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+<html>
+<head>
+<title>MayaChemTools:Code:ElementalAnalysisSDFiles.pl</title>
+<meta http-equiv="content-type" content="text/html;charset=utf-8">
+<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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+<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: ElementalAnalysisSDFiles.pl,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
+   5 <span class="c"># $Revision: 1.24 $</span>
+   6 <span class="c">#</span>
+   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+   8 <span class="c">#</span>
+   9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+  10 <span class="c">#</span>
+  11 <span class="c"># This file is part of MayaChemTools.</span>
+  12 <span class="c">#</span>
+  13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+  14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+  15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+  16 <span class="c"># later version.</span>
+  17 <span class="c">#</span>
+  18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+  19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+  20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+  21 <span class="c"># details.</span>
+  22 <span class="c">#</span>
+  23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+  24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+  25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+  26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+  27 <span class="c">#</span>
+  28 
+  29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+  30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</span><span class="sc">;</span>
+  31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
+  32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
+  33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
+  34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
+  36 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span>
+  37 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
+  38 <span class="k">use</span> <span class="w">MolecularFormula</span><span class="sc">;</span>
+  39 <span class="k">use</span> <span class="w">FileIO::SDFileIO</span><span class="sc">;</span>
+  40 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
+  41 
+  42 <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>
+  43 
+  44 <span class="c"># Autoflush STDOUT</span>
+  45 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+  46 
+  47 <span class="c"># Starting message...</span>
+  48 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
+  49 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
+  50 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  51 
+  52 <span class="c"># Get the options and setup script...</span>
+  53 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  54 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+  55   <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>
+  56 <span class="s">}</span>
+  57 
+  58 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
+  59 <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>
+  60 
+  61 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+  62 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+  63 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  64 
+  65 <span class="k">print</span> <span class="q">&quot;Checking input SD file(s)...\n&quot;</span><span class="sc">;</span>
+  66 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
+  67 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  68 
+  69 <span class="c"># Generate output files...</span>
+  70 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  71 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+  72   <span class="k">print</span> <span class="q">&quot;\nProcessing SD files...\n&quot;</span><span class="sc">;</span>
+  73 <span class="s">}</span>
+  74 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+  75   <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+  76     <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+  77     <span class="i">PerformElementalAnalysis</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  78   <span class="s">}</span>
+  79 <span class="s">}</span>
+  80 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+  81 
+  82 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  83 <span class="i">$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>
+  84 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+  85 
+  86 <span class="c">###############################################################################</span>
+  87 
+  88 <span class="c"># Perform analysis...</span>
+<a name="PerformElementalAnalysis-"></a>  89 <span class="k">sub </span><span class="m">PerformElementalAnalysis</span> <span class="s">{</span>
+  90   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  91   <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">$KeyDataFieldName</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$CurrentFormula</span><span class="cm">,</span> <span class="i">$FormulaFieldName</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$CalculationType</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldValuesMap</span><span class="s">)</span><span class="sc">;</span>
+  92 
+  93   <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+  94   <span class="i">$NewSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
+  95 
+  96   <span class="k">print</span> <span class="q">&quot;Generating new SD file $NewSDFile...\n&quot;</span><span class="sc">;</span>
