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   1 #!/usr/bin/perl -w
   2 <span class="c">#</span>
   3 <span class="c"># $RCSfile: InfoSDFiles.pl,v $</span>
   4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
   5 <span class="c"># $Revision: 1.35 $</span>
   6 <span class="c">#</span>
   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
   8 <span class="c">#</span>
   9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
  10 <span class="c">#</span>
  11 <span class="c"># This file is part of MayaChemTools.</span>
  12 <span class="c">#</span>
  13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
  14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
  15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
  16 <span class="c"># later version.</span>
  17 <span class="c">#</span>
  18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
  19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
  20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
  21 <span class="c"># details.</span>
  22 <span class="c">#</span>
  23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
  24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
  25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
  26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
  27 <span class="c">#</span>
  28 
  29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
  30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$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">Benchmark</span><span class="sc">;</span>
  34 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span>
  35 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
  36 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
  37 
  38 <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>
  39 
  40 <span class="c"># Autoflush STDOUT</span>
  41 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
  42 
  43 <span class="c"># Starting message...</span>
  44 <span class="i">$ScriptName</span> = <span class="w">basename</span> <span class="i">$0</span><span class="sc">;</span>
  45 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Starting...\n\n&quot;</span><span class="sc">;</span>
  46 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
  47 
  48 <span class="c"># Get the options and setup script...</span>
  49 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
  50 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
  51   <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>
  52 <span class="s">}</span>
  53 
  54 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
  55 <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>
  56 
  57 <span class="c"># Process options...</span>
  58 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
  59 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
  60 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
  61 
  62 <span class="c"># Setup information about input files...</span>
  63 <span class="k">print</span> <span class="q">&quot;Checking input SD file(s)...\n&quot;</span><span class="sc">;</span>
  64 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="cm">,</span> <span class="i">%SDCmpdsInfo</span><span class="s">)</span><span class="sc">;</span>
  65 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
  66 <span class="i">InitializeSDCmpdsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
  67 
  68 <span class="c"># Process input files..</span>
  69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
  70 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
  71   <span class="k">print</span> <span class="q">&quot;\nProcessing SD files...\n&quot;</span><span class="sc">;</span>
  72 <span class="s">}</span>
  73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
  74   <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
  75     <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
  76     <span class="i">ListSDFileInfo</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
  77   <span class="s">}</span>
  78 <span class="s">}</span>
  79 <span class="i">ListTotalSizeOfFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
  80 
  81 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
  82 
  83 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
  84 <span class="i">$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>
  85 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
  86 
  87 <span class="c">###############################################################################</span>
  88 
  89 <span class="c"># List appropriate information...</span>
<a name="ListSDFileInfo-"></a>  90 <span class="k">sub </span><span class="m">ListSDFileInfo</span> <span class="s">{</span>
  91   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
  92   <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
  93 
  94   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
  95 
  96   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ProcessCmpdInfo</span>}<span class="s">)</span> <span class="s">{</span>
  97     <span class="i">ListCompoundDetailsInfo</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
  98   <span class="s">}</span>
  99   <span class="k">else</span> <span class="s">{</span>
 100     <span class="i">ListCompoundCountInfo</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
 101   <span class="s">}</span>
 102 
 103   <span class="c"># File size and modification information...</span>
 104   <span class="k">print</span> <span class="q">&quot;\nFile size: &quot;</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="s">)</span><span class="cm">,</span> <span class="q">&quot; \n&quot;</span><span class="sc">;</span>
 105   <span class="k">print</span> <span class="q">&quot;Last modified: &quot;</span><span class="cm">,</span> <span class="i">$SDFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>]<span class="cm">,</span> <span class="q">&quot; \n&quot;</span><span class="sc">;</span>
 106 <span class="s">}</span>
 107 
 108 <span class="c"># List number of compounds in SD file...</span>
<a name="ListCompoundCountInfo-"></a> 109 <span class="k">sub </span><span class="m">ListCompoundCountInfo</span> <span class="s">{</span>
