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1 <html>
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2 <head>
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3 <title>MayaChemTools:Code:InfoSDFiles.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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8 <br/>
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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: InfoSDFiles.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">Benchmark</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">TextUtil</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="cm">,</span> <span class="i">%SDCmpdsInfo</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 <span class="i">InitializeSDCmpdsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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80 67
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81 68 <span class="c"># Process input files..</span>
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82 69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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83 70 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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84 71 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span>
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85 72 <span class="s">}</span>
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86 73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
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87 74 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
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88 75 <span class="k">print</span> <span class="q">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
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89 76 <span class="i">ListSDFileInfo</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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90 77 <span class="s">}</span>
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91 78 <span class="s">}</span>
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92 79 <span class="i">ListTotalSizeOfFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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93 80
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94 81 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
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95 82
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96 83 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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97 84 <span class="i">$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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98 85 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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99 86
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100 87 <span class="c">###############################################################################</span>
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101 88
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102 89 <span class="c"># List appropriate information...</span>
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103 <a name="ListSDFileInfo-"></a> 90 <span class="k">sub </span><span class="m">ListSDFileInfo</span> <span class="s">{</span>
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104 91 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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105 92 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
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106 93
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107 94 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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108 95
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109 96 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ProcessCmpdInfo</span>}<span class="s">)</span> <span class="s">{</span>
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110 97 <span class="i">ListCompoundDetailsInfo</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
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111 98 <span class="s">}</span>
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112 99 <span class="k">else</span> <span class="s">{</span>
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113 100 <span class="i">ListCompoundCountInfo</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
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114 101 <span class="s">}</span>
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115 102
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116 103 <span class="c"># File size and modification information...</span>
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117 104 <span class="k">print</span> <span class="q">"\nFile size: "</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="s">)</span><span class="cm">,</span> <span class="q">" \n"</span><span class="sc">;</span>
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118 105 <span class="k">print</span> <span class="q">"Last modified: "</span><span class="cm">,</span> <span class="i">$SDFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>]<span class="cm">,</span> <span class="q">" \n"</span><span class="sc">;</span>
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119 106 <span class="s">}</span>
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120 107
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121 108 <span class="c"># List number of compounds in SD file...</span>
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122 <a name="ListCompoundCountInfo-"></a> 109 <span class="k">sub </span><span class="m">ListCompoundCountInfo</span> <span class="s">{</span>
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123 110 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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124 111 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
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125 112
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126 113 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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127 114
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128 115 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
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129 116
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130 117 <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">"Couldn't open $SDFile: $! \n"</span><span class="sc">;</span>