+  97   <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewSDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $NewSDFile: $! \n&quot;</span><span class="sc">;</span>
+  98   <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
+  99 
+ 100 
+ 101   <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
+ 102   <span class="i">$FormulaFieldName</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FormulaFieldName</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
+ 103 
+ 104   <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$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>
+ 105     <span class="i">$CmpdCount</span>++<span class="sc">;</span>
+ 106     <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+ 107     <span class="i">%DataFieldValuesMap</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
+ 108 
+ 109     <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 110     <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="s">)</span> <span class="s">{</span>
+ 111       <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 112     <span class="s">}</span>
+ 113 
+ 114     <span class="i">$CurrentFormula</span> = <span class="k">undef</span><span class="sc">;</span>
+ 115 
+ 116     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseStructureData</span>}<span class="s">)</span> <span class="s">{</span>
+ 117       <span class="i">$Molecule</span> = <span class="i">FileIO::SDFileIO::ParseMoleculeString</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
+ 118       <span class="i">$CurrentFormula</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetMolecularFormula</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 119     <span class="s">}</span>
+ 120     <span class="k">else</span> <span class="s">{</span>
+ 121       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValuesMap</span>{<span class="i">$FormulaFieldName</span>}<span class="s">)</span> <span class="s">{</span>
+ 122         <span class="i">$ErrorMsg</span> = <span class="q">&quot;Ignoring compound record $CmpdCount: Formula field $FormulaFieldName not found&quot;</span><span class="sc">;</span>
+ 123         <span class="i">PrintErrorMsg</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
+ 124         <span class="i">WriteNewCompoundRecord</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> \<span class="i">*NEWSDFILE</span><span class="cm">,</span> \<span class="i">@CmpdLines</span><span class="cm">,</span> \<span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span>
+ 125         <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
+ 126       <span class="s">}</span>
+ 127 
+ 128       <span class="c"># Make sure it&#39;s a valid molecular formula...</span>
+ 129       <span class="i">$CurrentFormula</span> = <span class="i">$DataFieldValuesMap</span>{<span class="i">$FormulaFieldName</span>}<span class="sc">;</span>
+ 130       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckFormula</span>}<span class="s">)</span> <span class="s">{</span>
+ 131         <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span> = <span class="i">MolecularFormula::IsMolecularFormula</span><span class="s">(</span><span class="i">$CurrentFormula</span><span class="s">)</span><span class="sc">;</span>
+ 132         <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span>
+ 133           <span class="i">$ErrorMsg</span> = <span class="q">&quot;Ignoring compound record $CmpdCount: Formula field value $CurrentFormula is not valid: $ErrorMsg&quot;</span><span class="sc">;</span>
+ 134           <span class="i">PrintErrorMsg</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
+ 135           <span class="i">WriteNewCompoundRecord</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> \<span class="i">*NEWSDFILE</span><span class="cm">,</span> \<span class="i">@CmpdLines</span><span class="cm">,</span> \<span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span>
+ 136           <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
+ 137         <span class="s">}</span>
+ 138       <span class="s">}</span>
+ 139     <span class="s">}</span>
+ 140 
+ 141     <span class="c"># Calculate appropriate values and write &#39;em out...</span>
+ 142     <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 143     <span class="k">for</span> <span class="i">$CalculationType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="s">)</span> <span class="s">{</span>
+ 144       <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^ElementalAnalysis$/i</span><span class="s">)</span> <span class="s">{</span>
+ 145         <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="s">)</span> = <span class="i">MolecularFormula::CalculateElementalComposition</span><span class="s">(</span><span class="i">$CurrentFormula</span><span class="s">)</span><span class="sc">;</span>
+ 146         <span class="i">$CalculatedValue</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="s">)</span> &amp;&amp; <span class="k">defined</span><span class="s">(</span><span class="i">$ElementCompositionRef</span><span class="s">)</span><span class="s">)</span> ? <span class="i">MolecularFormula::FormatCompositionInfomation</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>}<span class="s">)</span> <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 147       <span class="s">}</span>
+ 148       <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^MolecularWeight$/i</span><span class="s">)</span> <span class="s">{</span>
+ 149         <span class="i">$CalculatedValue</span> = <span class="i">MolecularFormula::CalculateMolecularWeight</span><span class="s">(</span><span class="i">$CurrentFormula</span><span class="s">)</span><span class="sc">;</span>