 110   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
 111   <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
 112 
 113   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
 114 
 115   <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
 116 
 117   <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;Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
 118   <span class="k">while</span> <span class="s">(</span><span class="q">&lt;SDFILE&gt;</span><span class="s">)</span> <span class="s">{</span>
 119     <span class="k">if</span> <span class="s">(</span><span class="q">/^\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span>
 120       <span class="i">$CmpdCount</span>++<span class="sc">;</span>
 121     <span class="s">}</span>
 122   <span class="s">}</span>
 123   <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
 124 
 125   <span class="i">$SDCmpdsInfo</span>{<span class="w">TotalCmpdCount</span>} += <span class="i">$CmpdCount</span><span class="sc">;</span>
 126 
 127   <span class="k">print</span> <span class="q">&quot;\nNumber of compounds: $CmpdCount\n&quot;</span><span class="sc">;</span>
 128 <span class="s">}</span>
 129 
 130 <span class="c"># List detailed compound information...</span>
<a name="ListCompoundDetailsInfo-"></a> 131 <span class="k">sub </span><span class="m">ListCompoundDetailsInfo</span> <span class="s">{</span>
 132   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
 133   <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$EmptyCtabBlocksCount</span><span class="cm">,</span> <span class="i">$MismatchCtabBlockCount</span><span class="cm">,</span> <span class="i">$ChiralCtabBlockCount</span><span class="cm">,</span> <span class="i">$UnknownAtomsCtabBlockCount</span><span class="cm">,</span> <span class="i">$InvalidAtomNumbersCtabBlockCount</span><span class="cm">,</span> <span class="i">$SaltsCtabBlockCount</span><span class="cm">,</span> <span class="i">$CtabLinesCount</span><span class="cm">,</span> <span class="i">$PrintCmpdCounterHeader</span><span class="cm">,</span> <span class="i">$ProblematicCmpdData</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
 134 
 135   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
 136 
 137   <span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$EmptyCtabBlocksCount</span><span class="cm">,</span> <span class="i">$MismatchCtabBlockCount</span><span class="cm">,</span> <span class="i">$ChiralCtabBlockCount</span><span class="cm">,</span> <span class="i">$UnknownAtomsCtabBlockCount</span><span class="cm">,</span> <span class="i">$InvalidAtomNumbersCtabBlockCount</span><span class="cm">,</span> <span class="i">$SaltsCtabBlockCount</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="s">)</span> x <span class="n">7</span><span class="sc">;</span>
 138 
 139   <span class="i">InitializeSDCmpdsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 140 
 141   <span class="i">$PrintCmpdCounterHeader</span> = <span class="n">1</span><span class="sc">;</span>
 142 
 143   <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
 144   <span class="k">while</span> <span class="s">(</span><span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
 145     <span class="i">$CmpdCount</span>++<span class="sc">;</span>
 146     <span class="i">$ProblematicCmpdData</span> = <span class="n">0</span><span class="sc">;</span>
 147     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} &lt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
 148       <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$CmpdCount</span> % <span class="n">5000</span><span class="s">)</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
 149         <span class="k">if</span> <span class="s">(</span><span class="i">$PrintCmpdCounterHeader</span><span class="s">)</span> <span class="s">{</span>
 150           <span class="i">$PrintCmpdCounterHeader</span> = <span class="n">0</span><span class="sc">;</span>
 151           <span class="k">print</span> <span class="q">&quot;Processing compounds:&quot;</span><span class="sc">;</span>
 152         <span class="s">}</span>
 153         <span class="k">print</span> <span class="q">&quot;$CmpdCount...&quot;</span><span class="sc">;</span>
 154       <span class="s">}</span>
 155     <span class="s">}</span>
 156     <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
 157     <span class="i">$CtabLinesCount</span> = <span class="i">GetCtabLinesCount</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
 158     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Empty</span>}<span class="s">)</span> <span class="s">{</span>
 159       <span class="k">if</span> <span class="s">(</span><span class="i">$CtabLinesCount</span> &lt;= <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
 160         <span class="i">$EmptyCtabBlocksCount</span>++<span class="sc">;</span>
 161         <span class="i">$ProblematicCmpdData</span> = <span class="n">1</span><span class="sc">;</span>
 162       <span class="s">}</span>
 163     <span class="s">}</span>
 164     <span class="k">if</span> <span class="s">(</span><span class="i">$CtabLinesCount</span> &gt; <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
 165       <span class="k">my</span> <span class="s">(</span><span class="i">$AtomCount</span><span class="cm">,</span> <span class="i">$BondCount</span><span class="cm">,</span> <span class="i">$ChiralFlag</span><span class="s">)</span> = <span class="i">ParseCmpdCountsLine</span><span class="s">(</span><span class="i">$CmpdLines</span>[<span class="n">3</span>]<span class="s">)</span><span class="sc">;</span>
 166       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Mismatch</span>}<span class="s">)</span> <span class="s">{</span>
 167         <span class="k">if</span> <span class="s">(</span><span class="i">$CtabLinesCount</span> != <span class="s">(</span><span class="i">$AtomCount</span> + <span class="i">$BondCount</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
 168           <span class="i">$MismatchCtabBlockCount</span>++<span class="sc">;</span>
 169           <span class="i">$ProblematicCmpdData</span> = <span class="n">1</span><span class="sc">;</span>
