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+<html>
+<head>
+<title>MayaChemTools:Code:SplitSDFiles.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>
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+<br/>
+<pre>
+   1 #!/usr/bin/perl -w
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: SplitSDFiles.pl,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:46:21 $</span>
+   5 <span class="c"># $Revision: 1.36 $</span>
+   6 <span class="c">#</span>
+   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+   8 <span class="c">#</span>
+   9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+  10 <span class="c">#</span>
+  11 <span class="c"># This file is part of MayaChemTools.</span>
+  12 <span class="c">#</span>
+  13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+  14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+  15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+  16 <span class="c"># later version.</span>
+  17 <span class="c">#</span>
+  18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+  19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+  20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+  21 <span class="c"># details.</span>
+  22 <span class="c">#</span>
+  23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+  24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+  25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+  26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+  27 <span class="c">#</span>
+  28 
+  29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+  30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$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">FileUtil</span><span class="sc">;</span>
+  36 
+  37 <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>
+  38 
+  39 <span class="c"># Autoflush STDOUT</span>
+  40 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+  41 
+  42 <span class="c"># Starting message...</span>
+  43 <span class="i">$ScriptName</span> = <span class="w">basename</span> <span class="i">$0</span><span class="sc">;</span>
+  44 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Starting...\n\n&quot;</span><span class="sc">;</span>
+  45 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  46 
+  47 <span class="c"># Get the options and setup script...</span>
+  48 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  49 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+  50   <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>
+  51 <span class="s">}</span>
+  52 
+  53 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
+  54 <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>
+  55 
+  56 <span class="c"># Process options...</span>
+  57 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+  58 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+  59 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  60 
+  61 <span class="c"># Setup information about input files...</span>
+  62 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</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="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  65 
+  66 <span class="c"># Process input files..</span>
+  67 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  68 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+  69   <span class="k">print</span> <span class="q">&quot;\nProcessing SD files...\n&quot;</span><span class="sc">;</span>
+  70 <span class="s">}</span>
+  71 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+  72   <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+  73     <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+  74     <span class="i">SplitSDFile</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  75   <span class="s">}</span>
+  76 <span class="s">}</span>
+  77 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+  78 
+  79 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  80 <span class="i">$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>
+  81 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+  82 
+  83 <span class="c">###############################################################################</span>
+  84 
+  85 <span class="c"># Split a SD file...</span>
+  86 <span class="c">#</span>
+<a name="SplitSDFile-"></a>  87 <span class="k">sub </span><span class="m">SplitSDFile</span> <span class="s">{</span>
+  88   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  89 
+  90   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Files$/i</span><span class="s">)</span> <span class="s">{</span>
+  91     <span class="i">SplitSDFileByNumOfFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  92   <span class="s">}</span>
+  93   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Cmpds$/i</span><span class="s">)</span> <span class="s">{</span>
+  94     <span class="i">SplitSDFileByNumOfCmpds</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  95   <span class="s">}</span>
+  96 <span class="s">}</span>
+  97 
+  98 <span class="c"># Split SD into specified number of files...</span>
+  99 <span class="c">#</span>
