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1 <html>
2 <head>
3 <title>MayaChemTools:Code:ElementalAnalysisSDFiles.pl</title>
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
8 <br/>
9 <center>
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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13 <pre>
14 1 #!/usr/bin/perl -w
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: ElementalAnalysisSDFiles.pl,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
18 5 <span class="c"># $Revision: 1.24 $</span>
19 6 <span class="c">#</span>
20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
21 8 <span class="c">#</span>
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
23 10 <span class="c">#</span>
24 11 <span class="c"># This file is part of MayaChemTools.</span>
25 12 <span class="c">#</span>
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
29 16 <span class="c"># later version.</span>
30 17 <span class="c">#</span>
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
34 21 <span class="c"># details.</span>
35 22 <span class="c">#</span>
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
40 27 <span class="c">#</span>
41 28
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</span><span class="sc">;</span>
44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
49 36 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span>
50 37 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
51 38 <span class="k">use</span> <span class="w">MolecularFormula</span><span class="sc">;</span>
52 39 <span class="k">use</span> <span class="w">FileIO::SDFileIO</span><span class="sc">;</span>
53 40 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
54 41
55 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>
56 43
57 44 <span class="c"># Autoflush STDOUT</span>
58 45 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
59 46
60 47 <span class="c"># Starting message...</span>
61 48 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
62 49 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
63 50 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
64 51
65 52 <span class="c"># Get the options and setup script...</span>
66 53 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
67 54 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
68 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>
69 56 <span class="s">}</span>
70 57
71 58 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
72 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>
73 60
74 61 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
75 62 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
76 63 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
77 64
78 65 <span class="k">print</span> <span class="q">&quot;Checking input SD file(s)...\n&quot;</span><span class="sc">;</span>
79 66 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
80 67 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
81 68
82 69 <span class="c"># Generate output files...</span>
83 70 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
84 71 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
85 72 <span class="k">print</span> <span class="q">&quot;\nProcessing SD files...\n&quot;</span><span class="sc">;</span>
86 73 <span class="s">}</span>
87 74 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
88 75 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
89 76 <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
90 77 <span class="i">PerformElementalAnalysis</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
91 78 <span class="s">}</span>
92 79 <span class="s">}</span>
93 80 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
94 81
95 82 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
96 83 <span class="i">$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>
97 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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
98 85
99 86 <span class="c">###############################################################################</span>
100 87
101 88 <span class="c"># Perform analysis...</span>
102 <a name="PerformElementalAnalysis-"></a> 89 <span class="k">sub </span><span class="m">PerformElementalAnalysis</span> <span class="s">{</span>
103 90 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
104 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">$Molecule</span><span class="cm">,</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldValuesMap</span><span class="s">)</span><span class="sc">;</span>
105 92
106 93 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
107 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>
108 95
109 96 <span class="k">print</span> <span class="q">&quot;Generating new SD file $NewSDFile...\n&quot;</span><span class="sc">;</span>
110 97 <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewSDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $NewSDFile: $! \n&quot;</span><span class="sc">;</span>
111 98 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
112 99
113 100
114 101 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
115 102 <span class="i">$FormulaFieldName</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FormulaFieldName</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
116 103
117 104 <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$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>
118 105 <span class="i">$CmpdCount</span>++<span class="sc">;</span>
119 106 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
120 107 <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>
121 108
122 109 <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
123 110 <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>
124 111 <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
125 112 <span class="s">}</span>
126 113
127 114 <span class="i">$CurrentFormula</span> = <span class="k">undef</span><span class="sc">;</span>
128 115
129 116 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseStructureData</span>}<span class="s">)</span> <span class="s">{</span>
130 117 <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>
131 118 <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>
132 119 <span class="s">}</span>
133 120 <span class="k">else</span> <span class="s">{</span>
134 121 <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>
