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<html> <head> <title>MayaChemTools:Code:SDToMolFiles.pl</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> 1 #!/usr/bin/perl -w 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: SDToMolFiles.pl,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span> 5 <span class="c"># $Revision: 1.35 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$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">SDFileUtil</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> 37 38 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span> 39 40 <span class="c"># Autoflush STDOUT</span> 41 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> 42 43 <span class="c"># Starting message...</span> 44 <span class="i">$ScriptName</span> = <span class="w">basename</span> <span class="i">$0</span><span class="sc">;</span> 45 <span class="k">print</span> <span class="q">"\n$ScriptName:Starting...\n\n"</span><span class="sc">;</span> 46 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 47 48 <span class="c"># Get the options and setup script...</span> 49 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 50 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 51 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span> 52 <span class="s">}</span> 53 54 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span> 55 <span class="i">@SDFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"sdf sd"</span><span class="s">)</span><span class="sc">;</span> 56 57 <span class="c"># Process options...</span> 58 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> 59 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> 60 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 61 62 <span class="c"># Setup information about input files...</span> 63 <span class="k">print</span> <span class="q">"Checking input SD file(s)...\n"</span><span class="sc">;</span> 64 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span> 65 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 66 67 <span class="c"># Process input files..</span> 68 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 69 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 70 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span> 71 <span class="s">}</span> 72 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span> 73 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> 74 <span class="k">print</span> <span class="q">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span> 75 <span class="i">GenerateMolFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 76 <span class="s">}</span> 77 <span class="s">}</span> 78 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> 79 80 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 81 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span> 82 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 83 84 <span class="c">###############################################################################</span> 85 86 <span class="c"># Generate MOL files for a SD file...</span> 87 <span class="c">#</span> <a name="GenerateMolFiles-"></a> 88 <span class="k">sub </span><span class="m">GenerateMolFiles</span> <span class="s">{</span> 89 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 90 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$MOLFile</span><span class="cm">,</span> <span class="i">$MOLFileRoot</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OverwriteFiles</span><span class="cm">,</span> <span class="i">$UseDataField</span><span class="cm">,</span> <span class="i">$DataFieldName</span><span class="cm">,</span> <span class="i">$UseMolName</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$MolEndDelimiter</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldValues</span><span class="s">)</span><span class="sc">;</span> 91 92 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> 93 94 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span><span class="s">)</span> <span class="s">{</span> 95 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Couldn't open it: $! \n"</span><span class="sc">;</span> 96 <span class="k">return</span><span class="sc">;</span> 97 <span class="s">}</span> 98 99 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span> 100 <span class="i">$MolEndDelimiter</span> = <span class="q">"M END"</span><span class="sc">;</span> 101 102 <span class="i">$OutFileRoot</span> = <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 103 <span class="i">$OverwriteFiles</span> = <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="sc">;</span> 104 105 <span class="i">$UseDataField</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 106 <span class="i">$DataFieldName</span> = <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>}<span class="sc">;</span> 107 108 <span class="i">$UseMolName</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^MolName$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 109 110 <span class="j">CMPDSTRING:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 111 <span class="i">$CmpdCount</span>++<span class="sc">;</span> 112 113 <span class="c"># Setup MOL file name...</span> 114 <span class="i">$MOLFileRoot</span> = <span class="q">''</span><span class="sc">;</span> 115 <span class="k">if</span> <span class="s">(</span><span class="i">$UseDataField</span><span class="s">)</span> <span class="s">{</span> 116 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span> 117 <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span> 118 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$DataFieldName</span>}<span class="s">)</span> <span class="s">{</span> 119 <span class="i">$MOLFileRoot</span> = <span class="i">$DataFieldValues</span>{<span class="i">$DataFieldName</span>}<span class="sc">;</span> 120 <span class="s">}</span> 121 <span class="s">}</span> 122 <span class="k">elsif</span> <span class="s">(</span><span class="i">$UseMolName</span><span class="s">)</span> <span class="s">{</span> 123 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span> 124 <span class="i">$MOLFileRoot</span> = <span class="i">$CmpdLines</span>[<span class="n">0</span>]<span class="sc">;</span> 125 <span class="s">}</span> 126 127 <span class="c"># Check for any invalid file name characters in data field or molname values...</span> 128 <span class="k">if</span> <span class="s">(</span><span class="i">$MOLFileRoot</span> && <span class="i">$MOLFileRoot</span> =~ <span class="q">/[^a-zA-Z0-9_]/</span><span class="s">)</span> <span class="s">{</span> 129 <span class="i">$MOLFileRoot</span> =~ <span class="q">s/[^a-zA-Z0-9_]//g</span><span class="sc">;</span> 130 <span class="s">}</span> 131 <span class="c"># Fall back plan for MOL file name...