 170           <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
 171             <span class="k">print</span> <span class="q">&quot;\nMismatch found: Ctab lines count: $CtabLinesCount;  Atoms count: $AtomCount; Bond count: $BondCount\n&quot;</span><span class="sc">;</span>
 172           <span class="s">}</span>
 173         <span class="s">}</span>
 174       <span class="s">}</span>
 175       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Chiral</span>}<span class="s">)</span> <span class="s">{</span>
 176         <span class="k">if</span> <span class="s">(</span><span class="i">$ChiralFlag</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
 177           <span class="i">$ChiralCtabBlockCount</span>++<span class="sc">;</span>
 178         <span class="s">}</span>
 179       <span class="s">}</span>
 180       <span class="k">if</span> <span class="s">(</span><span class="i">$CtabLinesCount</span> == <span class="s">(</span><span class="i">$AtomCount</span> + <span class="i">$BondCount</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
 181         <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">UnknownAtoms</span>}<span class="s">)</span> <span class="s">{</span>
 182           <span class="k">my</span><span class="s">(</span><span class="i">$UnknownAtomCount</span><span class="cm">,</span> <span class="i">$UnknownAtoms</span><span class="cm">,</span> <span class="i">$UnknownAtomLines</span><span class="s">)</span> = <span class="i">GetUnknownAtoms</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
 183           <span class="k">if</span> <span class="s">(</span><span class="i">$UnknownAtomCount</span><span class="s">)</span> <span class="s">{</span>
 184             <span class="i">$UnknownAtomsCtabBlockCount</span>++<span class="sc">;</span>
 185             <span class="i">$ProblematicCmpdData</span> = <span class="n">1</span><span class="sc">;</span>
 186             <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
 187               <span class="k">print</span> <span class="q">&quot;\nUnknown atom(s) found: $UnknownAtomCount\nUnknown atom(s) symbols:$UnknownAtoms\nUnknown atom(s) data lines:\n$UnknownAtomLines\n&quot;</span><span class="sc">;</span>
 188             <span class="s">}</span>
 189           <span class="s">}</span>
 190         <span class="s">}</span>
 191         <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">InvalidAtomNumbers</span>}<span class="s">)</span> <span class="s">{</span>
 192           <span class="k">my</span><span class="s">(</span><span class="i">$InvalidAtomNumbersCount</span><span class="cm">,</span> <span class="i">$InvalidAtomNumbers</span><span class="cm">,</span> <span class="i">$InvalidAtomNumberLines</span><span class="s">)</span> = <span class="i">GetInvalidAtomNumbers</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
 193           <span class="k">if</span> <span class="s">(</span><span class="i">$InvalidAtomNumbersCount</span><span class="s">)</span> <span class="s">{</span>
 194             <span class="i">$InvalidAtomNumbersCtabBlockCount</span>++<span class="sc">;</span>
 195             <span class="i">$ProblematicCmpdData</span> = <span class="n">1</span><span class="sc">;</span>
 196             <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
 197               <span class="k">print</span> <span class="q">&quot;\nInvalid atom number(s) found: $InvalidAtomNumbersCount\nInvalid atom number(s):$InvalidAtomNumbers\nInvalid atom number(s) data lines:\n$InvalidAtomNumberLines\n&quot;</span><span class="sc">;</span>
 198             <span class="s">}</span>
 199           <span class="s">}</span>
 200         <span class="s">}</span>
 201         <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Salts</span>}<span class="s">)</span> <span class="s">{</span>
 202           <span class="k">my</span><span class="s">(</span><span class="i">$FragmentsCount</span><span class="cm">,</span> <span class="i">$Fragments</span><span class="s">)</span> = <span class="i">GetCmpdFragments</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
 203           <span class="k">if</span> <span class="s">(</span><span class="i">$FragmentsCount</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
 204             <span class="i">$SaltsCtabBlockCount</span>++<span class="sc">;</span>
 205             <span class="i">$ProblematicCmpdData</span> = <span class="n">1</span><span class="sc">;</span>
 206             <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
 207               <span class="k">print</span> <span class="q">&quot;\nSalts found: $FragmentsCount\nSalts atom numbers:\n$Fragments\n&quot;</span><span class="sc">;</span>
 208             <span class="s">}</span>
 209           <span class="s">}</span>
 210         <span class="s">}</span>
 211       <span class="s">}</span>
 212     <span class="s">}</span>
 213     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ProcessCmpdData</span>}<span class="s">)</span> <span class="s">{</span>
 214       <span class="i">ProcessCmpdInfo</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
 215     <span class="s">}</span>
 216     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} &gt;= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
 217       <span class="k">if</span> <span class="s">(</span><span class="i">$ProblematicCmpdData</span><span class="s">)</span> <span class="s">{</span>
 218         <span class="k">print</span> <span class="q">&quot;\nCompound data:\n$CmpdString\n\n&quot;</span><span class="sc">;</span>
 219       <span class="s">}</span>
 220     <span class="s">}</span>
 221   <span class="s">}</span>
 222   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} &lt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
 223     <span class="k">if</span> <span class="s">(</span>!<span class="i">$PrintCmpdCounterHeader</span><span class="s">)</span> <span class="s">{</span>
 224       <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
 225     <span class="s">}</span>
 226   <span class="s">}</span>
 227   <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
 228 