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131 118 <span class="k">while</span> <span class="s">(</span><span class="q"><SDFILE></span><span class="s">)</span> <span class="s">{</span>
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132 119 <span class="k">if</span> <span class="s">(</span><span class="q">/^\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span>
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133 120 <span class="i">$CmpdCount</span>++<span class="sc">;</span>
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134 121 <span class="s">}</span>
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135 122 <span class="s">}</span>
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136 123 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
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137 124
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138 125 <span class="i">$SDCmpdsInfo</span>{<span class="w">TotalCmpdCount</span>} += <span class="i">$CmpdCount</span><span class="sc">;</span>
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139 126
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140 127 <span class="k">print</span> <span class="q">"\nNumber of compounds: $CmpdCount\n"</span><span class="sc">;</span>
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141 128 <span class="s">}</span>
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142 129
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143 130 <span class="c"># List detailed compound information...</span>
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144 <a name="ListCompoundDetailsInfo-"></a> 131 <span class="k">sub </span><span class="m">ListCompoundDetailsInfo</span> <span class="s">{</span>
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145 132 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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146 133 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$EmptyCtabBlocksCount</span><span class="cm">,</span> <span class="i">$MismatchCtabBlockCount</span><span class="cm">,</span> <span class="i">$ChiralCtabBlockCount</span><span class="cm">,</span> <span class="i">$UnknownAtomsCtabBlockCount</span><span class="cm">,</span> <span class="i">$InvalidAtomNumbersCtabBlockCount</span><span class="cm">,</span> <span class="i">$SaltsCtabBlockCount</span><span class="cm">,</span> <span class="i">$CtabLinesCount</span><span class="cm">,</span> <span class="i">$PrintCmpdCounterHeader</span><span class="cm">,</span> <span class="i">$ProblematicCmpdData</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
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147 134
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148 135 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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149 136
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150 137 <span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$EmptyCtabBlocksCount</span><span class="cm">,</span> <span class="i">$MismatchCtabBlockCount</span><span class="cm">,</span> <span class="i">$ChiralCtabBlockCount</span><span class="cm">,</span> <span class="i">$UnknownAtomsCtabBlockCount</span><span class="cm">,</span> <span class="i">$InvalidAtomNumbersCtabBlockCount</span><span class="cm">,</span> <span class="i">$SaltsCtabBlockCount</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="s">)</span> x <span class="n">7</span><span class="sc">;</span>
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151 138
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152 139 <span class="i">InitializeSDCmpdsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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153 140
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154 141 <span class="i">$PrintCmpdCounterHeader</span> = <span class="n">1</span><span class="sc">;</span>
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155 142
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156 143 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $SDFile: $! \n"</span><span class="sc">;</span>
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157 144 <span class="k">while</span> <span class="s">(</span><span class="i">$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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158 145 <span class="i">$CmpdCount</span>++<span class="sc">;</span>
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159 146 <span class="i">$ProblematicCmpdData</span> = <span class="n">0</span><span class="sc">;</span>
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160 147 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} <= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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161 148 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$CmpdCount</span> % <span class="n">5000</span><span class="s">)</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
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162 149 <span class="k">if</span> <span class="s">(</span><span class="i">$PrintCmpdCounterHeader</span><span class="s">)</span> <span class="s">{</span>
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163 150 <span class="i">$PrintCmpdCounterHeader</span> = <span class="n">0</span><span class="sc">;</span>
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164 151 <span class="k">print</span> <span class="q">"Processing compounds:"</span><span class="sc">;</span>
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165 152 <span class="s">}</span>
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166 153 <span class="k">print</span> <span class="q">"$CmpdCount..."</span><span class="sc">;</span>
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167 154 <span class="s">}</span>
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168 155 <span class="s">}</span>
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169 156 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
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170 157 <span class="i">$CtabLinesCount</span> = <span class="i">GetCtabLinesCount</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
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171 158 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Empty</span>}<span class="s">)</span> <span class="s">{</span>
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172 159 <span class="k">if</span> <span class="s">(</span><span class="i">$CtabLinesCount</span> <= <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
