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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"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> 1 #!/usr/bin/perl -w 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: ElementalAnalysisSDFiles.pl,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span> 5 <span class="c"># $Revision: 1.24 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</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">$0</span><span class="s">)</span><span class="sc">;</span> 49 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</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> < <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">"$FindBin::Bin/$ScriptName"</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">"sdf sd"</span><span class="s">)</span><span class="sc">;</span> 60 61 <span class="k">print</span> <span class="q">"Processing options...\n"</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">"Checking input SD file(s)...\n"</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">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 71 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 72 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span> 73 <span class="s">}</span> 74 <span class="k">for</span> <span class="i">$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">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span> 77 <span class="i">PerformElementalAnalysis</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 78 <span class="s">}</span> 79 <span class="s">}</span> 80 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</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">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 85 86 <span class="c">###############################################################################</span> 87 88 <span class="c"># Perform analysis...</span> <a name="PerformElementalAnalysis-"></a> 89 <span class="k">sub </span><span class="m">PerformElementalAnalysis</span> <span class="s">{</span> 90 <span class="k">my</span><span class="s">(</span><span class="i">$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">"Generating new SD file $NewSDFile...\n"</span><span class="sc">;</span> 97 <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">">$NewSDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewSDFile: $! \n"</span><span class="sc">;</span> 98 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $SDFile: $! \n"</span><span class="sc">;</span> 99 100 101 <span class="i">$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">$CmpdCount</span>++<span class="sc">;</span> 106 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$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">''</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">->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">"Ignoring compound record $CmpdCount: Formula field $FormulaFieldName not found"</span><span class="sc">;</span> 123 <span class="i">PrintErrorMsg</span><span class="s">(</span><span class="i">$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'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">"Ignoring compound record $CmpdCount: Formula field value $CurrentFormula is not valid: $ErrorMsg"</span><span class="sc">;</span> 134 <span class="i">PrintErrorMsg</span><span class="s">(</span><span class="i">$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 '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">$ElementsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">Precision</span>}<span class="s">)</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> 147 <span class="s">}</span> 148 <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">$CalculatedValue</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$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">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">""</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> && <span class="k">length</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">""</span><span class="sc">;</span> 155 <span class="s">}</span> 156 <span class="k">else</span> <span class="s">{</span> 157 <span class="i">$CalculatedValue</span> = <span class="q">''</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">$SDFileRef</span> <span class="q">"$CmpdLinesRef->[$LineIndex]\n"</span><span class="sc">;</span> 175 <span class="s">}</span> 176 177 <span class="c"># Write out calculated values...</span> 178 <span class="k">my</span><span class="s">(</span><span class="i">$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>->[<span class="i">$CalcIndex</span>]<span class="sc">;</span> 182 <span class="k">print</span> <span class="i">$SDFileRef</span> <span class="q">"> <$FieldName>\n$FieldValue\n\n"</span><span class="sc">;</span> 183 <span class="s">}</span> 184 185 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseStructureData</span>} && <span class="i">$OptionsInfo</span>{<span class="w">WriteOutFormula</span>} && <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">$SDFileRef</span> <span class="q">"> <$FieldName>\n$FieldValue\n\n"</span><span class="sc">;</span> 189 <span class="s">}</span> 190 191 <span class="k">print</span> <span class="i">$SDFileRef</span> <span class="q">"\$\$\$\$\n"</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">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span> <span class="s">)</span> <span class="s">{</span> 199 <span class="k">print</span> <span class="q">"$ErrorMsg:\n$CmpdString\n"</span><span class="sc">;</span> 200 <span class="s">}</span> 201 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 202 <span class="k">print</span> <span class="q">"$ErrorMsg\n"</span><span class="sc">;</span> 203 <span class="s">}</span> 204 <span class="s">}</span> 205 206 <span class="c"># Retrieve information about input SD files...