 229   <span class="i">$SDCmpdsInfo</span>{<span class="w">TotalCmpdCount</span>} += <span class="i">$CmpdCount</span><span class="sc">;</span>
 230 
 231   <span class="k">print</span> <span class="q">&quot;\nNumber of compounds: $CmpdCount\n&quot;</span><span class="sc">;</span>
 232 
 233   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Empty</span>}<span class="s">)</span> <span class="s">{</span>
 234     <span class="k">print</span> <span class="q">&quot;Number of empty atom/bond blocks: $EmptyCtabBlocksCount\n&quot;</span><span class="sc">;</span>
 235   <span class="s">}</span>
 236   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Mismatch</span>}<span class="s">)</span> <span class="s">{</span>
 237     <span class="k">print</span> <span class="q">&quot;Number of mismatched atom/bond blocks: $MismatchCtabBlockCount\n&quot;</span><span class="sc">;</span>
 238   <span class="s">}</span>
 239   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">UnknownAtoms</span>}<span class="s">)</span> <span class="s">{</span>
 240     <span class="k">print</span> <span class="q">&quot;Number of atom blocks with unknown atom labels: $UnknownAtomsCtabBlockCount\n&quot;</span><span class="sc">;</span>
 241   <span class="s">}</span>
 242   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">InvalidAtomNumbers</span>}<span class="s">)</span> <span class="s">{</span>
 243     <span class="k">print</span> <span class="q">&quot;Number of bond blocks and atom property blocks with invalid atom numbers: $InvalidAtomNumbersCtabBlockCount\n&quot;</span><span class="sc">;</span>
 244   <span class="s">}</span>
 245   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Salts</span>}<span class="s">)</span> <span class="s">{</span>
 246     <span class="k">print</span> <span class="q">&quot;Number of atom blocks containing salts: $SaltsCtabBlockCount\n&quot;</span><span class="sc">;</span>
 247   <span class="s">}</span>
 248   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Chiral</span>}<span class="s">)</span> <span class="s">{</span>
 249     <span class="k">print</span> <span class="q">&quot;Number of chiral atom/bond blocks: $ChiralCtabBlockCount\n&quot;</span><span class="sc">;</span>
 250   <span class="s">}</span>
 251   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ProcessCmpdData</span>}<span class="s">)</span> <span class="s">{</span>
 252     <span class="i">PrintCmpdInfoSummary</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 253   <span class="s">}</span>
 254 
 255 <span class="s">}</span>
 256 
 257 <span class="c"># Initialize compound data information for a SD file...</span>
<a name="InitializeSDCmpdsInfo-"></a> 258 <span class="k">sub </span><span class="m">InitializeSDCmpdsInfo</span> <span class="s">{</span>
 259 
 260   <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$SDCmpdsInfo</span>{<span class="w">TotalCmpdCount</span>}<span class="s">)</span> <span class="s">{</span>
 261     <span class="i">$SDCmpdsInfo</span>{<span class="w">TotalCmpdCount</span>} = <span class="n">0</span><span class="sc">;</span>
 262   <span class="s">}</span>
 263 
 264   <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 265   <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 266   <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 267   <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 268   <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 269   <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 270 <span class="s">}</span>
 271 
 272 <span class="c"># Process compound data header labels and figure out which ones are present for</span>
 273 <span class="c"># all the compounds...</span>
<a name="ProcessCmpdInfo-"></a> 274 <span class="k">sub </span><span class="m">ProcessCmpdInfo</span> <span class="s">{</span>
 275   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdLinesRef</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
 276   <span class="k">my</span><span class="s">(</span><span class="i">$Label</span><span class="s">)</span><span class="sc">;</span>
 277 
 278   <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
 279     <span class="k">my</span> <span class="s">(</span><span class="i">@CmpdFieldLabels</span><span class="s">)</span> = <span class="i">GetCmpdDataHeaderLabels</span><span class="s">(</span><span class="i">$CmpdLinesRef</span><span class="s">)</span><span class="sc">;</span>
 280     <span class="k">my</span><span class="s">(</span><span class="i">%CmpdFieldLabelsMap</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 281     <span class="c"># Setup a map for the current labels...</span>
 282     <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="i">@CmpdFieldLabels</span><span class="s">)</span> <span class="s">{</span>
 283       <span class="i">$CmpdFieldLabelsMap</span>{<span class="i">$Label</span>} = <span class="q">&quot;PresentInSome&quot;</span><span class="sc">;</span>
 284     <span class="s">}</span>
 285     <span class="c"># Check the presence old labels for this compound; otherwise, mark &#39;em new...</span>
 286     <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
 287       <span class="k">if</span> <span class="s">(</span>!<span class="i">$CmpdFieldLabelsMap</span>{<span class="i">$Label</span>}<span class="s">)</span> <span class="s">{</span>
 288         <span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} = <span class="q">&quot;PresentInSome&quot;</span><span class="sc">;</span>
 289       <span class="s">}</span>
 290     <span class="s">}</span>
 291     <span class="c"># Check the presence this compound in the old labels; otherwise, add &#39;em...</span>
 292     <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="i">@CmpdFieldLabels</span> <span class="s">)</span> <span class="s">{</span>
 293       <span class="k">if</span> <span class="s">(</span>!<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>}<span class="s">)</span> <span class="s">{</span>
 294         <span class="c"># It&#39;s a new label...</span>
 295         <span class="k">push</span> <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> <span class="i">$Label</span><span class="sc">;</span>