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173 160 <span class="i">$EmptyCtabBlocksCount</span>++<span class="sc">;</span>
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174 161 <span class="i">$ProblematicCmpdData</span> = <span class="n">1</span><span class="sc">;</span>
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175 162 <span class="s">}</span>
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176 163 <span class="s">}</span>
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177 164 <span class="k">if</span> <span class="s">(</span><span class="i">$CtabLinesCount</span> > <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
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178 165 <span class="k">my</span> <span class="s">(</span><span class="i">$AtomCount</span><span class="cm">,</span> <span class="i">$BondCount</span><span class="cm">,</span> <span class="i">$ChiralFlag</span><span class="s">)</span> = <span class="i">ParseCmpdCountsLine</span><span class="s">(</span><span class="i">$CmpdLines</span>[<span class="n">3</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
179 166 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Mismatch</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
180 167 <span class="k">if</span> <span class="s">(</span><span class="i">$CtabLinesCount</span> != <span class="s">(</span><span class="i">$AtomCount</span> + <span class="i">$BondCount</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
181 168 <span class="i">$MismatchCtabBlockCount</span>++<span class="sc">;</span>
|
|
|
182 169 <span class="i">$ProblematicCmpdData</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
183 170 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
184 171 <span class="k">print</span> <span class="q">"\nMismatch found: Ctab lines count: $CtabLinesCount; Atoms count: $AtomCount; Bond count: $BondCount\n"</span><span class="sc">;</span>
|
|
|
185 172 <span class="s">}</span>
|
|
|
186 173 <span class="s">}</span>
|
|
|
187 174 <span class="s">}</span>
|
|
|
188 175 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Chiral</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
189 176 <span class="k">if</span> <span class="s">(</span><span class="i">$ChiralFlag</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
190 177 <span class="i">$ChiralCtabBlockCount</span>++<span class="sc">;</span>
|
|
|
191 178 <span class="s">}</span>
|
|
|
192 179 <span class="s">}</span>
|
|
|
193 180 <span class="k">if</span> <span class="s">(</span><span class="i">$CtabLinesCount</span> == <span class="s">(</span><span class="i">$AtomCount</span> + <span class="i">$BondCount</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
194 181 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">UnknownAtoms</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
195 182 <span class="k">my</span><span class="s">(</span><span class="i">$UnknownAtomCount</span><span class="cm">,</span> <span class="i">$UnknownAtoms</span><span class="cm">,</span> <span class="i">$UnknownAtomLines</span><span class="s">)</span> = <span class="i">GetUnknownAtoms</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
|
|
|
196 183 <span class="k">if</span> <span class="s">(</span><span class="i">$UnknownAtomCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
197 184 <span class="i">$UnknownAtomsCtabBlockCount</span>++<span class="sc">;</span>
|
|
|
198 185 <span class="i">$ProblematicCmpdData</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
199 186 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
200 187 <span class="k">print</span> <span class="q">"\nUnknown atom(s) found: $UnknownAtomCount\nUnknown atom(s) symbols:$UnknownAtoms\nUnknown atom(s) data lines:\n$UnknownAtomLines\n"</span><span class="sc">;</span>
|
|
|
201 188 <span class="s">}</span>
|
|
|
202 189 <span class="s">}</span>
|
|
|
203 190 <span class="s">}</span>
|
|
|
204 191 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">InvalidAtomNumbers</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
205 192 <span class="k">my</span><span class="s">(</span><span class="i">$InvalidAtomNumbersCount</span><span class="cm">,</span> <span class="i">$InvalidAtomNumbers</span><span class="cm">,</span> <span class="i">$InvalidAtomNumberLines</span><span class="s">)</span> = <span class="i">GetInvalidAtomNumbers</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
|
|
|
206 193 <span class="k">if</span> <span class="s">(</span><span class="i">$InvalidAtomNumbersCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
207 194 <span class="i">$InvalidAtomNumbersCtabBlockCount</span>++<span class="sc">;</span>
|
|
|
208 195 <span class="i">$ProblematicCmpdData</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
209 196 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
210 197 <span class="k">print</span> <span class="q">"\nInvalid atom number(s) found: $InvalidAtomNumbersCount\nInvalid atom number(s):$InvalidAtomNumbers\nInvalid atom number(s) data lines:\n$InvalidAtomNumberLines\n"</span><span class="sc">;</span>
|
|
|
211 198 <span class="s">}</span>
|
|
|
212 199 <span class="s">}</span>
|
|
|
213 200 <span class="s">}</span>
|
|
|
214 201 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Salts</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
215 202 <span class="k">my</span><span class="s">(</span><span class="i">$FragmentsCount</span><span class="cm">,</span> <span class="i">$Fragments</span><span class="s">)</span> = <span class="i">GetCmpdFragments</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
|
|
|
216 203 <span class="k">if</span> <span class="s">(</span><span class="i">$FragmentsCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
217 204 <span class="i">$SaltsCtabBlockCount</span>++<span class="sc">;</span>
|
|
|
218 205 <span class="i">$ProblematicCmpdData</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
219 206 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
220 207 <span class="k">print</span> <span class="q">"\nSalts found: $FragmentsCount\nSalts atom numbers:\n$Fragments\n"</span><span class="sc">;</span>
|
|
|
221 208 <span class="s">}</span>
|
|
|
222 209 <span class="s">}</span>
|
|
|
223 210 <span class="s">}</span>
|
|
|
224 211 <span class="s">}</span>
|
|
|
225 212 <span class="s">}</span>
|
|
|
226 213 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ProcessCmpdData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
227 214 <span class="i">ProcessCmpdInfo</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
228 215 <span class="s">}</span>
|
|
|
229 216 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
|
|