135 122 <span class="i">$ErrorMsg</span> = <span class="q">&quot;Ignoring compound record $CmpdCount: Formula field $FormulaFieldName not found&quot;</span><span class="sc">;</span>
136 123 <span class="i">PrintErrorMsg</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
137 124 <span class="i">WriteNewCompoundRecord</span><span class="s">(</span><span class="i">$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>
138 125 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
139 126 <span class="s">}</span>
140 127
141 128 <span class="c"># Make sure it&#39;s a valid molecular formula...</span>
142 129 <span class="i">$CurrentFormula</span> = <span class="i">$DataFieldValuesMap</span>{<span class="i">$FormulaFieldName</span>}<span class="sc">;</span>
143 130 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckFormula</span>}<span class="s">)</span> <span class="s">{</span>
144 131 <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">$CurrentFormula</span><span class="s">)</span><span class="sc">;</span>
145 132 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span>
146 133 <span class="i">$ErrorMsg</span> = <span class="q">&quot;Ignoring compound record $CmpdCount: Formula field value $CurrentFormula is not valid: $ErrorMsg&quot;</span><span class="sc">;</span>
147 134 <span class="i">PrintErrorMsg</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
148 135 <span class="i">WriteNewCompoundRecord</span><span class="s">(</span><span class="i">$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>
149 136 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
150 137 <span class="s">}</span>
151 138 <span class="s">}</span>
152 139 <span class="s">}</span>
153 140
154 141 <span class="c"># Calculate appropriate values and write &#39;em out...</span>
155 142 <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
156 143 <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>
157 144 <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>
158 145 <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">$CurrentFormula</span><span class="s">)</span><span class="sc">;</span>
159 146 <span class="i">$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">$OptionsInfo</span>{<span class="w">Precision</span>}<span class="s">)</span> <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
160 147 <span class="s">}</span>
161 148 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^MolecularWeight$/i</span><span class="s">)</span> <span class="s">{</span>
162 149 <span class="i">$CalculatedValue</span> = <span class="i">MolecularFormula::CalculateMolecularWeight</span><span class="s">(</span><span class="i">$CurrentFormula</span><span class="s">)</span><span class="sc">;</span>
163 150 <span class="i">$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>
164 151 <span class="s">}</span>
165 152 <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>
166 153 <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>
167 154 <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">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">&quot;&quot;</span><span class="sc">;</span>
168 155 <span class="s">}</span>
169 156 <span class="k">else</span> <span class="s">{</span>
170 157 <span class="i">$CalculatedValue</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
171 158 <span class="s">}</span>
172 159 <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="sc">;</span>
173 160 <span class="s">}</span>
174 161 <span class="i">WriteNewCompoundRecord</span><span class="s">(</span><span class="i">$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">$CurrentFormula</span><span class="s">)</span><span class="sc">;</span>
175 162 <span class="s">}</span>
176 163 <span class="k">close</span> <span class="w">NEWSDFILE</span><span class="sc">;</span>
177 164 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
178 165 <span class="s">}</span>
179 166
180 167 <span class="c"># Write out compound record with calculated values...</span>
181 <a name="WriteNewCompoundRecord-"></a> 168 <span class="k">sub </span><span class="m">WriteNewCompoundRecord</span> <span class="s">{</span>
182 169 <span class="k">my</span><span class="s">(</span><span class="i">$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>
183 170
184 171 <span class="c"># Write out compound lines except the last line which contains $$$$...</span>
185 172 <span class="k">my</span><span class="s">(</span><span class="i">$LineIndex</span><span class="s">)</span><span class="sc">;</span>
186 173 <span class="k">for</span> <span class="i">$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>
187 174 <span class="k">print</span> <span class="i">$SDFileRef</span> <span class="q">&quot;$CmpdLinesRef-&gt;[$LineIndex]\n&quot;</span><span class="sc">;</span>
188 175 <span class="s">}</span>
189 176
190 177 <span class="c"># Write out calculated values...</span>
191 178 <span class="k">my</span><span class="s">(</span><span class="i">$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>
192 179 <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">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="s">)</span> <span class="s">{</span>
193 180 <span class="i">$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>
194 181 <span class="i">$FieldValue</span> = <span class="i">$CalculatedValuesRef</span>-&gt;[<span class="i">$CalcIndex</span>]<span class="sc">;</span>
195 182 <span class="k">print</span> <span class="i">$SDFileRef</span> <span class="q">&quot;&gt; &lt;$FieldName&gt;\n$FieldValue\n\n&quot;</span><span class="sc">;</span>
196 183 <span class="s">}</span>
197 184
198 185 <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">$MolecularFormula</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
199 186 <span class="i">$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>
200 187 <span class="i">$FieldValue</span> = <span class="i">$MolecularFormula</span><span class="sc">;</span>
201 188 <span class="k">print</span> <span class="i">$SDFileRef</span> <span class="q">&quot;&gt; &lt;$FieldName&gt;\n$FieldValue\n\n&quot;</span><span class="sc">;</span>
202 189 <span class="s">}</span>
203 190
204 191 <span class="k">print</span> <span class="i">$SDFileRef</span> <span class="q">&quot;\$\$\$\$\n&quot;</span><span class="sc">;</span>
205 192 <span class="s">}</span>