 296         <span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} = <span class="q">&quot;PresentInSome&quot;</span><span class="sc">;</span>
 297       <span class="s">}</span>
 298     <span class="s">}</span>
 299   <span class="s">}</span>
 300   <span class="k">else</span> <span class="s">{</span>
 301     <span class="c"># Get the initial label set and set up a map...</span>
 302     <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}} = <span class="i">GetCmpdDataHeaderLabels</span><span class="s">(</span><span class="i">$CmpdLinesRef</span><span class="s">)</span><span class="sc">;</span>
 303     <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
 304       <span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} = <span class="q">&quot;PresentInAll&quot;</span><span class="sc">;</span>
 305     <span class="s">}</span>
 306   <span class="s">}</span>
 307   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountEmptyData</span>} || <span class="i">$OptionsInfo</span>{<span class="w">CheckData</span>}<span class="s">)</span> <span class="s">{</span>
 308     <span class="c"># Count empty data field values...</span>
 309     <span class="k">my</span><span class="s">(</span><span class="i">%DataFieldAndValues</span><span class="cm">,</span> <span class="i">$Label</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
 310 
 311     <span class="i">%DataFieldAndValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span><span class="i">$CmpdLinesRef</span><span class="s">)</span><span class="sc">;</span>
 312     <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%DataFieldAndValues</span><span class="s">)</span> <span class="s">{</span>
 313       <span class="i">$Value</span> = <span class="i">$DataFieldAndValues</span>{<span class="i">$Label</span>}<span class="sc">;</span>
 314       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountEmptyData</span>}<span class="s">)</span> <span class="s">{</span>
 315         <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
 316           <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
 317             <span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>} += <span class="n">1</span><span class="sc">;</span>
 318           <span class="s">}</span>
 319           <span class="k">else</span> <span class="s">{</span>
 320             <span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>} = <span class="n">1</span><span class="sc">;</span>
 321           <span class="s">}</span>
 322         <span class="s">}</span>
 323         <span class="k">else</span> <span class="s">{</span>
 324           <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
 325             <span class="k">print</span> <span class="q">&quot;Compound record $CmpdCount: Empty data field &lt;$Label&gt;\n&quot;</span><span class="sc">;</span>
 326           <span class="s">}</span>
 327           <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
 328             <span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>} += <span class="n">1</span><span class="sc">;</span>
 329           <span class="s">}</span>
 330           <span class="k">else</span> <span class="s">{</span>
 331             <span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>} = <span class="n">1</span><span class="sc">;</span>
 332           <span class="s">}</span>
 333         <span class="s">}</span>
 334       <span class="s">}</span>
 335       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckData</span>}<span class="s">)</span> <span class="s">{</span>
 336         <span class="k">if</span> <span class="s">(</span><span class="i">IsNumerical</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
 337           <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
 338             <span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>} += <span class="n">1</span><span class="sc">;</span>
 339           <span class="s">}</span>
 340           <span class="k">else</span> <span class="s">{</span>
 341             <span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>} = <span class="n">1</span><span class="sc">;</span>
 342           <span class="s">}</span>
 343         <span class="s">}</span>
 344         <span class="k">else</span> <span class="s">{</span>
 345           <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
 346             <span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>} += <span class="n">1</span><span class="sc">;</span>
 347           <span class="s">}</span>
 348           <span class="k">else</span> <span class="s">{</span>
 349             <span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>} = <span class="n">1</span><span class="sc">;</span>
 350           <span class="s">}</span>
 351         <span class="s">}</span>
 352       <span class="s">}</span>
 353     <span class="s">}</span>
 354   <span class="s">}</span>
 355 <span class="s">}</span>
 356 
 357 <span class="c"># Print compound summary...</span>
<a name="PrintCmpdInfoSummary-"></a> 358 <span class="k">sub </span><span class="m">PrintCmpdInfoSummary</span> <span class="s">{</span>
 359   <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
 360     <span class="k">my</span><span class="s">(</span><span class="i">$PresentInAllCount</span><span class="cm">,</span> <span class="i">$Label</span><span class="cm">,</span> <span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> <span class="i">@FieldLabelsPresentInAll</span><span class="s">)</span><span class="sc">;</span>
 361 
 362     <span class="i">@FieldLabelsPresentInSome</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 363     <span class="i">@FieldLabelsPresentInAll</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 364 
 365     <span class="i">$PresentInAllCount</span> = <span class="n">0</span><span class="sc">;</span>
 366     <span class="k">print</span> <span class="q">&quot;\nNumber of data fields: &quot;</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
 367     <span class="k">print</span> <span class="q">&quot;All data field labels: &quot;</span><span class="sc">;</span>
 368     <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}}<span class="s">)</span> <span class="s">{</span>
