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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/scripts/html/code/InfoSDFiles.html	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,566 @@
+<html>
+<head>
+<title>MayaChemTools:Code:InfoSDFiles.pl</title>
+<meta http-equiv="content-type" content="text/html;charset=utf-8">
+<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
+</head>
+<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
+<br/>
+<center>
+<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
+</center>
+<br/>
+<pre>
+   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>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>