+ 150         <span class="i">$CalculatedValue</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span> &amp;&amp; <span class="k">length</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.$OptionsInfo{Precision}f&quot;</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">&quot;&quot;</span><span class="sc">;</span>
+ 151       <span class="s">}</span>
+ 152       <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^ExactMass$/i</span><span class="s">)</span> <span class="s">{</span>
+ 153         <span class="i">$CalculatedValue</span> = <span class="i">MolecularFormula::CalculateExactMass</span><span class="s">(</span><span class="i">$CurrentFormula</span><span class="s">)</span><span class="sc">;</span>
+ 154         <span class="i">$CalculatedValue</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span> &amp;&amp; <span class="k">length</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.$OptionsInfo{Precision}f&quot;</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">&quot;&quot;</span><span class="sc">;</span>
+ 155       <span class="s">}</span>
+ 156       <span class="k">else</span> <span class="s">{</span>
+ 157         <span class="i">$CalculatedValue</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 158       <span class="s">}</span>
+ 159       <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="sc">;</span>
+ 160     <span class="s">}</span>
+ 161     <span class="i">WriteNewCompoundRecord</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> \<span class="i">*NEWSDFILE</span><span class="cm">,</span> \<span class="i">@CmpdLines</span><span class="cm">,</span> \<span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="i">$CurrentFormula</span><span class="s">)</span><span class="sc">;</span>
+ 162   <span class="s">}</span>
+ 163   <span class="k">close</span> <span class="w">NEWSDFILE</span><span class="sc">;</span>
+ 164   <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+ 165 <span class="s">}</span>
+ 166 
+ 167 <span class="c"># Write out compound record with calculated values...</span>
+<a name="WriteNewCompoundRecord-"></a> 168 <span class="k">sub </span><span class="m">WriteNewCompoundRecord</span> <span class="s">{</span>
+ 169   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SDFileRef</span><span class="cm">,</span> <span class="i">$CmpdLinesRef</span><span class="cm">,</span> <span class="i">$CalculatedValuesRef</span><span class="cm">,</span> <span class="i">$MolecularFormula</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 170 
+ 171   <span class="c"># Write out compound lines except the last line which contains $$$$...</span>
+ 172   <span class="k">my</span><span class="s">(</span><span class="i">$LineIndex</span><span class="s">)</span><span class="sc">;</span>
+ 173   <span class="k">for</span> <span class="i">$LineIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$#</span>{<span class="i">$CmpdLinesRef</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 174     <span class="k">print</span> <span class="i">$SDFileRef</span> <span class="q">&quot;$CmpdLinesRef-&gt;[$LineIndex]\n&quot;</span><span class="sc">;</span>
+ 175   <span class="s">}</span>
+ 176 
+ 177   <span class="c"># Write out calculated values...</span>
+ 178   <span class="k">my</span><span class="s">(</span><span class="i">$CalcIndex</span><span class="cm">,</span> <span class="i">$FieldName</span><span class="cm">,</span> <span class="i">$FieldValue</span><span class="s">)</span><span class="sc">;</span>
+ 179   <span class="k">for</span> <span class="i">$CalcIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="s">)</span> <span class="s">{</span>
+ 180     <span class="i">$FieldName</span> = <span class="i">$SDFilesInfo</span>{<span class="w">ValueFieldNamesMap</span>}[<span class="i">$Index</span>]{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}[<span class="i">$CalcIndex</span>]}<span class="sc">;</span>
+ 181     <span class="i">$FieldValue</span> = <span class="i">$CalculatedValuesRef</span>-&gt;[<span class="i">$CalcIndex</span>]<span class="sc">;</span>
+ 182     <span class="k">print</span>  <span class="i">$SDFileRef</span> <span class="q">&quot;&gt;  &lt;$FieldName&gt;\n$FieldValue\n\n&quot;</span><span class="sc">;</span>
+ 183   <span class="s">}</span>
+ 184 
+ 185   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseStructureData</span>} &amp;&amp; <span class="i">$OptionsInfo</span>{<span class="w">WriteOutFormula</span>} &amp;&amp; <span class="k">defined</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 186     <span class="i">$FieldName</span> = <span class="i">$SDFilesInfo</span>{<span class="w">ValueFieldNamesMap</span>}[<span class="i">$Index</span>]{<span class="w">MolecularFormula</span>}<span class="sc">;</span>
+ 187     <span class="i">$FieldValue</span> = <span class="i">$MolecularFormula</span><span class="sc">;</span>
+ 188     <span class="k">print</span>  <span class="i">$SDFileRef</span> <span class="q">&quot;&gt;  &lt;$FieldName&gt;\n$FieldValue\n\n&quot;</span><span class="sc">;</span>
+ 189   <span class="s">}</span>
+ 190 
+ 191   <span class="k">print</span> <span class="i">$SDFileRef</span>  <span class="q">&quot;\$\$\$\$\n&quot;</span><span class="sc">;</span>
+ 192 <span class="s">}</span>
+ 193 
+ 194 <span class="c"># Print out error message...</span>
+<a name="PrintErrorMsg-"></a> 195 <span class="k">sub </span><span class="m">PrintErrorMsg</span> <span class="s">{</span>
+ 196   <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 197 