+<a name="SplitSDFileByNumOfFiles-"></a> 100 <span class="k">sub </span><span class="m">SplitSDFileByNumOfFiles</span> <span class="s">{</span>
+ 101   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 102   <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$MaxCmpdsPerFile</span><span class="cm">,</span> <span class="i">$MaxNumOfFiles</span><span class="s">)</span><span class="sc">;</span>
+ 103 
+ 104   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+ 105 
+ 106   <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>
+ 107     <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+ 108     <span class="k">return</span><span class="sc">;</span>
+ 109   <span class="s">}</span>
+ 110 
+ 111   <span class="i">$MaxNumOfFiles</span> = <span class="i">$OptionsInfo</span>{<span class="w">NumOfFiles</span>}<span class="sc">;</span>
+ 112 
+ 113   <span class="c"># Count number of compounds to figure out maximum number of compound per file...</span>
+ 114   <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+ 115   <span class="k">while</span> <span class="s">(</span><span class="q">&lt;SDFILE&gt;</span><span class="s">)</span> <span class="s">{</span>
+ 116     <span class="k">if</span> <span class="s">(</span><span class="q">/^\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span>
+ 117       <span class="i">$CmpdCount</span>++<span class="sc">;</span>
+ 118     <span class="s">}</span>
+ 119   <span class="s">}</span>
+ 120   <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+ 121 
+ 122   <span class="k">if</span> <span class="s">(</span><span class="i">$CmpdCount</span> &lt; <span class="i">$MaxNumOfFiles</span><span class="s">)</span> <span class="s">{</span>
+ 123     <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Total number of compounds, $CmpdCount, is smaller than number of new files, $MaxNumOfFiles\n&quot;</span><span class="sc">;</span>
+ 124     <span class="k">return</span><span class="sc">;</span>
+ 125   <span class="s">}</span>
+ 126 
+ 127   <span class="i">$MaxCmpdsPerFile</span> = <span class="k">int</span> <span class="i">$CmpdCount</span> / <span class="i">$MaxNumOfFiles</span><span class="sc">;</span>
+ 128 
+ 129   <span class="i">SplitSDFileByNumOfFilesAndCmpds</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$MaxNumOfFiles</span><span class="cm">,</span> <span class="i">$MaxCmpdsPerFile</span><span class="s">)</span><span class="sc">;</span>
+ 130 <span class="s">}</span>
+ 131 
+ 132 <span class="c"># Split SD into files containing specified number of compounds...</span>
+ 133 <span class="c">#</span>
+<a name="SplitSDFileByNumOfCmpds-"></a> 134 <span class="k">sub </span><span class="m">SplitSDFileByNumOfCmpds</span> <span class="s">{</span>
+ 135   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 136 
+ 137   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">NumOfCmpds</span>} == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+ 138     <span class="i">SplitSDFileByOneCmpdPerFile</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+ 139   <span class="s">}</span>
+ 140   <span class="k">else</span> <span class="s">{</span>
+ 141     <span class="i">SplitSDFileByNumOfCmpdsPerFile</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+ 142   <span class="s">}</span>
+ 143 <span class="s">}</span>
+ 144 
+ 145 <span class="c"># Split SD into files containing one compound per file...</span>
+ 146 <span class="c">#</span>
+<a name="SplitSDFileByOneCmpdPerFile-"></a> 147 <span class="k">sub </span><span class="m">SplitSDFileByOneCmpdPerFile</span> <span class="s">{</span>
+ 148   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 149   <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$NewSDFile</span><span class="cm">,</span> <span class="i">$NewSDFileRoot</span><span class="cm">,</span> <span class="i">$FileExt</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">$CmpdString</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldValues</span><span class="s">)</span><span class="sc">;</span>
+ 150 
+ 151   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+ 152 
+ 153   <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>
+ 154     <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+ 155     <span class="k">return</span><span class="sc">;</span>
+ 156   <span class="s">}</span>
+ 157 
+ 158   <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+ 159 
+ 160   <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+ 161 
+ 162   <span class="i">$FileExt</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+ 163 
+ 164   <span class="i">$OutFileRoot</span> = <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+ 165   <span class="i">$OverwriteFiles</span> = <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="sc">;</span>
+ 166 
+ 167   <span class="i">$UseDataField</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CmpdsMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 168   <span class="i">$DataFieldName</span> = <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>}<span class="sc">;</span>
+ 169 