</span> 132 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MOLFileRoot</span><span class="s">)</span> <span class="s">{</span> 133 <span class="i">$MOLFileRoot</span> = <span class="q">"${OutFileRoot}Cmpd${CmpdCount}"</span><span class="sc">;</span> 134 <span class="s">}</span> 135 136 <span class="i">$MOLFile</span> = <span class="q">"${MOLFileRoot}.mol"</span><span class="sc">;</span> 137 138 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OverwriteFiles</span><span class="s">)</span> <span class="s">{</span> 139 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$MOLFile</span><span class="s">)</span> <span class="s">{</span> 140 <span class="k">warn</span> <span class="q">"Warning: Ignoring compound number, $CmpdCount, in $SDFile: New MOL file, $MOLFile, already exists\n"</span><span class="sc">;</span> 141 <span class="k">next</span> <span class="j">CMPDSTRING</span><span class="sc">;</span> 142 <span class="s">}</span> 143 <span class="s">}</span> 144 145 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$CmpdString</span> =~ <span class="q">/$MolEndDelimiter/</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 146 <span class="k">warn</span> <span class="q">"Warning: Ignoring compound number, $CmpdCount, in $SDFile: Invalid compound data\n"</span><span class="sc">;</span> 147 <span class="k">next</span> <span class="j">CMPDSTRING</span><span class="sc">;</span> 148 <span class="s">}</span> 149 150 <span class="c"># Write out MOL file...</span> 151 152 <span class="k">print</span> <span class="q">"Generating $MOLFile file...\n"</span><span class="sc">;</span> 153 <span class="k">open</span> <span class="w">MOLFILE</span><span class="cm">,</span> <span class="q">">$MOLFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $MOLFile: $! \n"</span><span class="sc">;</span> 154 <span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span> = <span class="k">split</span> <span class="q">"$MolEndDelimiter"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span> 155 <span class="k">print</span> <span class="i">MOLFILE</span> <span class="q">"$CmpdString"</span><span class="sc">;</span> 156 <span class="k">print</span> <span class="i">MOLFILE</span> <span class="q">"$MolEndDelimiter\n"</span><span class="sc">;</span> 157 <span class="k">close</span> <span class="w">MOLFILE</span><span class="sc">;</span> 158 159 <span class="s">}</span> 160 161 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> 162 <span class="s">}</span> 163 164 <span class="c"># Retrieve information about SD files...</span> 165 <span class="c">#</span> <a name="RetrieveSDFilesInfo-"></a> 166 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span> 167 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="s">)</span><span class="sc">;</span> 168 169 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 170 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 171 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 172 173 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span> 174 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 175 176 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> 177 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 178 179 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 180 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 181 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span> 182 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 183 <span class="s">}</span> 184 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 185 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span> 186 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 187 <span class="s">}</span> 188 189 <span class="c"># Setup output file root...</span> 190 <span class="i">$FileDir</span> = <span class="q">""</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> 191 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span> 192 193 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 194 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> 195 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> 196 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> 197 <span class="s">}</span> 198 <span class="k">else</span> <span class="s">{</span> 199 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> 200 <span class="s">}</span> 201 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> 202 <span class="s">}</span> 203 <span class="k">else</span> <span class="s">{</span> 204 <span class="i">$OutFileRoot</span> = <span class="q">"$FileName"</span><span class="sc">;</span> 205 <span class="s">}</span> 206 207 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> 208 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> 209 <span class="s">}</span> 210 <span class="s">}</span> 211 212 <span class="c"># Process option values...</span> <a name="ProcessOptions-"></a> 213 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> 214 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 215 216 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> 217 218 <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>} = <span class="q">''</span><span class="sc">;</span> 219 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span> 220 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafield</span>}<span class="s">)</span> <span class="s">{</span> 221 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"-d, --DataField\" option in \"DataField\" \"-m, --mode\". \n"</span><span class="sc">;</span> 222 <span class="s">}</span> 223 <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>} = <span class="i">$Options</span>{<span class="w">datafield</span>}<span class="sc">;</span> 224 <span class="s">}</span> 225 226 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 227 228 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 229 <span class="s">}</span> 230 231 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> <a name="SetupScriptUsage-"></a> 232 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> 233 234 <span class="c"># Retrieve all the options...</span> 235 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 236 237 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'RootPrefix'</span><span class="sc">;</span> 238 239 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"datafield|d=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"root|r=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> 240 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> 241 <span class="s">}</span> 242 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 243 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 244 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> 245 <span class="s">}</span> 246 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span> 247 <span class="s">}</span> 248 249 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(DataField|MolName|RootPrefix)$/i</span><span class="s">)</span> <span class="s">{</span> 250 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: DataField, MolName, RootPrefix\n"</span><span class="sc">;</span> 251 <span class="s">}</span> 252 <span class="s">}</span> 253 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>