+ 198   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
+ 199     <span class="k">print</span> <span class="q">&quot;$ErrorMsg:\n$CmpdString\n&quot;</span><span class="sc">;</span>
+ 200   <span class="s">}</span>
+ 201   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+ 202     <span class="k">print</span> <span class="q">&quot;$ErrorMsg\n&quot;</span><span class="sc">;</span>
+ 203   <span class="s">}</span>
+ 204 <span class="s">}</span>
+ 205 
+ 206 <span class="c"># Retrieve information about input SD files...</span>
+<a name="RetrieveSDFilesInfo-"></a> 207 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
+ 208   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$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">$OutFileRoot</span><span class="cm">,</span>  <span class="i">$OutFile</span><span class="cm">,</span> <span class="i">$FormulaFieldName</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$FieldName</span><span class="cm">,</span> <span class="i">$NewFieldName</span><span class="cm">,</span> <span class="i">$Count</span><span class="s">)</span><span class="sc">;</span>
+ 209 
+ 210   <span class="k">my</span><span class="s">(</span><span class="i">%NewValueFieldNames</span><span class="s">)</span> = <span class="s">(</span><span class="w">ElementalAnalysis</span> <span class="cm">=&gt;</span> <span class="q">&#39;ElementalAnalysis&#39;</span><span class="cm">,</span> <span class="w">MolecularWeight</span> <span class="cm">=&gt;</span> <span class="q">&#39;MolecularWeight&#39;</span><span class="cm">,</span> <span class="w">ExactMass</span> <span class="cm">=&gt;</span> <span class="q">&#39;ExactMass&#39;</span><span class="cm">,</span> <span class="w">MolecularFormula</span> <span class="cm">=&gt;</span> <span class="q">&#39;MolecularFormula&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 211   <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueFieldNames</span>}}<span class="s">)</span> <span class="s">{</span>
+ 212     <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> &lt; <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueFieldNames</span>}}<span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+ 213       <span class="i">$Value</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueFieldNames</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
+ 214       <span class="i">$FieldName</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueFieldNames</span>}[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
+ 215       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NewValueFieldNames</span>{<span class="i">$Value</span>}<span class="s">)</span> <span class="s">{</span>
+ 216         <span class="i">$NewValueFieldNames</span>{<span class="i">$Value</span>} = <span class="i">$FieldName</span><span class="sc">;</span>
+ 217       <span class="s">}</span>
+ 218     <span class="s">}</span>
+ 219   <span class="s">}</span>
+ 220 
+ 221   <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 222 
+ 223   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 224   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFile</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 225   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FormulaFieldName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 226   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">ValueFieldNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 227 
+ 228   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+ 229     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 230 
+ 231     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+ 232     <span class="i">$SDFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 233     <span class="i">$SDFilesInfo</span>{<span class="w">FormulaFieldName</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 234 
+ 235     <span class="i">%</span>{<span class="i">$SDFilesInfo</span>{<span class="w">ValueFieldNamesMap</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 236 
+ 237     <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>
+ 238       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+ 239       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 240     <span class="s">}</span>
+ 241     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$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>
+ 242       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
+ 243       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 244     <span class="s">}</span>
+ 245     <span class="i">$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>
+ 246     <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>
+ 247     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>} &amp;&amp; <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 248       <span class="k">my</span> <span class="s">(</span><span class="i">$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">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span>
+ 249       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+ 250         <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+ 251       <span class="s">}</span>
+ 252       <span class="k">else</span> <span class="s">{</span>
+ 253         <span class="i">$FileName</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span>
+ 254       <span class="s">}</span>
+ 255       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+ 256     <span class="s">}</span>
+ 257     <span class="k">else</span> <span class="s">{</span>