|
230 217 <span class="k">if</span> <span class="s">(</span><span class="i">$ProblematicCmpdData</span><span class="s">)</span> <span class="s">{</span>
|
|
|
231 218 <span class="k">print</span> <span class="q">"\nCompound data:\n$CmpdString\n\n"</span><span class="sc">;</span>
|
|
|
232 219 <span class="s">}</span>
|
|
|
233 220 <span class="s">}</span>
|
|
|
234 221 <span class="s">}</span>
|
|
|
235 222 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} <= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
236 223 <span class="k">if</span> <span class="s">(</span>!<span class="i">$PrintCmpdCounterHeader</span><span class="s">)</span> <span class="s">{</span>
|
|
|
237 224 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
238 225 <span class="s">}</span>
|
|
|
239 226 <span class="s">}</span>
|
|
|
240 227 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
|
|
|
241 228
|
|
|
242 229 <span class="i">$SDCmpdsInfo</span>{<span class="w">TotalCmpdCount</span>} += <span class="i">$CmpdCount</span><span class="sc">;</span>
|
|
|
243 230
|
|
|
244 231 <span class="k">print</span> <span class="q">"\nNumber of compounds: $CmpdCount\n"</span><span class="sc">;</span>
|
|
|
245 232
|
|
|
246 233 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Empty</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
247 234 <span class="k">print</span> <span class="q">"Number of empty atom/bond blocks: $EmptyCtabBlocksCount\n"</span><span class="sc">;</span>
|
|
|
248 235 <span class="s">}</span>
|
|
|
249 236 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Mismatch</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
250 237 <span class="k">print</span> <span class="q">"Number of mismatched atom/bond blocks: $MismatchCtabBlockCount\n"</span><span class="sc">;</span>
|
|
|
251 238 <span class="s">}</span>
|
|
|
252 239 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">UnknownAtoms</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
253 240 <span class="k">print</span> <span class="q">"Number of atom blocks with unknown atom labels: $UnknownAtomsCtabBlockCount\n"</span><span class="sc">;</span>
|
|
|
254 241 <span class="s">}</span>
|
|
|
255 242 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">InvalidAtomNumbers</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
256 243 <span class="k">print</span> <span class="q">"Number of bond blocks and atom property blocks with invalid atom numbers: $InvalidAtomNumbersCtabBlockCount\n"</span><span class="sc">;</span>
|
|
|
257 244 <span class="s">}</span>
|
|
|
258 245 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Salts</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
259 246 <span class="k">print</span> <span class="q">"Number of atom blocks containing salts: $SaltsCtabBlockCount\n"</span><span class="sc">;</span>
|
|
|
260 247 <span class="s">}</span>
|
|
|
261 248 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Chiral</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
262 249 <span class="k">print</span> <span class="q">"Number of chiral atom/bond blocks: $ChiralCtabBlockCount\n"</span><span class="sc">;</span>
|
|
|
263 250 <span class="s">}</span>
|
|
|
264 251 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ProcessCmpdData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
265 252 <span class="i">PrintCmpdInfoSummary</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
266 253 <span class="s">}</span>
|
|
|
267 254
|
|
|
268 255 <span class="s">}</span>
|
|
|
269 256
|
|
|
270 257 <span class="c"># Initialize compound data information for a SD file...</span>
|
|
|
271 <a name="InitializeSDCmpdsInfo-"></a> 258 <span class="k">sub </span><span class="m">InitializeSDCmpdsInfo</span> <span class="s">{</span>
|
|
|
272 259
|
|
|
273 260 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$SDCmpdsInfo</span>{<span class="w">TotalCmpdCount</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
274 261 <span class="i">$SDCmpdsInfo</span>{<span class="w">TotalCmpdCount</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
275 262 <span class="s">}</span>
|
|
|
276 263
|
|
|
277 264 <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
278 265 <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
279 266 <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
280 267 <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
281 268 <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
282 269 <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
283 270 <span class="s">}</span>
|
|
|
284 271
|
|
|
285 272 <span class="c"># Process compound data header labels and figure out which ones are present for</span>
|
|
|
286 273 <span class="c"># all the compounds...</span>
|
|
|
287 <a name="ProcessCmpdInfo-"></a> 274 <span class="k">sub </span><span class="m">ProcessCmpdInfo</span> <span class="s">{</span>
|
|
|
288 275 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdLinesRef</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
289 276 <span class="k">my</span><span class="s">(</span><span class="i">$Label</span><span class="s">)</span><span class="sc">;</span>
|
|
|
290 277
|
|
|
291 278 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
292 279 <span class="k">my</span> <span class="s">(</span><span class="i">@CmpdFieldLabels</span><span class="s">)</span> = <span class="i">GetCmpdDataHeaderLabels</span><span class="s">(</span><span class="i">$CmpdLinesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
293 280 <span class="k">my</span><span class="s">(</span><span class="i">%CmpdFieldLabelsMap</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
294 281 <span class="c"># Setup a map for the current labels...</span>
|
|
|
295 282 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="i">@CmpdFieldLabels</span><span class="s">)</span> <span class="s">{</span>
|
|
|
296 283 <span class="i">$CmpdFieldLabelsMap</span>{<span class="i">$Label</span>} = <span class="q">"PresentInSome"</span><span class="sc">;</span>
|
|
|
297 284 <span class="s">}</span>
|
|
|
298 285 <span class="c"># Check the presence old labels for this compound; otherwise, mark 'em new...</span>
|
|
|
299 286 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
300 287 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CmpdFieldLabelsMap</span>{<span class="i">$Label</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
301 288 <span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} = <span class="q">"PresentInSome"</span><span class="sc">;</span>
|
|
|
302 289 <span class="s">}</span>
|
|
|
303 290 <span class="s">}</span>
|
|
|
304 291 <span class="c"># Check the presence this compound in the old labels; otherwise, add 'em...</span>