</span> <a name="RetrieveSDFilesInfo-"></a> 207 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span> 208 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Count</span><span class="s">)</span><span class="sc">;</span> 209 210 <span class="k">my</span><span class="s">(</span><span class="i">%NewValueFieldNames</span><span class="s">)</span> = <span class="s">(</span><span class="w">ElementalAnalysis</span> <span class="cm">=></span> <span class="q">'ElementalAnalysis'</span><span class="cm">,</span> <span class="w">MolecularWeight</span> <span class="cm">=></span> <span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="w">ExactMass</span> <span class="cm">=></span> <span class="q">'ExactMass'</span><span class="cm">,</span> <span class="w">MolecularFormula</span> <span class="cm">=></span> <span class="q">'MolecularFormula'</span><span class="s">)</span><span class="sc">;</span> 211 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$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> < <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">''</span><span class="sc">;</span> 233 <span class="i">$SDFilesInfo</span>{<span class="w">FormulaFieldName</span>}[<span class="i">$Index</span>] = <span class="q">''</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">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span> 239 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 240 <span class="s">}</span> 241 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 242 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span> 243 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 244 <span class="s">}</span> 245 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</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">$Options</span>{<span class="w">root</span>} && <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 248 <span class="k">my</span> <span class="s">(</span><span class="i">$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> && <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">$FileName</span> . <span class="q">"ElementalAnalysis"</span><span class="sc">;</span> 259 <span class="s">}</span> 260 261 <span class="i">$OutFile</span> = <span class="i">$OutFileRoot</span> . <span class="q">".$FileExt"</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">"Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n"</span><span class="sc">;</span> 264 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 265 <span class="s">}</span> 266 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">"Warning: Ignoring file $SDFile: The file $OutFile already exists\n"</span><span class="sc">;</span> 269 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 270 <span class="s">}</span> 271 <span class="s">}</span> 272 <span class="c"># Get data field names and values...</span> 273 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$FieldName</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">@DataFieldNames</span><span class="cm">,</span> <span class="i">%DataFieldNamesMap</span><span class="s">)</span><span class="sc">;</span> 274 <span class="i">@DataFieldNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 275 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span><span class="s">(</span><span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 276 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Couldn't open it: $! \n"</span><span class="sc">;</span> 277 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 278 <span class="s">}</span> 279 <span class="i">$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">"\n"</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">''</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">"Warning: Ignoring file $SDFile: Data field label containing the word Formula doesn't exist\n"</span><span class="sc">;</span> 301 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 302 <span class="s">}</span> 303 <span class="s">}</span> 304 <span class="s">}</span> 305 <span class="i">$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">$Value</span>}<span class="sc">;</span> 312 313 <span class="c"># Make sure it doesn't already exists...</span> 314 <span class="i">$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">$OptionsInfo</span>{<span class="w">SpecifiedFormulaFieldName</span>} = <span class="q">""</span><span class="sc">;</span> 347 348 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$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">"Error: All value for option \"-m --mode\" is not allowed with other valid values.\n"</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">"Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n"</span><span class="sc">;</span> 368 <span class="s">}</span> 369 <span class="s">}</span> 370 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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">"Error: The value specified, $Options{valuefieldnames}, for option \"-v --valuefieldnames\" is not valid: It must contain even number of comma delimited values\n"</span><span class="sc">;</span> 382 <span class="s">}</span> 383 <span class="k">my</span><span class="s">(</span><span class="i">$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> < <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">"Error: The value specified, $Value, using option \"-v --valuefieldnames\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, ExactMass, or MolecularFormula\n"</span><span class="sc">;</span> 390 <span class="s">}</span> 391 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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">"DataField"</span><span class="sc">;</span> 403 <span class="i">$Options</span>{<span class="w">formulaout</span>} = <span class="q">"No"</span><span class="sc">;</span> 404 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">"All"</span><span class="sc">;</span> 405 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span> 406 407 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"detail|d=i"</span><span class="cm">,</span> <span class="q">"fast"</span><span class="cm">,</span> <span class="q">"formulafield=s"</span><span class="cm">,</span> <span class="q">"formulamode|f=s"</span><span class="cm">,</span> <span class="q">"formulaout=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"precision|p=i"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"valuefieldnames|v=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 408 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> 409 <span class="s">}</span> 410 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> 413 <span class="s">}</span> 414 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span> 415 <span class="s">}</span> 416 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n"</span><span class="sc">;</span> 418 <span class="s">}</span> 419 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{formulamode}, for option \"-f, --formulamode\" is not valid. Allowed values: StructureData or DataField \n"</span><span class="sc">;</span> 421 <span class="s">}</span> 422 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{formulaout}, for option \"--formulaout\" is not valid. Allowed values: Yes or No \n"</span><span class="sc">;</span> 424 <span class="s">}</span> 425 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> 427 <span class="s">}</span> 428 <span class="s">}</span> 429 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>