 369       <span class="k">print</span> <span class="q">&quot;&lt;$Label&gt; &quot;</span><span class="sc">;</span>
 370     <span class="s">}</span>
 371     <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
 372     <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}}<span class="s">)</span> <span class="s">{</span>
 373       <span class="k">if</span> <span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} <span class="k">eq</span> <span class="q">&quot;PresentInAll&quot;</span><span class="s">)</span> <span class="s">{</span>
 374         <span class="i">$PresentInAllCount</span>++<span class="sc">;</span>
 375         <span class="k">push</span> <span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> <span class="i">$Label</span><span class="sc">;</span>
 376       <span class="s">}</span>
 377     <span class="s">}</span>
 378     <span class="k">if</span> <span class="s">(</span><span class="i">$PresentInAllCount</span> != <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
 379       <span class="k">print</span> <span class="q">&quot;Data field labels present in all compounds: &quot;</span><span class="sc">;</span>
 380       <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}}<span class="s">)</span> <span class="s">{</span>
 381         <span class="k">if</span> <span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} <span class="k">eq</span> <span class="q">&quot;PresentInAll&quot;</span><span class="s">)</span> <span class="s">{</span>
 382           <span class="k">print</span> <span class="q">&quot;&lt;$Label&gt; &quot;</span><span class="sc">;</span>
 383         <span class="s">}</span>
 384       <span class="s">}</span>
 385       <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
 386       <span class="k">print</span> <span class="q">&quot;Data field labels present in some compounds: &quot;</span><span class="sc">;</span>
 387       <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}}<span class="s">)</span> <span class="s">{</span>
 388         <span class="k">if</span> <span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} <span class="k">eq</span> <span class="q">&quot;PresentInSome&quot;</span><span class="s">)</span> <span class="s">{</span>
 389           <span class="k">print</span> <span class="q">&quot;&lt;$Label&gt; &quot;</span><span class="sc">;</span>
 390           <span class="k">push</span> <span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> <span class="i">$Label</span><span class="sc">;</span>
 391         <span class="s">}</span>
 392       <span class="s">}</span>
 393       <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
 394     <span class="s">}</span>
 395     <span class="c"># List empty data field values count...</span>
 396     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountEmptyData</span>}<span class="s">)</span> <span class="s">{</span>
 397       <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
 398       <span class="k">if</span> <span class="s">(</span><span class="i">$PresentInAllCount</span> == <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
 399         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of non-empty values for data field(s)&quot;</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 400         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of empty values for data field(s)&quot;</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 401       <span class="s">}</span>
 402       <span class="k">else</span> <span class="s">{</span>
 403         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of non-empty values for data field(s) present in all compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 404         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of empty values for data field(s) present in all compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 405         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of non-empty values for data field(s) present in some compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 406         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of empty values for data field(s) present in some compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 407       <span class="s">}</span>
 408       <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
 409     <span class="s">}</span>
 410     <span class="c"># List numerical data values count...</span>
 411     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckData</span>}<span class="s">)</span> <span class="s">{</span>
 412       <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
 413       <span class="k">if</span> <span class="s">(</span><span class="i">$PresentInAllCount</span> == <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
 414         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of non-numerical values for data field(s)&quot;</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 415         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of numerical values for data field(s)&quot;</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 416       <span class="s">}</span>
 417       <span class="k">else</span> <span class="s">{</span>
 418         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of non-numerical values for data field(s) present in all compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 419         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of numerical values for data field(s) present in all compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 420         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of non-numerical values for data field(s) present in some compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 421         <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of numerical values for data field(s) present in some compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
 422       <span class="s">}</span>
 423       <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
 424     <span class="s">}</span>
 425   <span class="s">}</span>
 426   <span class="k">else</span> <span class="s">{</span>
 427     <span class="k">print</span> <span class="q">&quot;\nNumber of data fields: 0\n&quot;</span><span class="sc">;</span>