|
|
|
305 292 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="i">@CmpdFieldLabels</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
306 293 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
307 294 <span class="c"># It's a new label...</span>
|
|
|
308 295 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> <span class="i">$Label</span><span class="sc">;</span>
|
|
|
309 296 <span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} = <span class="q">"PresentInSome"</span><span class="sc">;</span>
|
|
|
310 297 <span class="s">}</span>
|
|
|
311 298 <span class="s">}</span>
|
|
|
312 299 <span class="s">}</span>
|
|
|
313 300 <span class="k">else</span> <span class="s">{</span>
|
|
|
314 301 <span class="c"># Get the initial label set and set up a map...</span>
|
|
|
315 302 <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}} = <span class="i">GetCmpdDataHeaderLabels</span><span class="s">(</span><span class="i">$CmpdLinesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
316 303 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
317 304 <span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} = <span class="q">"PresentInAll"</span><span class="sc">;</span>
|
|
|
318 305 <span class="s">}</span>
|
|
|
319 306 <span class="s">}</span>
|
|
|
320 307 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountEmptyData</span>} || <span class="i">$OptionsInfo</span>{<span class="w">CheckData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
321 308 <span class="c"># Count empty data field values...</span>
|
|
|
322 309 <span class="k">my</span><span class="s">(</span><span class="i">%DataFieldAndValues</span><span class="cm">,</span> <span class="i">$Label</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
323 310
|
|
|
324 311 <span class="i">%DataFieldAndValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span><span class="i">$CmpdLinesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
325 312 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%DataFieldAndValues</span><span class="s">)</span> <span class="s">{</span>
|
|
|
326 313 <span class="i">$Value</span> = <span class="i">$DataFieldAndValues</span>{<span class="i">$Label</span>}<span class="sc">;</span>
|
|
|
327 314 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountEmptyData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
328 315 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
329 316 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
330 317 <span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
331 318 <span class="s">}</span>
|
|
|
332 319 <span class="k">else</span> <span class="s">{</span>
|
|
|
333 320 <span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
334 321 <span class="s">}</span>
|
|
|
335 322 <span class="s">}</span>
|
|
|
336 323 <span class="k">else</span> <span class="s">{</span>
|
|
|
337 324 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
338 325 <span class="k">print</span> <span class="q">"Compound record $CmpdCount: Empty data field <$Label>\n"</span><span class="sc">;</span>
|
|
|
339 326 <span class="s">}</span>
|
|
|
340 327 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
341 328 <span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
342 329 <span class="s">}</span>
|
|
|
343 330 <span class="k">else</span> <span class="s">{</span>
|
|
|
344 331 <span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}{<span class="i">$Label</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
345 332 <span class="s">}</span>
|
|
|
346 333 <span class="s">}</span>
|
|
|
347 334 <span class="s">}</span>
|
|
|
348 335 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
349 336 <span class="k">if</span> <span class="s">(</span><span class="i">IsNumerical</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
350 337 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
351 338 <span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
352 339 <span class="s">}</span>
|
|
|
353 340 <span class="k">else</span> <span class="s">{</span>
|
|
|
354 341 <span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
355 342 <span class="s">}</span>
|
|
|
356 343 <span class="s">}</span>
|
|
|
357 344 <span class="k">else</span> <span class="s">{</span>
|
|
|
358 345 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
359 346 <span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
360 347 <span class="s">}</span>
|
|
|
361 348 <span class="k">else</span> <span class="s">{</span>
|
|
|
362 349 <span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}{<span class="i">$Label</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
363 350 <span class="s">}</span>
|
|
|
364 351 <span class="s">}</span>
|
|
|
365 352 <span class="s">}</span>
|
|
|
366 353 <span class="s">}</span>
|
|
|
367 354 <span class="s">}</span>
|
|
|
368 355 <span class="s">}</span>
|
|
|
369 356
|
|
|
370 357 <span class="c"># Print compound summary...</span>
|
|
|
371 <a name="PrintCmpdInfoSummary-"></a> 358 <span class="k">sub </span><span class="m">PrintCmpdInfoSummary</span> <span class="s">{</span>
|
|
|
372 359 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
373 360 <span class="k">my</span><span class="s">(</span><span class="i">$PresentInAllCount</span><span class="cm">,</span> <span class="i">$Label</span><span class="cm">,</span> <span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> <span class="i">@FieldLabelsPresentInAll</span><span class="s">)</span><span class="sc">;</span>
|
|
|
374 361
|
|
|
375 362 <span class="i">@FieldLabelsPresentInSome</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
376 363 <span class="i">@FieldLabelsPresentInAll</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
377 364
|
|
|
378 365 <span class="i">$PresentInAllCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
379 366 <span class="k">print</span> <span class="q">"\nNumber of data fields: "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
380 367 <span class="k">print</span> <span class="q">"All data field labels: "</span><span class="sc">;</span>
|
|
|
381 368 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
382 369 <span class="k">print</span> <span class="q">"<$Label> "</span><span class="sc">;</span>
|
|
|
383 370 <span class="s">}</span>
|
|
|
384 371 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
385 372 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
386 373 <span class="k">if</span> <span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} <span class="k">eq</span> <span class="q">"PresentInAll"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