+ 258       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span> . <span class="q">&quot;ElementalAnalysis&quot;</span><span class="sc">;</span>
+ 259     <span class="s">}</span>
+ 260 
+ 261     <span class="i">$OutFile</span> = <span class="i">$OutFileRoot</span> . <span class="q">&quot;.$FileExt&quot;</span><span class="sc">;</span>
+ 262     <span class="k">if</span> <span class="s">(</span><span class="k">lc</span><span class="s">(</span><span class="i">$OutFile</span><span class="s">)</span> <span class="k">eq</span> <span class="k">lc</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 263       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n&quot;</span><span class="sc">;</span>
+ 264       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 265     <span class="s">}</span>
+ 266     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
+ 267       <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFile</span><span class="s">)</span> <span class="s">{</span>
+ 268         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $OutFile already exists\n&quot;</span><span class="sc">;</span>
+ 269         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 270       <span class="s">}</span>
+ 271     <span class="s">}</span>
+ 272     <span class="c"># Get data field names and values...</span>
+ 273     <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$FieldName</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">@DataFieldNames</span><span class="cm">,</span> <span class="i">%DataFieldNamesMap</span><span class="s">)</span><span class="sc">;</span>
+ 274     <span class="i">@DataFieldNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 275     <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span><span class="s">(</span><span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 276       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+ 277       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 278     <span class="s">}</span>
+ 279     <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
+ 280     <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+ 281 
+ 282     <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
+ 283     <span class="i">@DataFieldNames</span> = <span class="i">GetCmpdDataHeaderLabels</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
+ 284     <span class="i">%DataFieldNamesMap</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
+ 285 
+ 286     <span class="c"># Setup formula field name...</span>
+ 287     <span class="i">$FormulaFieldName</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 288     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseDataField</span>}<span class="s">)</span> <span class="s">{</span>
+ 289       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaFieldName</span>}<span class="s">)</span> <span class="s">{</span>
+ 290         <span class="i">$FormulaFieldName</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaFieldName</span>}<span class="sc">;</span>
+ 291       <span class="s">}</span>
+ 292       <span class="k">else</span> <span class="s">{</span>
+ 293       <span class="j">FIELDNAME:</span> <span class="k">for</span> <span class="i">$FieldName</span> <span class="s">(</span><span class="i">@DataFieldNames</span><span class="s">)</span> <span class="s">{</span>
+ 294           <span class="k">if</span> <span class="s">(</span><span class="i">$FieldName</span> =~ <span class="q">/Formula/i</span><span class="s">)</span> <span class="s">{</span>
+ 295             <span class="i">$FormulaFieldName</span> = <span class="i">$FieldName</span><span class="sc">;</span>
+ 296             <span class="k">last</span> <span class="j">FIELDNAME</span><span class="sc">;</span>
+ 297           <span class="s">}</span>
+ 298         <span class="s">}</span>
+ 299         <span class="k">if</span> <span class="s">(</span>!<span class="i">$FormulaFieldName</span><span class="s">)</span> <span class="s">{</span>
+ 300           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Data field label containing the word Formula doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+ 301           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 302         <span class="s">}</span>
+ 303       <span class="s">}</span>
+ 304     <span class="s">}</span>
+ 305     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+ 306     <span class="i">$SDFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="i">$OutFile</span><span class="sc">;</span>
+ 307     <span class="i">$SDFilesInfo</span>{<span class="w">FormulaFieldName</span>}[<span class="i">$Index</span>] = <span class="i">$FormulaFieldName</span><span class="sc">;</span>
+ 308 
+ 309     <span class="c"># Setup value data field names for calculated values...</span>
+ 310     <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%NewValueFieldNames</span><span class="s">)</span> <span class="s">{</span>
+ 311       <span class="i">$FieldName</span> = <span class="i">$NewValueFieldNames</span>{<span class="i">$Value</span>}<span class="sc">;</span>
+ 312 
+ 313       <span class="c"># Make sure it doesn&#39;t already exists...</span>
+ 314       <span class="i">$Count</span> = <span class="n">1</span><span class="sc">;</span>
+ 315       <span class="i">$NewFieldName</span> = <span class="i">$FieldName</span><span class="sc">;</span>
+ 316       <span class="k">while</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataFieldNamesMap</span>{<span class="i">$NewFieldName</span>}<span class="s">)</span> <span class="s">{</span>
+ 317         <span class="i">$Count</span>++<span class="sc">;</span>
