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1 <html>
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2 <head>
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3 <title>MayaChemTools:Code:SDToMolFiles.pl</title>
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4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
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5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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6 </head>
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7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
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8 <br/>
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9 <center>
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10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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11 </center>
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12 <br/>
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13 <pre>
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14 1 #!/usr/bin/perl -w
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: SDToMolFiles.pl,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
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18 5 <span class="c"># $Revision: 1.35 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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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">"$FindBin::Bin/../lib"</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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50 37
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51 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>
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52 39
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53 40 <span class="c"># Autoflush STDOUT</span>
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54 41 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
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55 42
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56 43 <span class="c"># Starting message...</span>
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57 44 <span class="i">$ScriptName</span> = <span class="w">basename</span> <span class="i">$0</span><span class="sc">;</span>
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58 45 <span class="k">print</span> <span class="q">"\n$ScriptName:Starting...\n\n"</span><span class="sc">;</span>
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59 46 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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60 47
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61 48 <span class="c"># Get the options and setup script...</span>
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62 49 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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63 50 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
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64 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>
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65 52 <span class="s">}</span>
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66 53
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67 54 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
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68 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>
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69 56
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70 57 <span class="c"># Process options...</span>
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71 58 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
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72 59 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
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73 60 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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74 61
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75 62 <span class="c"># Setup information about input files...</span>
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76 63 <span class="k">print</span> <span class="q">"Checking input SD file(s)...\n"</span><span class="sc">;</span>
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77 64 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
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78 65 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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79 66
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80 67 <span class="c"># Process input files..</span>
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81 68 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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82 69 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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83 70 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span>
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84 71 <span class="s">}</span>
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85 72 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
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86 73 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
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87 74 <span class="k">print</span> <span class="q">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
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88 75 <span class="i">GenerateMolFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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89 76 <span class="s">}</span>
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90 77 <span class="s">}</span>
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91 78 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
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92 79
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93 80 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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94 81 <span class="i">$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>
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95 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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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96 83
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97 84 <span class="c">###############################################################################</span>
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98 85
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99 86 <span class="c"># Generate MOL files for a SD file...</span>
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100 87 <span class="c">#</span>
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101 <a name="GenerateMolFiles-"></a> 88 <span class="k">sub </span><span class="m">GenerateMolFiles</span> <span class="s">{</span>
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102 89 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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103 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">$CmpdString</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldValues</span><span class="s">)</span><span class="sc">;</span>
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104 91
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105 92 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
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106 93
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107 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>
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108 95 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Couldn't open it: $! \n"</span><span class="sc">;</span>
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109 96 <span class="k">return</span><span class="sc">;</span>
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110 97 <span class="s">}</span>
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111 98
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112 99 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
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113 100 <span class="i">$MolEndDelimiter</span> = <span class="q">"M END"</span><span class="sc">;</span>
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114 101
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115 102 <span class="i">$OutFileRoot</span> = <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
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116 103 <span class="i">$OverwriteFiles</span> = <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="sc">;</span>
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117 104
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118 105 <span class="i">$UseDataField</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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119 106 <span class="i">$DataFieldName</span> = <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>}<span class="sc">;</span>
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120 107
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121 108 <span class="i">$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>
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122 109
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123 110 <span class="j">CMPDSTRING:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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124 111 <span class="i">$CmpdCount</span>++<span class="sc">;</span>
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125 112
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126 113 <span class="c"># Setup MOL file name...</span>
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127 114 <span class="i">$MOLFileRoot</span> = <span class="q">''</span><span class="sc">;</span>
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128 115 <span class="k">if</span> <span class="s">(</span><span class="i">$UseDataField</span><span class="s">)</span> <span class="s">{</span>
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129 116 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
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130 117 <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
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131 118 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$DataFieldName</span>}<span class="s">)</span> <span class="s">{</span>
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132 119 <span class="i">$MOLFileRoot</span> = <span class="i">$DataFieldValues</span>{<span class="i">$DataFieldName</span>}<span class="sc">;</span>
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133 120 <span class="s">}</span>
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134 121 <span class="s">}</span>
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135 122 <span class="k">elsif</span> <span class="s">(</span><span class="i">$UseMolName</span><span class="s">)</span> <span class="s">{</span>
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136 123 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
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137 124 <span class="i">$MOLFileRoot</span> = <span class="i">$CmpdLines</span>[<span class="n">0</span>]<span class="sc">;</span>
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138 125 <span class="s">}</span>
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139 126
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140 127 <span class="c"># Check for any invalid file name characters in data field or molname values...</span>
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141 128 <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>
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142 129 <span class="i">$MOLFileRoot</span> =~ <span class="q">s/[^a-zA-Z0-9_]//g</span><span class="sc">;</span>
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143 130 <span class="s">}</span>
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144 131 <span class="c"># Fall back plan for MOL file name...</span>
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145 132 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MOLFileRoot</span><span class="s">)</span> <span class="s">{</span>
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146 133 <span class="i">$MOLFileRoot</span> = <span class="q">"${OutFileRoot}Cmpd${CmpdCount}"</span><span class="sc">;</span>
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147 134 <span class="s">}</span>
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148 135
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149 136 <span class="i">$MOLFile</span> = <span class="q">"${MOLFileRoot}.mol"</span><span class="sc">;</span>
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150 137
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151 138 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OverwriteFiles</span><span class="s">)</span> <span class="s">{</span>