387 374 <span class="i">$PresentInAllCount</span>++<span class="sc">;</span>
|
|
|
388 375 <span class="k">push</span> <span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> <span class="i">$Label</span><span class="sc">;</span>
|
|
|
389 376 <span class="s">}</span>
|
|
|
390 377 <span class="s">}</span>
|
|
|
391 378 <span class="k">if</span> <span class="s">(</span><span class="i">$PresentInAllCount</span> != <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
392 379 <span class="k">print</span> <span class="q">"Data field labels present in all compounds: "</span><span class="sc">;</span>
|
|
|
393 380 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
394 381 <span class="k">if</span> <span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} <span class="k">eq</span> <span class="q">"PresentInAll"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
395 382 <span class="k">print</span> <span class="q">"<$Label> "</span><span class="sc">;</span>
|
|
|
396 383 <span class="s">}</span>
|
|
|
397 384 <span class="s">}</span>
|
|
|
398 385 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
399 386 <span class="k">print</span> <span class="q">"Data field labels present in some compounds: "</span><span class="sc">;</span>
|
|
|
400 387 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
401 388 <span class="k">if</span> <span class="s">(</span><span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}{<span class="i">$Label</span>} <span class="k">eq</span> <span class="q">"PresentInSome"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
402 389 <span class="k">print</span> <span class="q">"<$Label> "</span><span class="sc">;</span>
|
|
|
403 390 <span class="k">push</span> <span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> <span class="i">$Label</span><span class="sc">;</span>
|
|
|
404 391 <span class="s">}</span>
|
|
|
405 392 <span class="s">}</span>
|
|
|
406 393 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
407 394 <span class="s">}</span>
|
|
|
408 395 <span class="c"># List empty data field values count...</span>
|
|
|
409 396 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountEmptyData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
410 397 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
411 398 <span class="k">if</span> <span class="s">(</span><span class="i">$PresentInAllCount</span> == <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
412 399 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of non-empty values for data field(s)"</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
413 400 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of empty values for data field(s)"</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
414 401 <span class="s">}</span>
|
|
|
415 402 <span class="k">else</span> <span class="s">{</span>
|
|
|
416 403 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of non-empty values for data field(s) present in all compounds"</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
417 404 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of empty values for data field(s) present in all compounds"</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
418 405 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of non-empty values for data field(s) present in some compounds"</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
419 406 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of empty values for data field(s) present in some compounds"</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">EmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
420 407 <span class="s">}</span>
|
|
|
421 408 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
422 409 <span class="s">}</span>
|
|
|
423 410 <span class="c"># List numerical data values count...</span>
|
|
|
424 411 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
425 412 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
426 413 <span class="k">if</span> <span class="s">(</span><span class="i">$PresentInAllCount</span> == <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
427 414 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of non-numerical values for data field(s)"</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
428 415 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of numerical values for data field(s)"</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
429 416 <span class="s">}</span>
|
|
|
430 417 <span class="k">else</span> <span class="s">{</span>
|
|
|
431 418 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of non-numerical values for data field(s) present in all compounds"</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
432 419 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of numerical values for data field(s) present in all compounds"</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
433 420 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of non-numerical values for data field(s) present in some compounds"</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
434 421 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">"Number of numerical values for data field(s) present in some compounds"</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
435 422 <span class="s">}</span>
|
|
|
436 423 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
437 424 <span class="s">}</span>
|
|
|
438 425 <span class="s">}</span>
|
|
|
439 426 <span class="k">else</span> <span class="s">{</span>
|
|
|
440 427 <span class="k">print</span> <span class="q">"\nNumber of data fields: 0\n"</span><span class="sc">;</span>
|
|
|
441 428 <span class="s">}</span>
|
|
|
442 429 <span class="s">}</span>
|
|
|
443 430 <span class="c"># List data information...</span>
|
|
|
444 <a name="PrintDataInformation-"></a> 431 <span class="k">sub </span><span class="m">PrintDataInformation</span> <span class="s">{</span>
|
|
|
445 432 <span class="k">my</span><span class="s">(</span><span class="i">$InfoLabel</span><span class="cm">,</span> <span class="i">$DataLabelRef</span><span class="cm">,</span> <span class="i">$DataLabelToValueMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
446 433 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$Label</span><span class="s">)</span><span class="sc">;</span>
|
|
|
447 434
|
|
|
448 435 <span class="i">$Line</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
449 436 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$DataLabelRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
