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+++ b/docs/scripts/html/code/SDToMolFiles.html	Wed Jan 20 09:23:18 2016 -0500
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+<html>
+<head>
+<title>MayaChemTools:Code:SDToMolFiles.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: SDToMolFiles.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">Text::ParseWords</span><span class="sc">;</span>
+  34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  35 <span class="k">use</span> <span class="w">SDFileUtil</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="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 
+  67 <span class="c"># Process input files..</span>
+  68 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  69 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+  70   <span class="k">print</span> <span class="q">&quot;\nProcessing SD files...\n&quot;</span><span class="sc">;</span>
+  71 <span class="s">}</span>
+  72 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+  73   <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+  74     <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+  75     <span class="i">GenerateMolFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  76   <span class="s">}</span>
+  77 <span class="s">}</span>
+  78 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+  79 
+  80 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  81 <span class="i">$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>
+  82 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+  83 
+  84 <span class="c">###############################################################################</span>
+  85 
+  86 <span class="c"># Generate MOL files for a SD file...</span>
+  87 <span class="c">#</span>
+<a name="GenerateMolFiles-"></a>  88 <span class="k">sub </span><span class="m">GenerateMolFiles</span> <span class="s">{</span>
+  89   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  90   <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$MOLFile</span><span class="cm">,</span> <span class="i">$MOLFileRoot</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OverwriteFiles</span><span class="cm">,</span> <span class="i">$UseDataField</span><span class="cm">,</span> <span class="i">$DataFieldName</span><span class="cm">,</span> <span class="i">$UseMolName</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$MolEndDelimiter</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldValues</span><span class="s">)</span><span class="sc">;</span>
+  91 
+  92   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+  93 
+  94   <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>
+  95     <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+  96     <span class="k">return</span><span class="sc">;</span>
+  97   <span class="s">}</span>
+  98 
+  99   <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+ 100   <span class="i">$MolEndDelimiter</span> = <span class="q">&quot;M  END&quot;</span><span class="sc">;</span>
+ 101 
+ 102   <span class="i">$OutFileRoot</span> = <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+ 103   <span class="i">$OverwriteFiles</span> = <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="sc">;</span>
+ 104 
+ 105   <span class="i">$UseDataField</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 106   <span class="i">$DataFieldName</span> = <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>}<span class="sc">;</span>
+ 107 
+ 108   <span class="i">$UseMolName</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^MolName$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 109 
+ 110   <span class="j">CMPDSTRING:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 111     <span class="i">$CmpdCount</span>++<span class="sc">;</span>
+ 112 
+ 113     <span class="c"># Setup MOL file name...</span>
+ 114     <span class="i">$MOLFileRoot</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 115     <span class="k">if</span> <span class="s">(</span><span class="i">$UseDataField</span><span class="s">)</span> <span class="s">{</span>
+ 116       <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+ 117       <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
+ 118       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$DataFieldName</span>}<span class="s">)</span> <span class="s">{</span>
+ 119         <span class="i">$MOLFileRoot</span> = <span class="i">$DataFieldValues</span>{<span class="i">$DataFieldName</span>}<span class="sc">;</span>
+ 120       <span class="s">}</span>
+ 121     <span class="s">}</span>
+ 122     <span class="k">elsif</span> <span class="s">(</span><span class="i">$UseMolName</span><span class="s">)</span> <span class="s">{</span>
+ 123       <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+ 124       <span class="i">$MOLFileRoot</span> = <span class="i">$CmpdLines</span>[<span class="n">0</span>]<span class="sc">;</span>
+ 125     <span class="s">}</span>
+ 126 
+ 127     <span class="c"># Check for any invalid file name characters in data field or molname values...</span>
+ 128     <span class="k">if</span> <span class="s">(</span><span class="i">$MOLFileRoot</span> &amp;&amp; <span class="i">$MOLFileRoot</span> =~ <span class="q">/[^a-zA-Z0-9_]/</span><span class="s">)</span> <span class="s">{</span>
+ 129       <span class="i">$MOLFileRoot</span> =~ <span class="q">s/[^a-zA-Z0-9_]//g</span><span class="sc">;</span>
+ 130     <span class="s">}</span>
+ 131     <span class="c"># Fall back plan for MOL file name...</span>
+ 132     <span class="k">if</span> <span class="s">(</span>!<span class="i">$MOLFileRoot</span><span class="s">)</span> <span class="s">{</span>
+ 133       <span class="i">$MOLFileRoot</span> = <span class="q">&quot;${OutFileRoot}Cmpd${CmpdCount}&quot;</span><span class="sc">;</span>
+ 134     <span class="s">}</span>
+ 135 
+ 136     <span class="i">$MOLFile</span> = <span class="q">&quot;${MOLFileRoot}.mol&quot;</span><span class="sc">;</span>
+ 137 
+ 138     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OverwriteFiles</span><span class="s">)</span> <span class="s">{</span>
+ 139       <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$MOLFile</span><span class="s">)</span> <span class="s">{</span>
+ 140         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring compound number, $CmpdCount, in $SDFile: New MOL file, $MOLFile, already exists\n&quot;</span><span class="sc">;</span>
+ 141         <span class="k">next</span> <span class="j">CMPDSTRING</span><span class="sc">;</span>
+ 142       <span class="s">}</span>
+ 143     <span class="s">}</span>
+ 144 