+ 170   <span class="i">$UseMolName</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CmpdsMode</span>} =~ <span class="q">/^MolName$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 171 
+ 172   <span class="j">CMPDSTRING:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 173     <span class="i">$CmpdCount</span>++<span class="sc">;</span>
+ 174 
+ 175     <span class="c"># Setup SD file name...</span>
+ 176     <span class="i">$NewSDFileRoot</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 177     <span class="k">if</span> <span class="s">(</span><span class="i">$UseDataField</span><span class="s">)</span> <span class="s">{</span>
+ 178       <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+ 179       <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
+ 180       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$DataFieldName</span>}<span class="s">)</span> <span class="s">{</span>
+ 181         <span class="i">$NewSDFileRoot</span> = <span class="i">$DataFieldValues</span>{<span class="i">$DataFieldName</span>}<span class="sc">;</span>
+ 182       <span class="s">}</span>
+ 183     <span class="s">}</span>
+ 184     <span class="k">elsif</span> <span class="s">(</span><span class="i">$UseMolName</span><span class="s">)</span> <span class="s">{</span>
+ 185       <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+ 186       <span class="i">$NewSDFileRoot</span> = <span class="i">$CmpdLines</span>[<span class="n">0</span>]<span class="sc">;</span>
+ 187     <span class="s">}</span>
+ 188 
+ 189     <span class="c"># Check for any invalid file name characters in data field or molname values...</span>
+ 190     <span class="k">if</span> <span class="s">(</span><span class="i">$NewSDFileRoot</span> &amp;&amp; <span class="i">$NewSDFileRoot</span> =~ <span class="q">/[^a-zA-Z0-9_]/</span><span class="s">)</span> <span class="s">{</span>
+ 191       <span class="i">$NewSDFileRoot</span> =~ <span class="q">s/[^a-zA-Z0-9_]//g</span><span class="sc">;</span>
+ 192     <span class="s">}</span>
+ 193 
+ 194     <span class="c"># Fall back plan for SD file name...</span>
+ 195     <span class="k">if</span> <span class="s">(</span>!<span class="i">$NewSDFileRoot</span><span class="s">)</span> <span class="s">{</span>
+ 196       <span class="i">$NewSDFileRoot</span> = <span class="q">&quot;${OutFileRoot}Cmpd${CmpdCount}&quot;</span><span class="sc">;</span>
+ 197     <span class="s">}</span>
+ 198 
+ 199     <span class="i">$NewSDFile</span> = <span class="q">&quot;${NewSDFileRoot}.${FileExt}&quot;</span><span class="sc">;</span>
+ 200 
+ 201     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OverwriteFiles</span><span class="s">)</span> <span class="s">{</span>
+ 202       <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFile</span><span class="s">)</span> <span class="s">{</span>
+ 203         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring compound number, $CmpdCount, in $SDFile: New SD file, $NewSDFile, already exists\n&quot;</span><span class="sc">;</span>
+ 204         <span class="k">next</span> <span class="j">CMPDSTRING</span><span class="sc">;</span>
+ 205       <span class="s">}</span>
+ 206     <span class="s">}</span>
+ 207 
+ 208     <span class="c"># Write out new SD file...</span>
+ 209 
+ 210     <span class="k">print</span> <span class="q">&quot;Generating $NewSDFile file\n&quot;</span><span class="sc">;</span>
+ 211     <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewSDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $NewSDFile: $! \n&quot;</span><span class="sc">;</span>
+ 212     <span class="k">print</span> <span class="i">NEWSDFILE</span> <span class="q">&quot;$CmpdString\n&quot;</span><span class="sc">;</span>
+ 213     <span class="k">close</span> <span class="w">NEWSDFILE</span><span class="sc">;</span>
+ 214 
+ 215   <span class="s">}</span>
+ 216   <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+ 217 <span class="s">}</span>
+ 218 
+ 219 <span class="c"># Split SD into files containing specified number of compounds per file...</span>
+ 220 <span class="c">#</span>
+<a name="SplitSDFileByNumOfCmpdsPerFile-"></a> 221 <span class="k">sub </span><span class="m">SplitSDFileByNumOfCmpdsPerFile</span> <span class="s">{</span>
+ 222   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 223   <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$MaxCmpdsPerFile</span><span class="cm">,</span> <span class="i">$MaxNumOfFiles</span><span class="s">)</span><span class="sc">;</span>
+ 224 
+ 225   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+ 226 
+ 227   <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>
+ 228     <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+ 229     <span class="k">return</span><span class="sc">;</span>
+ 230   <span class="s">}</span>
+ 231 
+ 232   <span class="i">$MaxCmpdsPerFile</span> = <span class="i">$OptionsInfo</span>{<span class="w">NumOfCmpds</span>}<span class="sc">;</span>
+ 233 
+ 234   <span class="c"># Count number of compounds to figure out maximum number of files...</span>
