span class="q">&quot;ruleof3violations=s&quot;</span><span class="cm">,</span> <span class="q">&quot;ruleof5violations=s&quot;</span><span class="cm">,</span> <span class="q">&quot;quote|q=s&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;tpsa=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>
+1266     <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 $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+1267   <span class="s">}</span>
+1268   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+1269     <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>
+1270       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+1271     <span class="s">}</span>
+1272     <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
+1273   <span class="s">}</span>
+1274   <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1275     <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>
+1276     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{aromaticitymodel}, for option \&quot;--AromaticityModel\&quot; is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n&quot;</span><span class="sc">;</span>
+1277   <span class="s">}</span>
+1278   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
+1279     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{compoundidmode}, for option \&quot;--CompoundIDMode\&quot; is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n&quot;</span><span class="sc">;</span>
+1280   <span class="s">}</span>
+1281   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span>
+1282     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{datafieldsmode}, for option \&quot;-d, --DataFieldsMode\&quot; is not valid. Allowed values: All, Common, Specify or CompoundID\n&quot;</span><span class="sc">;</span>
+1283   <span class="s">}</span>
+1284   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+1285     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{filter}, for option \&quot;-f, --Filter\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+1286   <span class="s">}</span>
+1287   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">hydrogenbonds</span>} !~ <span class="q">/^(HBondsType1|HydrogenBondsType1|HBondsType2|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span>
+1288     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{hydrogenbonds}, for option \&quot;--HydrogenBonds\&quot; is not valid. Allowed values: HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2\n&quot;</span><span class="sc">;</span>
+1289   <span class="s">}</span>
+1290   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+1291     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{keeplargestcomponent}, for option \&quot;-k, --KeepLargestComponent\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+1292   <span class="s">}</span>
+1293   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|text|both)$/i</span><span class="s">)</span> <span class="s">{</span>
+1294     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{output}, for option \&quot;--output\&quot; is not valid. Allowed values: SD, text, or both\n&quot;</span><span class="sc">;</span>
+1295   <span class="s">}</span>
+1296   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
+1297     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--outdelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
+1298   <span class="s">}</span>
+1299   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+1300     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+1301   <span class="s">}</span>
+1302   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+1303     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{ruleof3violations}, for option \&quot;--RuleOf3Violations\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+1304   <span class="s">}</span>
+1305   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+1306     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{ruleof5violations}, for option \&quot;--RuleOf5Violations\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+1307   <span class="s">}</span>
+1308 <span class="s">}</span>
+1309
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>

Mercurial > repos > deepakjadmin > mayatool3_test3

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