+ 145     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$CmpdString</span> =~ <span class="q">/$MolEndDelimiter/</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 146       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring compound number, $CmpdCount, in $SDFile: Invalid compound data\n&quot;</span><span class="sc">;</span>
+ 147       <span class="k">next</span> <span class="j">CMPDSTRING</span><span class="sc">;</span>
+ 148     <span class="s">}</span>
+ 149 
+ 150     <span class="c"># Write out MOL file...</span>
+ 151 
+ 152     <span class="k">print</span> <span class="q">&quot;Generating $MOLFile file...\n&quot;</span><span class="sc">;</span>
+ 153     <span class="k">open</span> <span class="w">MOLFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$MOLFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $MOLFile: $! \n&quot;</span><span class="sc">;</span>
+ 154     <span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span> = <span class="k">split</span> <span class="q">&quot;$MolEndDelimiter&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+ 155     <span class="k">print</span> <span class="i">MOLFILE</span> <span class="q">&quot;$CmpdString&quot;</span><span class="sc">;</span>
+ 156     <span class="k">print</span> <span class="i">MOLFILE</span> <span class="q">&quot;$MolEndDelimiter\n&quot;</span><span class="sc">;</span>
+ 157     <span class="k">close</span> <span class="w">MOLFILE</span><span class="sc">;</span>
+ 158 
+ 159   <span class="s">}</span>
+ 160 
+ 161   <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+ 162 <span class="s">}</span>
+ 163 
+ 164 <span class="c"># Retrieve information about SD files...</span>
+ 165 <span class="c">#</span>
+<a name="RetrieveSDFilesInfo-"></a> 166 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
+ 167   <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="s">)</span><span class="sc">;</span>
+ 168 
+ 169   <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 170   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 171   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 172 
+ 173   <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>
+ 174     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 175 
+ 176     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+ 177     <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 178 
+ 179     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 180     <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>
+ 181       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+ 182       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 183     <span class="s">}</span>
+ 184     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">&quot;sd sdf&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 185       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
+ 186       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 187     <span class="s">}</span>
+ 188 
+ 189     <span class="c"># Setup output file root...</span>
+ 190     <span class="i">$FileDir</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+ 191     <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
+ 192 
+ 193     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 194       <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
+ 195       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+ 196         <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+ 197       <span class="s">}</span>
+ 198       <span class="k">else</span> <span class="s">{</span>
+ 199         <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
+ 200       <span class="s">}</span>
+ 201       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+ 202     <span class="s">}</span>
+ 203     <span class="k">else</span> <span class="s">{</span>
+ 204       <span class="i">$OutFileRoot</span> = <span class="q">&quot;$FileName&quot;</span><span class="sc">;</span>
+ 205     <span class="s">}</span>
+ 206 
+ 207     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+ 208     <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
+ 209   <span class="s">}</span>
+ 210 <span class="s">}</span>
+ 211 
+ 212 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 213 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+ 214   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 215 
+ 216   <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+ 217 
+ 218   <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 219   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
+ 220     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafield</span>}<span class="s">)</span> <span class="s">{</span>
+ 221       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;-d, --DataField\&quot; option in \&quot;DataField\&quot; \&quot;-m, --mode\&quot;. \n&quot;</span><span class="sc">;</span>
+ 222     <span class="s">}</span>
+ 223     <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>} = <span class="i">$Options</span>{<span class="w">datafield</span>}<span class="sc">;</span>
+ 224   <span class="s">}</span>
+ 225 
+ 226   <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 227 
+ 228   <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 229 <span class="s">}</span>
+ 230 
+ 231 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 232 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+ 233 
+ 234   <span class="c"># Retrieve all the options...</span>
+ 235   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 236 
+ 237   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;RootPrefix&#39;</span><span class="sc">;</span>
+ 238 
+ 239   <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;datafield|d=s&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 240     <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 $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+ 241   <span class="s">}</span>
+ 242   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+ 243     <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>
+ 244       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+ 245     <span class="s">}</span>
+ 246     <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
+ 247   <span class="s">}</span>
+ 248 
+ 249   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(DataField|MolName|RootPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 250     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m, --mode\&quot; is not valid. Allowed values: DataField, MolName, RootPrefix\n&quot;</span><span class="sc">;</span>
+ 251   <span class="s">}</span>
+ 252 <span class="s">}</span>
+ 253 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>