+ 235   <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+ 236   <span class="k">while</span> <span class="s">(</span><span class="q">&lt;SDFILE&gt;</span><span class="s">)</span> <span class="s">{</span>
+ 237     <span class="k">if</span> <span class="s">(</span><span class="q">/^\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span>
+ 238       <span class="i">$CmpdCount</span>++<span class="sc">;</span>
+ 239     <span class="s">}</span>
+ 240   <span class="s">}</span>
+ 241   <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+ 242 
+ 243   <span class="i">$MaxNumOfFiles</span> = <span class="k">int</span> <span class="i">$CmpdCount</span> / <span class="i">$MaxCmpdsPerFile</span><span class="sc">;</span>
+ 244 
+ 245   <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$MaxNumOfFiles</span> * <span class="i">$MaxCmpdsPerFile</span><span class="s">)</span> &lt; <span class="i">$CmpdCount</span><span class="s">)</span> <span class="s">{</span>
+ 246     <span class="i">$MaxNumOfFiles</span>++<span class="sc">;</span>
+ 247   <span class="s">}</span>
+ 248 
+ 249   <span class="k">if</span> <span class="s">(</span><span class="i">$CmpdCount</span> &lt;= <span class="i">$MaxCmpdsPerFile</span><span class="s">)</span> <span class="s">{</span>
+ 250     <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Total number of compounds, $CmpdCount, is &lt;= specified number of compunds per file, $MaxCmpdsPerFile\n&quot;</span><span class="sc">;</span>
+ 251     <span class="k">return</span><span class="sc">;</span>
+ 252   <span class="s">}</span>
+ 253 
+ 254   <span class="i">SplitSDFileByNumOfFilesAndCmpds</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$MaxNumOfFiles</span><span class="cm">,</span> <span class="i">$MaxCmpdsPerFile</span><span class="s">)</span><span class="sc">;</span>
+ 255 <span class="s">}</span>
+ 256 
+ 257 <span class="c"># Split SD files into specified number of files with specified number of compounds</span>
+ 258 <span class="c"># in each file...</span>
+ 259 <span class="c">#</span>
+<a name="SplitSDFileByNumOfFilesAndCmpds-"></a> 260 <span class="k">sub </span><span class="m">SplitSDFileByNumOfFilesAndCmpds</span> <span class="s">{</span>
+ 261   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$NumOfFiles</span><span class="cm">,</span> <span class="i">$NumOfCmpdsPerFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 262   <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$NewFileIndex</span><span class="cm">,</span> <span class="i">$NewFileName</span><span class="cm">,</span> <span class="i">$MaxCmpdsCount</span><span class="cm">,</span> <span class="i">@NewSDFilesList</span><span class="s">)</span><span class="sc">;</span>
+ 263 
+ 264   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+ 265 
+ 266   <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span><span class="s">)</span> <span class="s">{</span>
+ 267     <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+ 268     <span class="k">return</span><span class="sc">;</span>
+ 269   <span class="s">}</span>
+ 270 
+ 271   <span class="c"># Setup new file names list...</span>
+ 272   <span class="i">@NewSDFilesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 273   <span class="k">for</span> <span class="i">$NewFileIndex</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$NumOfFiles</span><span class="s">)</span> <span class="s">{</span>
+ 274     <span class="i">$NewFileName</span> = <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>] . <span class="q">&quot;Part${NewFileIndex}.&quot;</span> . <span class="i">$SDFilesInfo</span>{<span class="w">FileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+ 275     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
+ 276       <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewFileName</span><span class="s">)</span> <span class="s">{</span>
+ 277         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: New SD file, $NewFileName, already exists\n&quot;</span><span class="sc">;</span>
+ 278         <span class="k">return</span><span class="sc">;</span>
+ 279       <span class="s">}</span>
+ 280     <span class="s">}</span>
+ 281     <span class="k">push</span> <span class="i">@NewSDFilesList</span><span class="cm">,</span> <span class="i">$NewFileName</span><span class="sc">;</span>
+ 282   <span class="s">}</span>
+ 283 
+ 284   <span class="i">$MaxCmpdsCount</span> = <span class="i">$NumOfCmpdsPerFile</span><span class="sc">;</span>
+ 285 
+ 286   <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+ 287   <span class="i">$NewFileIndex</span> = <span class="n">1</span><span class="sc">;</span>
+ 288 
+ 289   <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewSDFilesList[$NewFileIndex - 1]&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $NewSDFilesList[$NewFileIndex -1]: $! \n&quot;</span><span class="sc">;</span>
+ 290   <span class="k">print</span> <span class="q">&quot;\nGenerating $NewSDFilesList[$NewFileIndex - 1] file\n&quot;</span><span class="sc">;</span>
+ 291 
+ 292   <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
+ 293 