 428   <span class="s">}</span>
 429 <span class="s">}</span>
 430 <span class="c"># List data information...</span>
<a name="PrintDataInformation-"></a> 431 <span class="k">sub </span><span class="m">PrintDataInformation</span> <span class="s">{</span>
 432   <span class="k">my</span><span class="s">(</span><span class="i">$InfoLabel</span><span class="cm">,</span> <span class="i">$DataLabelRef</span><span class="cm">,</span> <span class="i">$DataLabelToValueMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
 433   <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$Label</span><span class="s">)</span><span class="sc">;</span>
 434 
 435   <span class="i">$Line</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
 436   <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$DataLabelRef</span>}<span class="s">)</span> <span class="s">{</span>
 437     <span class="i">$Line</span> .= <span class="q">&quot; &lt;$Label&gt; - &quot;</span> . <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$DataLabelToValueMapRef</span>-&gt;{<span class="i">$Label</span>}<span class="s">)</span> ? <span class="i">$DataLabelToValueMapRef</span>-&gt;{<span class="i">$Label</span>} <span class="co">:</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;,&quot;</span><span class="sc">;</span>
 438   <span class="s">}</span>
 439   <span class="i">$Line</span> =~ <span class="q">s/\,$//g</span><span class="sc">;</span>
 440   <span class="k">print</span> <span class="q">&quot;$InfoLabel: $Line\n&quot;</span><span class="sc">;</span>
 441 <span class="s">}</span>
 442 
 443 <span class="c"># Total size of all the files...</span>
<a name="ListTotalSizeOfFiles-"></a> 444 <span class="k">sub </span><span class="m">ListTotalSizeOfFiles</span> <span class="s">{</span>
 445   <span class="k">my</span><span class="s">(</span><span class="i">$FileOkayCount</span><span class="cm">,</span> <span class="i">$TotalSize</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
 446 
 447   <span class="i">$FileOkayCount</span> = <span class="n">0</span><span class="sc">;</span>
 448   <span class="i">$TotalSize</span> = <span class="n">0</span><span class="sc">;</span>
 449 
 450   <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>
 451     <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span>
 452       <span class="i">$FileOkayCount</span>++<span class="sc">;</span>
 453       <span class="i">$TotalSize</span> += <span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
 454     <span class="s">}</span>
 455   <span class="s">}</span>
 456   <span class="k">if</span> <span class="s">(</span><span class="i">$FileOkayCount</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
 457     <span class="k">print</span> <span class="q">&quot;\nTotal number of compounds in  $FileOkayCount SD files: $SDCmpdsInfo{TotalCmpdCount}\n&quot;</span><span class="sc">;</span>
 458     <span class="k">print</span> <span class="q">&quot;\nTotal size of $FileOkayCount SD files: &quot;</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$TotalSize</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
 459   <span class="s">}</span>
 460 
 461 <span class="s">}</span>
 462 
 463 <span class="c"># Retrieve information about SD files...</span>
<a name="RetrieveSDFilesInfo-"></a> 464 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
 465   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$ModifiedTimeString</span><span class="cm">,</span> <span class="i">$ModifiedDateString</span><span class="s">)</span><span class="sc">;</span>
 466 
 467   <span class="i">%SDCmpdsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 468 
 469   <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 470   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 471   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 472   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileLastModified</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 473 
 474   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
 475     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
 476     <span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
 477     <span class="i">$SDFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
 478 
 479     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
 480     <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>
 481       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
 482       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
 483     <span class="s">}</span>
 484     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">&quot;sdf sd&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
 485       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
 486       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
 487     <span class="s">}</span>
 488     <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span><span class="s">)</span> <span class="s">{</span>
 489       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
 490       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
 491     <span class="s">}</span>
 492     <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
 493 
 494     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
 495     <span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>] = <span class="i">FileSize</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
 496     <span class="s">(</span><span class="i">$ModifiedTimeString</span><span class="cm">,</span> <span class="i">$ModifiedDateString</span><span class="s">)</span> = <span class="i">FormattedFileModificationTimeAndDate</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
 497     <span class="i">$SDFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">&quot;$ModifiedTimeString; $ModifiedDateString&quot;</span><span class="sc">;</span>
 498   <span class="s">}</span>
 499 <span class="s">}</span>
 500 
 501 <span class="c"># Process option values...</span>
<a name="ProcessOptions-"></a> 502 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
 503   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 504 