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152 139 <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>
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153 140 <span class="k">warn</span> <span class="q">"Warning: Ignoring compound number, $CmpdCount, in $SDFile: New MOL file, $MOLFile, already exists\n"</span><span class="sc">;</span>
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154 141 <span class="k">next</span> <span class="j">CMPDSTRING</span><span class="sc">;</span>
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155 142 <span class="s">}</span>
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156 143 <span class="s">}</span>
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157 144
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158 145 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$CmpdString</span> =~ <span class="q">/$MolEndDelimiter/</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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159 146 <span class="k">warn</span> <span class="q">"Warning: Ignoring compound number, $CmpdCount, in $SDFile: Invalid compound data\n"</span><span class="sc">;</span>
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160 147 <span class="k">next</span> <span class="j">CMPDSTRING</span><span class="sc">;</span>
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161 148 <span class="s">}</span>
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162 149
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163 150 <span class="c"># Write out MOL file...</span>
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164 151
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165 152 <span class="k">print</span> <span class="q">"Generating $MOLFile file...\n"</span><span class="sc">;</span>
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166 153 <span class="k">open</span> <span class="w">MOLFILE</span><span class="cm">,</span> <span class="q">">$MOLFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $MOLFile: $! \n"</span><span class="sc">;</span>
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167 154 <span class="s">(</span><span class="i">$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>
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168 155 <span class="k">print</span> <span class="i">MOLFILE</span> <span class="q">"$CmpdString"</span><span class="sc">;</span>
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169 156 <span class="k">print</span> <span class="i">MOLFILE</span> <span class="q">"$MolEndDelimiter\n"</span><span class="sc">;</span>
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170 157 <span class="k">close</span> <span class="w">MOLFILE</span><span class="sc">;</span>
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171 158
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172 159 <span class="s">}</span>
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173 160
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174 161 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
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175 162 <span class="s">}</span>
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176 163
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177 164 <span class="c"># Retrieve information about SD files...</span>
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178 165 <span class="c">#</span>
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179 <a name="RetrieveSDFilesInfo-"></a> 166 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
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180 167 <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>
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181 168
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182 169 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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183 170 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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184 171 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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185 172
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186 173 <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>
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187 174 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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188 175
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189 176 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
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190 177 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
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191 178
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192 179 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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193 180 <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>
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194 181 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span>
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195 182 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
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196 183 <span class="s">}</span>
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197 184 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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198 185 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span>
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199 186 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
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200 187 <span class="s">}</span>
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201 188
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202 189 <span class="c"># Setup output file root...</span>
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203 190 <span class="i">$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>
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204 191 <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>
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205 192
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206 193 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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207 194 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
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208 195 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
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209 196 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
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210 197 <span class="s">}</span>
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211 198 <span class="k">else</span> <span class="s">{</span>
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212 199 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
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213 200 <span class="s">}</span>
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214 201 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
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215 202 <span class="s">}</span>
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216 203 <span class="k">else</span> <span class="s">{</span>
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217 204 <span class="i">$OutFileRoot</span> = <span class="q">"$FileName"</span><span class="sc">;</span>
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218 205 <span class="s">}</span>
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219 206
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220 207 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
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221 208 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
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222 209 <span class="s">}</span>
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223 210 <span class="s">}</span>
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224 211
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225 212 <span class="c"># Process option values...</span>
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226 <a name="ProcessOptions-"></a> 213 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
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227 214 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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228 215
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229 216 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
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230 217
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231 218 <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>} = <span class="q">''</span><span class="sc">;</span>
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232 219 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
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233 220 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafield</span>}<span class="s">)</span> <span class="s">{</span>
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234 221 <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>
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235 222 <span class="s">}</span>
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236 223 <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>} = <span class="i">$Options</span>{<span class="w">datafield</span>}<span class="sc">;</span>
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237 224 <span class="s">}</span>
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238 225
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239 226 <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>
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240 227
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241 228 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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242 229 <span class="s">}</span>
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243 230
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244 231 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
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245 <a name="SetupScriptUsage-"></a> 232 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
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246 233
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247 234 <span class="c"># Retrieve all the options...</span>
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248 235 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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249 236
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250 237 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'RootPrefix'</span><span class="sc">;</span>
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251 238
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252 239 <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>
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253 240 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
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254 241 <span class="s">}</span>
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255 242 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
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256 243 <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>
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257 244 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
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258 245 <span class="s">}</span>
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259 246 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span>
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260 247 <span class="s">}</span>
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261 248
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262 249 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(DataField|MolName|RootPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
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263 250 <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>
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264 251 <span class="s">}</span>
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265 252 <span class="s">}</span>
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266 253
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267 <a name="EOF-"></a></pre>
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268 <p> </p>
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269 <br />
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270 <center>
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271 <img src="../../../images/h2o2.png">
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272 </center>
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273 </body>
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274 </html>
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