450 437 <span class="i">$Line</span> .= <span class="q">" <$Label> - "</span> . <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$DataLabelToValueMapRef</span>->{<span class="i">$Label</span>}<span class="s">)</span> ? <span class="i">$DataLabelToValueMapRef</span>->{<span class="i">$Label</span>} <span class="co">:</span> <span class="n">0</span><span class="s">)</span> . <span class="q">","</span><span class="sc">;</span>
|
|
|
451 438 <span class="s">}</span>
|
|
|
452 439 <span class="i">$Line</span> =~ <span class="q">s/\,$//g</span><span class="sc">;</span>
|
|
|
453 440 <span class="k">print</span> <span class="q">"$InfoLabel: $Line\n"</span><span class="sc">;</span>
|
|
|
454 441 <span class="s">}</span>
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455 442
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456 443 <span class="c"># Total size of all the files...</span>
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457 <a name="ListTotalSizeOfFiles-"></a> 444 <span class="k">sub </span><span class="m">ListTotalSizeOfFiles</span> <span class="s">{</span>
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458 445 <span class="k">my</span><span class="s">(</span><span class="i">$FileOkayCount</span><span class="cm">,</span> <span class="i">$TotalSize</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
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459 446
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460 447 <span class="i">$FileOkayCount</span> = <span class="n">0</span><span class="sc">;</span>
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461 448 <span class="i">$TotalSize</span> = <span class="n">0</span><span class="sc">;</span>
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462 449
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463 450 <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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464 451 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span>
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465 452 <span class="i">$FileOkayCount</span>++<span class="sc">;</span>
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|
466 453 <span class="i">$TotalSize</span> += <span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
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467 454 <span class="s">}</span>
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468 455 <span class="s">}</span>
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469 456 <span class="k">if</span> <span class="s">(</span><span class="i">$FileOkayCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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470 457 <span class="k">print</span> <span class="q">"\nTotal number of compounds in $FileOkayCount SD files: $SDCmpdsInfo{TotalCmpdCount}\n"</span><span class="sc">;</span>
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471 458 <span class="k">print</span> <span class="q">"\nTotal size of $FileOkayCount SD files: "</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$TotalSize</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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472 459 <span class="s">}</span>
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473 460
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474 461 <span class="s">}</span>
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475 462
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476 463 <span class="c"># Retrieve information about SD files...</span>
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477 <a name="RetrieveSDFilesInfo-"></a> 464 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
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478 465 <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">$ModifiedTimeString</span><span class="cm">,</span> <span class="i">$ModifiedDateString</span><span class="s">)</span><span class="sc">;</span>
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479 466
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|
480 467 <span class="i">%SDCmpdsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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481 468
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|
482 469 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
483 470 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
484 471 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
|
485 472 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileLastModified</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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486 473
|
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|
487 474 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
|
|
|
488 475 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
489 476 <span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
490 477 <span class="i">$SDFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
|
|
|
491 478
|
|
|
492 479 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
493 480 <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>
|
|
|
494 481 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span>
|
|
|
495 482 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
496 483 <span class="s">}</span>
|
|
|
497 484 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sdf sd"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
498 485 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span>
|
|
|
499 486 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
500 487 <span class="s">}</span>
|
|
|
501 488 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
502 489 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Couldn't open it: $! \n"</span><span class="sc">;</span>
|
|
|
503 490 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
504 491 <span class="s">}</span>
|
|
|
505 492 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
|
|
|
506 493
|
|
|
507 494 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
|
|
|
508 495 <span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>] = <span class="i">FileSize</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
509 496 <span class="s">(</span><span class="i">$ModifiedTimeString</span><span class="cm">,</span> <span class="i">$ModifiedDateString</span><span class="s">)</span> = <span class="i">FormattedFileModificationTimeAndDate</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
510 497 <span class="i">$SDFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">"$ModifiedTimeString; $ModifiedDateString"</span><span class="sc">;</span>
|
|
|
511 498 <span class="s">}</span>
|
|
|
512 499 <span class="s">}</span>
|
|
|
513 500
|
|
|
514 501 <span class="c"># Process option values...</span>