 505   <span class="i">$OptionsInfo</span>{<span class="w">All</span>} = <span class="i">$Options</span>{<span class="w">all</span>} ? <span class="i">$Options</span>{<span class="w">all</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 506   <span class="i">$OptionsInfo</span>{<span class="w">Chiral</span>} = <span class="i">$Options</span>{<span class="w">chiral</span>} ? <span class="i">$Options</span>{<span class="w">chiral</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 507   <span class="i">$OptionsInfo</span>{<span class="w">Count</span>} = <span class="i">$Options</span>{<span class="w">count</span>} ? <span class="i">$Options</span>{<span class="w">count</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 508   <span class="i">$OptionsInfo</span>{<span class="w">DataCheck</span>} = <span class="i">$Options</span>{<span class="w">datacheck</span>} ? <span class="i">$Options</span>{<span class="w">datacheck</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 509   <span class="i">$OptionsInfo</span>{<span class="w">Empty</span>} = <span class="i">$Options</span>{<span class="w">empty</span>} ? <span class="i">$Options</span>{<span class="w">empty</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 510   <span class="i">$OptionsInfo</span>{<span class="w">Fields</span>} = <span class="i">$Options</span>{<span class="w">fields</span>} ? <span class="i">$Options</span>{<span class="w">fields</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 511   <span class="i">$OptionsInfo</span>{<span class="w">InvalidAtomNumbers</span>} = <span class="i">$Options</span>{<span class="w">invalidatomnumbers</span>} ? <span class="i">$Options</span>{<span class="w">invalidatomnumbers</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 512   <span class="i">$OptionsInfo</span>{<span class="w">Mismatch</span>} = <span class="i">$Options</span>{<span class="w">mismatch</span>} ? <span class="i">$Options</span>{<span class="w">mismatch</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 513   <span class="i">$OptionsInfo</span>{<span class="w">Salts</span>} = <span class="i">$Options</span>{<span class="w">salts</span>} ? <span class="i">$Options</span>{<span class="w">salts</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 514   <span class="i">$OptionsInfo</span>{<span class="w">UnknownAtoms</span>} = <span class="i">$Options</span>{<span class="w">unknownatoms</span>} ? <span class="i">$Options</span>{<span class="w">unknownatoms</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 515 
 516   <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span>
 517 
 518   <span class="i">$OptionsInfo</span>{<span class="w">ProcessCmpdInfo</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} ||  <span class="i">$Options</span>{<span class="w">chiral</span>} || <span class="i">$Options</span>{<span class="w">empty</span>} || <span class="i">$Options</span>{<span class="w">fields</span>} || <span class="i">$Options</span>{<span class="w">invalidatomnumbers</span>}  || <span class="i">$Options</span>{<span class="w">mismatch</span>} || <span class="i">$Options</span>{<span class="w">salts</span>} || <span class="i">$Options</span>{<span class="w">unknownatoms</span>} || <span class="i">$Options</span>{<span class="w">datacheck</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 519 
 520   <span class="i">$OptionsInfo</span>{<span class="w">ProcessCmpdData</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">fields</span>} || <span class="i">$Options</span>{<span class="w">empty</span>} || <span class="i">$Options</span>{<span class="w">datacheck</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 521 
 522   <span class="i">$OptionsInfo</span>{<span class="w">CountEmptyData</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">empty</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 523   <span class="i">$OptionsInfo</span>{<span class="w">CheckData</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">datacheck</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
 524 <span class="s">}</span>
 525 
 526 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
<a name="SetupScriptUsage-"></a> 527 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
 528 
 529   <span class="c"># Setup default and retrieve all the options...</span>
 530   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
 531   <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
 532   <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;all|a&quot;</span><span class="cm">,</span> <span class="q">&quot;count|c&quot;</span><span class="cm">,</span> <span class="q">&quot;chiral&quot;</span><span class="cm">,</span> <span class="q">&quot;datacheck&quot;</span><span class="cm">,</span> <span class="q">&quot;detail|d:i&quot;</span><span class="cm">,</span> <span class="q">&quot;empty|e&quot;</span><span class="cm">,</span> <span class="q">&quot;fields|f&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;invalidatomnumbers|i&quot;</span><span class="cm">,</span> <span class="q">&quot;mismatch|m&quot;</span><span class="cm">,</span> <span class="q">&quot;salts|s&quot;</span><span class="cm">,</span> <span class="q">&quot;unknownatoms|u&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
 533     <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
 534   <span class="s">}</span>
 535   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
 536     <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>
 537       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
 538     <span class="s">}</span>
 539     <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
 540   <span class="s">}</span>
 541   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>} &lt;= <span class="n">0</span> || <span class="i">$Options</span>{<span class="w">detail</span>} &gt; <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
 542     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{detail}, for option \&quot;-d --detail\&quot; is not valid. Possible values: 1 to 3\n&quot;</span><span class="sc">;</span>
 543   <span class="s">}</span>
 544 <span class="s">}</span>
 545 
<a name="EOF-"></a></pre>
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