+ 294   <span class="k">while</span> <span class="s">(</span><span class="q">&lt;SDFILE&gt;</span><span class="s">)</span> <span class="s">{</span>
+ 295     <span class="q">s/(\r\n)|(\r)/\n/g</span><span class="sc">;</span>
+ 296     <span class="k">print</span> <span class="i">NEWSDFILE</span><span class="sc">;</span>
+ 297 
+ 298     <span class="k">if</span> <span class="s">(</span> <span class="q">/^\$\$\$\$/</span> <span class="s">)</span> <span class="s">{</span>
+ 299       <span class="i">$CmpdCount</span>++<span class="sc">;</span>
+ 300       <span class="k">if</span> <span class="s">(</span><span class="i">$NewFileIndex</span> &lt;= <span class="i">$NumOfFiles</span><span class="s">)</span> <span class="s">{</span>
+ 301         <span class="k">if</span> <span class="s">(</span><span class="i">$CmpdCount</span> &gt;= <span class="i">$MaxCmpdsCount</span><span class="s">)</span> <span class="s">{</span>
+ 302           <span class="k">if</span> <span class="s">(</span><span class="i">$NewFileIndex</span> &lt; <span class="i">$NumOfFiles</span><span class="s">)</span> <span class="s">{</span>
+ 303             <span class="k">close</span> <span class="w">NEWSDFILE</span><span class="sc">;</span>
+ 304           <span class="s">}</span>
+ 305           <span class="i">$NewFileIndex</span>++<span class="sc">;</span>
+ 306           <span class="i">$MaxCmpdsCount</span> = <span class="i">$NumOfCmpdsPerFile</span> * <span class="i">$NewFileIndex</span><span class="sc">;</span>
+ 307 
+ 308           <span class="k">if</span> <span class="s">(</span><span class="i">$NewFileIndex</span> &lt;= <span class="i">$NumOfFiles</span><span class="s">)</span> <span class="s">{</span>
+ 309             <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewSDFilesList[$NewFileIndex - 1]&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $NewSDFilesList[$NewFileIndex - 1]: $! \n&quot;</span><span class="sc">;</span>
+ 310             <span class="k">print</span> <span class="q">&quot;Generating $NewSDFilesList[$NewFileIndex - 1] file...\n&quot;</span><span class="sc">;</span>
+ 311           <span class="s">}</span>
+ 312         <span class="s">}</span>
+ 313       <span class="s">}</span>
+ 314     <span class="s">}</span>
+ 315   <span class="s">}</span>
+ 316   <span class="k">close</span> <span class="w">NEWSDFILE</span><span class="sc">;</span>
+ 317 <span class="s">}</span>
+ 318 
+ 319 <span class="c"># Retrieve information about SD files...</span>
+ 320 <span class="c">#</span>
+<a name="RetrieveSDFilesInfo-"></a> 321 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
+ 322   <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>
+ 323 
+ 324   <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 325   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 326   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileExt</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 327   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 328 
+ 329   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+ 330     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 331 
+ 332     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+ 333     <span class="i">$SDFilesInfo</span>{<span class="w">FileExt</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 334     <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>
+ 335 
+ 336     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 337     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 338       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+ 339       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 340     <span class="s">}</span>
+ 341     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$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>
+ 342       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
+ 343       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 344     <span class="s">}</span>
+ 345 
+ 346     <span class="c"># Setup output file root...</span>
+ 347     <span class="i">$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>
+ 348     <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>
+ 349 
+ 350     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 351       <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
+ 352       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+ 353         <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+ 354       <span class="s">}</span>
+ 355       <span class="k">else</span> <span class="s">{</span>
+ 356         <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
+ 357       <span class="s">}</span>
+ 358       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+ 359     <span class="s">}</span>
+ 360     <span class="k">else</span> <span class="s">{</span>
+ 361       <span class="i">$OutFileRoot</span> = <span class="q">&quot;$FileName&quot;</span><span class="sc">;</span>
+ 362     <span class="s">}</span>
+ 363 
+ 364     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+ 365     <span class="i">$SDFilesInfo</span>{<span class="w">FileExt</span>}[<span class="i">$Index</span>] = <span class="i">$FileExt</span><span class="sc">;</span>