206 193
207 194 <span class="c"># Print out error message...</span>
208 <a name="PrintErrorMsg-"></a> 195 <span class="k">sub </span><span class="m">PrintErrorMsg</span> <span class="s">{</span>
209 196 <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>
210 197
211 198 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
212 199 <span class="k">print</span> <span class="q">&quot;$ErrorMsg:\n$CmpdString\n&quot;</span><span class="sc">;</span>
213 200 <span class="s">}</span>
214 201 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
215 202 <span class="k">print</span> <span class="q">&quot;$ErrorMsg\n&quot;</span><span class="sc">;</span>
216 203 <span class="s">}</span>
217 204 <span class="s">}</span>
218 205
219 206 <span class="c"># Retrieve information about input SD files...</span>
220 <a name="RetrieveSDFilesInfo-"></a> 207 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
221 208 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Count</span><span class="s">)</span><span class="sc">;</span>
222 209
223 210 <span class="k">my</span><span class="s">(</span><span class="i">%NewValueFieldNames</span><span class="s">)</span> = <span class="s">(</span><span class="w">ElementalAnalysis</span> <span class="cm">=&gt;</span> <span class="q">&#39;ElementalAnalysis&#39;</span><span class="cm">,</span> <span class="w">MolecularWeight</span> <span class="cm">=&gt;</span> <span class="q">&#39;MolecularWeight&#39;</span><span class="cm">,</span> <span class="w">ExactMass</span> <span class="cm">=&gt;</span> <span class="q">&#39;ExactMass&#39;</span><span class="cm">,</span> <span class="w">MolecularFormula</span> <span class="cm">=&gt;</span> <span class="q">&#39;MolecularFormula&#39;</span><span class="s">)</span><span class="sc">;</span>
224 211 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueFieldNames</span>}}<span class="s">)</span> <span class="s">{</span>
225 212 <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>
226 213 <span class="i">$Value</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueFieldNames</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
227 214 <span class="i">$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>
228 215 <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>
229 216 <span class="i">$NewValueFieldNames</span>{<span class="i">$Value</span>} = <span class="i">$FieldName</span><span class="sc">;</span>
230 217 <span class="s">}</span>
231 218 <span class="s">}</span>
232 219 <span class="s">}</span>
233 220
234 221 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
235 222
236 223 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
237 224 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFile</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
238 225 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FormulaFieldName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
239 226 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">ValueFieldNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
240 227
241 228 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
242 229 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
243 230
244 231 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
245 232 <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>
246 233 <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>
247 234
248 235 <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>
249 236
250 237 <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>
251 238 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
252 239 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
253 240 <span class="s">}</span>
254 241 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$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>
255 242 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
256 243 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
257 244 <span class="s">}</span>
258 245 <span class="i">$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>
259 246 <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>
260 247 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>} &amp;&amp; <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
261 248 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span>
262 249 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
263 250 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
264 251 <span class="s">}</span>
265 252 <span class="k">else</span> <span class="s">{</span>
266 253 <span class="i">$FileName</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span>
267 254 <span class="s">}</span>
268 255 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
269 256 <span class="s">}</span>
270 257 <span class="k">else</span> <span class="s">{</span>
271 258 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span> . <span class="q">&quot;ElementalAnalysis&quot;</span><span class="sc">;</span>
272 259 <span class="s">}</span>
273 260
274 261 <span class="i">$OutFile</span> = <span class="i">$OutFileRoot</span> . <span class="q">&quot;.$FileExt&quot;</span><span class="sc">;</span>
275 262 <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>
276 263 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n&quot;</span><span class="sc">;</span>
277 264 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
278 265 <span class="s">}</span>
279 266 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
280 267 <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>
281 268 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $OutFile already exists\n&quot;</span><span class="sc">;</span>
282 269 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
283 270 <span class="s">}</span>
284 271 <span class="s">}</span>
285 272 <span class="c"># Get data field names and values...</span>
286 273 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$FieldName</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">@DataFieldNames</span><span class="cm">,</span> <span class="i">%DataFieldNamesMap</span><span class="s">)</span><span class="sc">;</span>
287 274 <span class="i">@DataFieldNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
288 275 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span><span class="s">(</span><span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
