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