|
|
|
515 <a name="ProcessOptions-"></a> 502 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
|
|
|
516 503 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
517 504
|
|
|
518 505 <span class="i">$OptionsInfo</span>{<span class="w">All</span>} = <span class="i">$Options</span>{<span class="w">all</span>} ? <span class="i">$Options</span>{<span class="w">all</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
519 506 <span class="i">$OptionsInfo</span>{<span class="w">Chiral</span>} = <span class="i">$Options</span>{<span class="w">chiral</span>} ? <span class="i">$Options</span>{<span class="w">chiral</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
520 507 <span class="i">$OptionsInfo</span>{<span class="w">Count</span>} = <span class="i">$Options</span>{<span class="w">count</span>} ? <span class="i">$Options</span>{<span class="w">count</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
521 508 <span class="i">$OptionsInfo</span>{<span class="w">DataCheck</span>} = <span class="i">$Options</span>{<span class="w">datacheck</span>} ? <span class="i">$Options</span>{<span class="w">datacheck</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
522 509 <span class="i">$OptionsInfo</span>{<span class="w">Empty</span>} = <span class="i">$Options</span>{<span class="w">empty</span>} ? <span class="i">$Options</span>{<span class="w">empty</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
523 510 <span class="i">$OptionsInfo</span>{<span class="w">Fields</span>} = <span class="i">$Options</span>{<span class="w">fields</span>} ? <span class="i">$Options</span>{<span class="w">fields</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
524 511 <span class="i">$OptionsInfo</span>{<span class="w">InvalidAtomNumbers</span>} = <span class="i">$Options</span>{<span class="w">invalidatomnumbers</span>} ? <span class="i">$Options</span>{<span class="w">invalidatomnumbers</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
525 512 <span class="i">$OptionsInfo</span>{<span class="w">Mismatch</span>} = <span class="i">$Options</span>{<span class="w">mismatch</span>} ? <span class="i">$Options</span>{<span class="w">mismatch</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
526 513 <span class="i">$OptionsInfo</span>{<span class="w">Salts</span>} = <span class="i">$Options</span>{<span class="w">salts</span>} ? <span class="i">$Options</span>{<span class="w">salts</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
527 514 <span class="i">$OptionsInfo</span>{<span class="w">UnknownAtoms</span>} = <span class="i">$Options</span>{<span class="w">unknownatoms</span>} ? <span class="i">$Options</span>{<span class="w">unknownatoms</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
528 515
|
|
|
529 516 <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span>
|
|
|
530 517
|
|
|
531 518 <span class="i">$OptionsInfo</span>{<span class="w">ProcessCmpdInfo</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">chiral</span>} || <span class="i">$Options</span>{<span class="w">empty</span>} || <span class="i">$Options</span>{<span class="w">fields</span>} || <span class="i">$Options</span>{<span class="w">invalidatomnumbers</span>} || <span class="i">$Options</span>{<span class="w">mismatch</span>} || <span class="i">$Options</span>{<span class="w">salts</span>} || <span class="i">$Options</span>{<span class="w">unknownatoms</span>} || <span class="i">$Options</span>{<span class="w">datacheck</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
532 519
|
|
|
533 520 <span class="i">$OptionsInfo</span>{<span class="w">ProcessCmpdData</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">fields</span>} || <span class="i">$Options</span>{<span class="w">empty</span>} || <span class="i">$Options</span>{<span class="w">datacheck</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
534 521
|
|
|
535 522 <span class="i">$OptionsInfo</span>{<span class="w">CountEmptyData</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">empty</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
536 523 <span class="i">$OptionsInfo</span>{<span class="w">CheckData</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">datacheck</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
537 524 <span class="s">}</span>
|
|
|
538 525
|
|
|
539 526 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
|
|
|
540 <a name="SetupScriptUsage-"></a> 527 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
|
|
|
541 528
|
|
|
542 529 <span class="c"># Setup default and retrieve all the options...</span>
|
|
|
543 530 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
544 531 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
545 532 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"all|a"</span><span class="cm">,</span> <span class="q">"count|c"</span><span class="cm">,</span> <span class="q">"chiral"</span><span class="cm">,</span> <span class="q">"datacheck"</span><span class="cm">,</span> <span class="q">"detail|d:i"</span><span class="cm">,</span> <span class="q">"empty|e"</span><span class="cm">,</span> <span class="q">"fields|f"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"invalidatomnumbers|i"</span><span class="cm">,</span> <span class="q">"mismatch|m"</span><span class="cm">,</span> <span class="q">"salts|s"</span><span class="cm">,</span> <span class="q">"unknownatoms|u"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
546 533 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
|
|
|
547 534 <span class="s">}</span>
|
|
|
548 535 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
549 536 <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>
|
|
|
550 537 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
|
|
|
551 538 <span class="s">}</span>
|
|
|
552 539 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span>
|
|
|
553 540 <span class="s">}</span>
|
|
|
554 541 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>} <= <span class="n">0</span> || <span class="i">$Options</span>{<span class="w">detail</span>} > <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
|
|
|
555 542 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Possible values: 1 to 3\n"</span><span class="sc">;</span>
|
|
|
556 543 <span class="s">}</span>
|
|
|
557 544 <span class="s">}</span>
|
|
|
558 545
|
|
|
559 <a name="EOF-"></a></pre>
|
|
|
560 <p> </p>
|
|
|
561 <br />
|
|
|
562 <center>
|
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|
563 <img src="../../../images/h2o2.png">
|
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|
564 </center>
|
|
|
565 </body>
|
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|
566 </html>
|