289 276 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
290 277 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
291 278 <span class="s">}</span>
292 279 <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
293 280 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
294 281
295 282 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
296 283 <span class="i">@DataFieldNames</span> = <span class="i">GetCmpdDataHeaderLabels</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
297 284 <span class="i">%DataFieldNamesMap</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
298 285
299 286 <span class="c"># Setup formula field name...</span>
300 287 <span class="i">$FormulaFieldName</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
301 288 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseDataField</span>}<span class="s">)</span> <span class="s">{</span>
302 289 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaFieldName</span>}<span class="s">)</span> <span class="s">{</span>
303 290 <span class="i">$FormulaFieldName</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaFieldName</span>}<span class="sc">;</span>
304 291 <span class="s">}</span>
305 292 <span class="k">else</span> <span class="s">{</span>
306 293 <span class="j">FIELDNAME:</span> <span class="k">for</span> <span class="i">$FieldName</span> <span class="s">(</span><span class="i">@DataFieldNames</span><span class="s">)</span> <span class="s">{</span>
307 294 <span class="k">if</span> <span class="s">(</span><span class="i">$FieldName</span> =~ <span class="q">/Formula/i</span><span class="s">)</span> <span class="s">{</span>
308 295 <span class="i">$FormulaFieldName</span> = <span class="i">$FieldName</span><span class="sc">;</span>
309 296 <span class="k">last</span> <span class="j">FIELDNAME</span><span class="sc">;</span>
310 297 <span class="s">}</span>
311 298 <span class="s">}</span>
312 299 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FormulaFieldName</span><span class="s">)</span> <span class="s">{</span>
313 300 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Data field label containing the word Formula doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
314 301 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
315 302 <span class="s">}</span>
316 303 <span class="s">}</span>
317 304 <span class="s">}</span>
318 305 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
319 306 <span class="i">$SDFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="i">$OutFile</span><span class="sc">;</span>
320 307 <span class="i">$SDFilesInfo</span>{<span class="w">FormulaFieldName</span>}[<span class="i">$Index</span>] = <span class="i">$FormulaFieldName</span><span class="sc">;</span>
321 308
322 309 <span class="c"># Setup value data field names for calculated values...</span>
323 310 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%NewValueFieldNames</span><span class="s">)</span> <span class="s">{</span>
324 311 <span class="i">$FieldName</span> = <span class="i">$NewValueFieldNames</span>{<span class="i">$Value</span>}<span class="sc">;</span>
325 312
326 313 <span class="c"># Make sure it doesn&#39;t already exists...</span>
327 314 <span class="i">$Count</span> = <span class="n">1</span><span class="sc">;</span>
328 315 <span class="i">$NewFieldName</span> = <span class="i">$FieldName</span><span class="sc">;</span>
329 316 <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>
330 317 <span class="i">$Count</span>++<span class="sc">;</span>
331 318 <span class="i">$NewFieldName</span> = <span class="i">$FieldName</span> . <span class="i">$Count</span><span class="sc">;</span>
332 319 <span class="s">}</span>
333 320 <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>
334 321 <span class="s">}</span>
335 322 <span class="s">}</span>
336 323 <span class="s">}</span>
337 324
338 325 <span class="c"># Process option values...</span>
339 <a name="ProcessOptions-"></a> 326 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
340 327 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
341 328
342 329 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
343 330 <span class="i">$OptionsInfo</span>{<span class="w">FormulaMode</span>} = <span class="i">$Options</span>{<span class="w">formulamode</span>}<span class="sc">;</span>
344 331
345 332 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
346 333
347 334 <span class="i">$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>
348 335 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
349 336
350 337 <span class="i">$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>
351 338
352 339 <span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span>
353 340 <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>
354 341 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
355 342
356 343 <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">$Options</span>{<span class="w">overwrite</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
357 344
358 345 <span class="i">$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>
359 346 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaFieldName</span>} = <span class="q">&quot;&quot;</span><span class="sc">;</span>
360 347
361 348 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$Options</span>{<span class="w">formulafield</span>}<span class="s">)</span> <span class="s">{</span>
362 349 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaFieldName</span>} = <span class="i">$Options</span>{<span class="w">formulafield</span>}<span class="sc">;</span>
363 350 <span class="s">}</span>
364 351 <span class="c"># Setup what to calculate...</span>
365 352 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
366 353 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
367 354 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}} = <span class="q">qw(ElementalAnalysis MolecularWeight ExactMass)</span><span class="sc">;</span>
368 355 <span class="s">}</span>
369 356 <span class="k">else</span> <span class="s">{</span>
370 357 <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>
371 358 <span class="i">$Mode</span> = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
372 359 <span class="i">$Mode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
373 360 <span class="i">@SpecifiedModeValues</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Mode</span><span class="sc">;</span>