+ 318         <span class="i">$NewFieldName</span> = <span class="i">$FieldName</span> . <span class="i">$Count</span><span class="sc">;</span>
+ 319       <span class="s">}</span>
+ 320       <span class="i">$SDFilesInfo</span>{<span class="w">ValueFieldNamesMap</span>}[<span class="i">$Index</span>]{<span class="i">$Value</span>} = <span class="i">$NewFieldName</span><span class="sc">;</span>
+ 321     <span class="s">}</span>
+ 322   <span class="s">}</span>
+ 323 <span class="s">}</span>
+ 324 
+ 325 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 326 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+ 327   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 328 
+ 329   <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+ 330   <span class="i">$OptionsInfo</span>{<span class="w">FormulaMode</span>} = <span class="i">$Options</span>{<span class="w">formulamode</span>}<span class="sc">;</span>
+ 331 
+ 332   <span class="i">$OptionsInfo</span>{<span class="w">WriteOutFormula</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">formulaout</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 333 
+ 334   <span class="i">$OptionsInfo</span>{<span class="w">UseStructureData</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">formulamode</span>} =~ <span class="q">/^StructureData$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 335   <span class="i">$OptionsInfo</span>{<span class="w">UseDataField</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">formulamode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 336 
+ 337   <span class="i">$OptionsInfo</span>{<span class="w">Fast</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="i">$Options</span>{<span class="w">fast</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 338 
+ 339   <span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span>
+ 340   <span class="i">$OptionsInfo</span>{<span class="w">CheckFormula</span>} = <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
+ 341   <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
+ 342 
+ 343   <span class="i">$OptionsInfo</span>{<span class="w">Overwrite</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="i">$Options</span>{<span class="w">overwrite</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 344 
+ 345   <span class="i">$OptionsInfo</span>{<span class="w">FormulaField</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">formulafield</span>} ? <span class="i">$Options</span>{<span class="w">formulafield</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 346   <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaFieldName</span>} = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+ 347 
+ 348   <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$Options</span>{<span class="w">formulafield</span>}<span class="s">)</span> <span class="s">{</span>
+ 349     <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaFieldName</span>} = <span class="i">$Options</span>{<span class="w">formulafield</span>}<span class="sc">;</span>
+ 350   <span class="s">}</span>
+ 351   <span class="c"># Setup what to calculate...</span>
+ 352   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 353   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+ 354     <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}} = <span class="q">qw(ElementalAnalysis MolecularWeight ExactMass)</span><span class="sc">;</span>
+ 355   <span class="s">}</span>
+ 356   <span class="k">else</span> <span class="s">{</span>
+ 357     <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$ModeValue</span><span class="cm">,</span> <span class="i">@SpecifiedModeValues</span><span class="s">)</span><span class="sc">;</span>
+ 358     <span class="i">$Mode</span> = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+ 359     <span class="i">$Mode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+ 360     <span class="i">@SpecifiedModeValues</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Mode</span><span class="sc">;</span>
+ 361     <span class="k">for</span> <span class="i">$ModeValue</span> <span class="s">(</span><span class="i">@SpecifiedModeValues</span><span class="s">)</span> <span class="s">{</span>
+ 362       <span class="k">if</span> <span class="s">(</span><span class="i">$ModeValue</span> !~ <span class="q">/^(ElementalAnalysis|MolecularWeight|ExactMass)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 363         <span class="k">if</span> <span class="s">(</span><span class="i">$ModeValue</span> =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+ 364           <span class="k">die</span> <span class="q">&quot;Error: All value for option \&quot;-m --mode\&quot; is not allowed with other valid values.\n&quot;</span><span class="sc">;</span>
+ 365         <span class="s">}</span>
+ 366         <span class="k">else</span> <span class="s">{</span>
+ 367           <span class="k">die</span> <span class="q">&quot;Error: The value specified, $ModeValue, for option \&quot;-m --mode\&quot; is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n&quot;</span><span class="sc">;</span>
+ 368         <span class="s">}</span>
+ 369       <span class="s">}</span>
+ 370       <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="cm">,</span> <span class="i">$ModeValue</span><span class="sc">;</span>
+ 371     <span class="s">}</span>
+ 372   <span class="s">}</span>
+ 373 
+ 374   <span class="i">$OptionsInfo</span>{<span class="w">ValueFieldNames</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">valuefieldnames</span>} ? <span class="i">$Options</span>{<span class="w">valuefieldnames</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 375   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueFieldNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 376 