+ 366     <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
+ 367   <span class="s">}</span>
+ 368 <span class="s">}</span>
+ 369 
+ 370 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 371 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+ 372   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 373 
+ 374   <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+ 375 
+ 376   <span class="i">$OptionsInfo</span>{<span class="w">CmpdsMode</span>} = <span class="i">$Options</span>{<span class="w">cmpdsmode</span>}<span class="sc">;</span>
+ 377 
+ 378   <span class="i">$OptionsInfo</span>{<span class="w">NumOfFiles</span>} = <span class="i">$Options</span>{<span class="w">numfiles</span>}<span class="sc">;</span>
+ 379   <span class="i">$OptionsInfo</span>{<span class="w">NumOfCmpds</span>} = <span class="i">$Options</span>{<span class="w">numcmpds</span>}<span class="sc">;</span>
+ 380 
+ 381   <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 382   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^Cmpds$/i</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">cmpdsmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
+ 383     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafield</span>}<span class="s">)</span> <span class="s">{</span>
+ 384       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;-d, --DataField\&quot; option in \&quot;DataField\&quot; value of \&quot;-c, --CmpdsMode\&quot; during \&quot;Cmpds\&quot; \&quot;-m, --mode\&quot; value. \n&quot;</span><span class="sc">;</span>
+ 385     <span class="s">}</span>
+ 386     <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>} = <span class="i">$Options</span>{<span class="w">datafield</span>}<span class="sc">;</span>
+ 387   <span class="s">}</span>
+ 388 
+ 389   <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 390 
+ 391   <span class="i">$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>
+ 392 <span class="s">}</span>
+ 393 
+ 394 
+ 395 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 396 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+ 397 
+ 398   <span class="c"># Retrieve all the options...</span>
+ 399   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 400 
+ 401   <span class="i">$Options</span>{<span class="w">cmpdsmode</span>} = <span class="q">&#39;RootPrefix&#39;</span><span class="sc">;</span>
+ 402   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;Files&#39;</span><span class="sc">;</span>
+ 403 
+ 404   <span class="i">$Options</span>{<span class="w">numfiles</span>} = <span class="n">2</span><span class="sc">;</span>
+ 405   <span class="i">$Options</span>{<span class="w">numcmpds</span>} = <span class="n">1</span><span class="sc">;</span>
+ 406 
+ 407 
+ 408   <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;cmpdsmode|c=s&quot;</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;numfiles|n=i&quot;</span><span class="cm">,</span> <span class="q">&quot;numcmpds=i&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>
+ 409     <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 $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+ 410   <span class="s">}</span>
+ 411   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+ 412     <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>
+ 413       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+ 414     <span class="s">}</span>
+ 415     <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
+ 416   <span class="s">}</span>
+ 417   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">cmpdsmode</span>} !~ <span class="q">/^(DataField|MolName|RootPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 418     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{cmpdsmode}, for option \&quot;-c, --CmpdsMode\&quot; is not valid. Allowed values: DataField, MolName, RootPrefix\n&quot;</span><span class="sc">;</span>
+ 419   <span class="s">}</span>
+ 420   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(Cmpds|Files)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 421     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m, --mode\&quot; is not valid. Allowed values: Cmpds, Files\n&quot;</span><span class="sc">;</span>
+ 422   <span class="s">}</span>
+ 423   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">numfiles</span>} &lt; <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+ 424     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{numfiles}, for option \&quot;-n --numfiles\&quot; is not valid. Allowed values: &gt;= 2 \n&quot;</span><span class="sc">;</span>
+ 425   <span class="s">}</span>
+ 426   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">numcmpds</span>} &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+ 427     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{numcmpds}, for option \&quot;-n --numcmpds\&quot; is not valid. Allowed values: &gt;= 1 \n&quot;</span><span class="sc">;</span>
+ 428   <span class="s">}</span>
+ 429 <span class="s">}</span>
+ 430 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>