374 361 <span class="k">for</span> <span class="i">$ModeValue</span> <span class="s">(</span><span class="i">@SpecifiedModeValues</span><span class="s">)</span> <span class="s">{</span>
375 362 <span class="k">if</span> <span class="s">(</span><span class="i">$ModeValue</span> !~ <span class="q">/^(ElementalAnalysis|MolecularWeight|ExactMass)$/i</span><span class="s">)</span> <span class="s">{</span>
376 363 <span class="k">if</span> <span class="s">(</span><span class="i">$ModeValue</span> =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
377 364 <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>
378 365 <span class="s">}</span>
379 366 <span class="k">else</span> <span class="s">{</span>
380 367 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $ModeValue, for option \&quot;-m --mode\&quot; is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n&quot;</span><span class="sc">;</span>
381 368 <span class="s">}</span>
382 369 <span class="s">}</span>
383 370 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="cm">,</span> <span class="i">$ModeValue</span><span class="sc">;</span>
384 371 <span class="s">}</span>
385 372 <span class="s">}</span>
386 373
387 374 <span class="i">$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>
388 375 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueFieldNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
389 376
390 377 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">valuefieldnames</span>}<span class="s">)</span> <span class="s">{</span>
391 378 <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>
392 379 <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>
393 380 <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>
394 381 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{valuefieldnames}, for option \&quot;-v --valuefieldnames\&quot; is not valid: It must contain even number of comma delimited values\n&quot;</span><span class="sc">;</span>
395 382 <span class="s">}</span>
396 383 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
397 384 <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">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
398 385 <span class="i">$Value</span> = <span class="i">$ValueLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span>
399 386 <span class="i">$Value</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
400 387 <span class="i">$Label</span> = <span class="i">$ValueLabels</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
401 388 <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>
402 389 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Value, using option \&quot;-v --valuefieldnames\&quot; is not valid. Allowed values: ElementalAnalysis, MolecularWeight, ExactMass, or MolecularFormula\n&quot;</span><span class="sc">;</span>
403 390 <span class="s">}</span>
404 391 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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>
405 392 <span class="s">}</span>
406 393 <span class="s">}</span>
407 394 <span class="s">}</span>
408 395
409 396 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
410 <a name="SetupScriptUsage-"></a> 397 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
411 398
412 399 <span class="c"># Retrieve all the options...</span>
413 400 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
414 401 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
415 402 <span class="i">$Options</span>{<span class="w">formulamode</span>} = <span class="q">&quot;DataField&quot;</span><span class="sc">;</span>
416 403 <span class="i">$Options</span>{<span class="w">formulaout</span>} = <span class="q">&quot;No&quot;</span><span class="sc">;</span>
417 404 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&quot;All&quot;</span><span class="sc">;</span>
418 405 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span>
419 406
420 407 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;detail|d=i&quot;</span><span class="cm">,</span> <span class="q">&quot;fast&quot;</span><span class="cm">,</span> <span class="q">&quot;formulafield=s&quot;</span><span class="cm">,</span> <span class="q">&quot;formulamode|f=s&quot;</span><span class="cm">,</span> <span class="q">&quot;formulaout=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;precision|p=i&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;valuefieldnames|v=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
421 408 <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
422 409 <span class="s">}</span>
423 410 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
424 411 <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>
425 412 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
426 413 <span class="s">}</span>
427 414 <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
428 415 <span class="s">}</span>
429 416 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
430 417 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{detail}, for option \&quot;-d --detail\&quot; is not valid. Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
431 418 <span class="s">}</span>
432 419 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">formulamode</span>} !~ <span class="q">/^(StructureData|DataField)$/i</span><span class="s">)</span> <span class="s">{</span>
433 420 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{formulamode}, for option \&quot;-f, --formulamode\&quot; is not valid. Allowed values: StructureData or DataField \n&quot;</span><span class="sc">;</span>
434 421 <span class="s">}</span>
435 422 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">formulaout</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
436 423 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{formulaout}, for option \&quot;--formulaout\&quot; is not valid. Allowed values: Yes or No \n&quot;</span><span class="sc">;</span>
437 424 <span class="s">}</span>
438 425 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
439 426 <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>
440 427 <span class="s">}</span>
441 428 <span class="s">}</span>
442 429
443 <a name="EOF-"></a></pre>
444 <p>&nbsp;</p>
445 <br />
446 <center>
447 <img src="../../../images/h2o2.png">
448 </center>
449 </body>
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