+ 377   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">valuefieldnames</span>}<span class="s">)</span> <span class="s">{</span>
+ 378     <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="cm">,</span> <span class="i">$Label</span><span class="cm">,</span> <span class="i">@ValueLabels</span><span class="s">)</span><span class="sc">;</span>
+ 379     <span class="i">@ValueLabels</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">valuefieldnames</span>}<span class="sc">;</span>
+ 380     <span class="k">if</span> <span class="s">(</span><span class="i">@ValueLabels</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+ 381       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{valuefieldnames}, for option \&quot;-v --valuefieldnames\&quot; is not valid: It must contain even number of comma delimited values\n&quot;</span><span class="sc">;</span>
+ 382     <span class="s">}</span>
+ 383     <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
+ 384     <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> &lt; <span class="i">@ValueLabels</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+ 385       <span class="i">$Value</span> = <span class="i">$ValueLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 386       <span class="i">$Value</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+ 387       <span class="i">$Label</span> = <span class="i">$ValueLabels</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
+ 388       <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ElementalAnalysis|MolecularWeight|ExactMass|MolecularFormula)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 389         <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Value, using option \&quot;-v --valuefieldnames\&quot; is not valid. Allowed values: ElementalAnalysis, MolecularWeight, ExactMass, or MolecularFormula\n&quot;</span><span class="sc">;</span>
+ 390       <span class="s">}</span>
+ 391       <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueFieldNames</span>}}<span class="cm">,</span> <span class="s">(</span><span class="i">$Value</span><span class="cm">,</span> <span class="i">$Label</span><span class="s">)</span><span class="sc">;</span>
+ 392     <span class="s">}</span>
+ 393   <span class="s">}</span>
+ 394 <span class="s">}</span>
+ 395 
+ 396 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 397 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+ 398 
+ 399   <span class="c"># Retrieve all the options...</span>
+ 400   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 401   <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
+ 402   <span class="i">$Options</span>{<span class="w">formulamode</span>} = <span class="q">&quot;DataField&quot;</span><span class="sc">;</span>
+ 403   <span class="i">$Options</span>{<span class="w">formulaout</span>} = <span class="q">&quot;No&quot;</span><span class="sc">;</span>
+ 404   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&quot;All&quot;</span><span class="sc">;</span>
+ 405   <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span>
+ 406 
+ 407   <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;detail|d=i&quot;</span><span class="cm">,</span> <span class="q">&quot;fast&quot;</span><span class="cm">,</span> <span class="q">&quot;formulafield=s&quot;</span><span class="cm">,</span> <span class="q">&quot;formulamode|f=s&quot;</span><span class="cm">,</span> <span class="q">&quot;formulaout=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;precision|p=i&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;valuefieldnames|v=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 408     <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+ 409   <span class="s">}</span>
+ 410   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+ 411     <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>
+ 412       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+ 413     <span class="s">}</span>
+ 414     <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
+ 415   <span class="s">}</span>
+ 416   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 417     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{detail}, for option \&quot;-d --detail\&quot; is not valid. Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
+ 418   <span class="s">}</span>
+ 419   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">formulamode</span>} !~ <span class="q">/^(StructureData|DataField)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 420     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{formulamode}, for option \&quot;-f, --formulamode\&quot; is not valid. Allowed values: StructureData or DataField \n&quot;</span><span class="sc">;</span>
+ 421   <span class="s">}</span>
+ 422   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">formulaout</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 423     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{formulaout}, for option \&quot;--formulaout\&quot; is not valid. Allowed values: Yes or No \n&quot;</span><span class="sc">;</span>
+ 424   <span class="s">}</span>
+ 425   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 426     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{precision}, for option \&quot;-p --precision\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+ 427   <span class="s">}</span>
+ 428 <span class="s">}</span>
+ 429 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>