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1 <html>
2 <head>
3 <title>MayaChemTools:Code:InfoSDFiles.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">
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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: InfoSDFiles.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">Benchmark</span><span class="sc">;</span>
47 34 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span>
48 35 <span class="k">use</span> <span class="w">TextUtil</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="cm">,</span> <span class="i">%SDCmpdsInfo</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 <span class="i">InitializeSDCmpdsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
80 67
81 68 <span class="c"># Process input files..</span>
82 69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
83 70 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
84 71 <span class="k">print</span> <span class="q">&quot;\nProcessing SD files...\n&quot;</span><span class="sc">;</span>
85 72 <span class="s">}</span>
86 73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
87 74 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
88 75 <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
89 76 <span class="i">ListSDFileInfo</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
90 77 <span class="s">}</span>
91 78 <span class="s">}</span>
92 79 <span class="i">ListTotalSizeOfFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
93 80
94 81 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
95 82
96 83 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
97 84 <span class="i">$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>
98 85 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
99 86
100 87 <span class="c">###############################################################################</span>
101 88
102 89 <span class="c"># List appropriate information...</span>
103 <a name="ListSDFileInfo-"></a> 90 <span class="k">sub </span><span class="m">ListSDFileInfo</span> <span class="s">{</span>
104 91 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
105 92 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
106 93
107 94 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
108 95
109 96 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ProcessCmpdInfo</span>}<span class="s">)</span> <span class="s">{</span>
110 97 <span class="i">ListCompoundDetailsInfo</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
111 98 <span class="s">}</span>
112 99 <span class="k">else</span> <span class="s">{</span>
113 100 <span class="i">ListCompoundCountInfo</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
114 101 <span class="s">}</span>
115 102
116 103 <span class="c"># File size and modification information...</span>
117 104 <span class="k">print</span> <span class="q">&quot;\nFile size: &quot;</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="s">)</span><span class="cm">,</span> <span class="q">&quot; \n&quot;</span><span class="sc">;</span>
118 105 <span class="k">print</span> <span class="q">&quot;Last modified: &quot;</span><span class="cm">,</span> <span class="i">$SDFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>]<span class="cm">,</span> <span class="q">&quot; \n&quot;</span><span class="sc">;</span>
119 106 <span class="s">}</span>
120 107
121 108 <span class="c"># List number of compounds in SD file...</span>
122 <a name="ListCompoundCountInfo-"></a> 109 <span class="k">sub </span><span class="m">ListCompoundCountInfo</span> <span class="s">{</span>
123 110 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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>
125 112
126 113 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
127 114
128 115 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
129 116
130 117 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
131 118 <span class="k">while</span> <span class="s">(</span><span class="q">&lt;SDFILE&gt;</span><span class="s">)</span> <span class="s">{</span>
132 119 <span class="k">if</span> <span class="s">(</span><span class="q">/^\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span>
133 120 <span class="i">$CmpdCount</span>++<span class="sc">;</span>
134 121 <span class="s">}</span>
135 122 <span class="s">}</span>
136 123 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
137 124
138 125 <span class="i">$SDCmpdsInfo</span>{<span class="w">TotalCmpdCount</span>} += <span class="i">$CmpdCount</span><span class="sc">;</span>
139 126
140 127 <span class="k">print</span> <span class="q">&quot;\nNumber of compounds: $CmpdCount\n&quot;</span><span class="sc">;</span>
141 128 <span class="s">}</span>
142 129
143 130 <span class="c"># List detailed compound information...</span>
144 <a name="ListCompoundDetailsInfo-"></a> 131 <span class="k">sub </span><span class="m">ListCompoundDetailsInfo</span> <span class="s">{</span>
145 132 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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>
147 134
148 135 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
149 136
150 137 <span class="s">(</span><span class="i">$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>
151 138
152 139 <span class="i">InitializeSDCmpdsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
153 140
154 141 <span class="i">$PrintCmpdCounterHeader</span> = <span class="n">1</span><span class="sc">;</span>
155 142
156 143 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
157 144 <span class="k">while</span> <span class="s">(</span><span class="i">$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>
158 145 <span class="i">$CmpdCount</span>++<span class="sc">;</span>
159 146 <span class="i">$ProblematicCmpdData</span> = <span class="n">0</span><span class="sc">;</span>
160 147 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} &lt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
161 148 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$CmpdCount</span> % <span class="n">5000</span><span class="s">)</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
162 149 <span class="k">if</span> <span class="s">(</span><span class="i">$PrintCmpdCounterHeader</span><span class="s">)</span> <span class="s">{</span>
163 150 <span class="i">$PrintCmpdCounterHeader</span> = <span class="n">0</span><span class="sc">;</span>
164 151 <span class="k">print</span> <span class="q">&quot;Processing compounds:&quot;</span><span class="sc">;</span>
165 152 <span class="s">}</span>
166 153 <span class="k">print</span> <span class="q">&quot;$CmpdCount...&quot;</span><span class="sc">;</span>
167 154 <span class="s">}</span>
168 155 <span class="s">}</span>
169 156 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
170 157 <span class="i">$CtabLinesCount</span> = <span class="i">GetCtabLinesCount</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
171 158 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">All</span>} || <span class="i">$OptionsInfo</span>{<span class="w">Empty</span>}<span class="s">)</span> <span class="s">{</span>
172 159 <span class="k">if</span> <span class="s">(</span><span class="i">$CtabLinesCount</span> &lt;= <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
173 160 <span class="i">$EmptyCtabBlocksCount</span>++<span class="sc">;</span>
174 161 <span class="i">$ProblematicCmpdData</span> = <span class="n">1</span><span class="sc">;</span>
175 162 <span class="s">}</span>
176 163 <span class="s">}</span>
177 164 <span class="k">if</span> <span class="s">(</span><span class="i">$CtabLinesCount</span> &gt; <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
178 165 <span class="k">my</span> <span class="s">(</span><span class="i">$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>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
184 171 <span class="k">print</span> <span class="q">&quot;\nMismatch found: Ctab lines count: $CtabLinesCount; Atoms count: $AtomCount; Bond count: $BondCount\n&quot;</span><span class="sc">;</span>
185 172 <span class="s">}</span>
186 173 <span class="s">}</span>
187 174 <span class="s">}</span>
188 175 <span class="k">if</span> <span class="s">(</span><span class="i">$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>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
200 187 <span class="k">print</span> <span class="q">&quot;\nUnknown atom(s) found: $UnknownAtomCount\nUnknown atom(s) symbols:$UnknownAtoms\nUnknown atom(s) data lines:\n$UnknownAtomLines\n&quot;</span><span class="sc">;</span>
201 188 <span class="s">}</span>
202 189 <span class="s">}</span>
203 190 <span class="s">}</span>
204 191 <span class="k">if</span> <span class="s">(</span><span class="i">$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>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
210 197 <span class="k">print</span> <span class="q">&quot;\nInvalid atom number(s) found: $InvalidAtomNumbersCount\nInvalid atom number(s):$InvalidAtomNumbers\nInvalid atom number(s) data lines:\n$InvalidAtomNumberLines\n&quot;</span><span class="sc">;</span>
211 198 <span class="s">}</span>
212 199 <span class="s">}</span>
213 200 <span class="s">}</span>
214 201 <span class="k">if</span> <span class="s">(</span><span class="i">$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> &gt; <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>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
220 207 <span class="k">print</span> <span class="q">&quot;\nSalts found: $FragmentsCount\nSalts atom numbers:\n$Fragments\n&quot;</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">$OptionsInfo</span>{<span class="w">Detail</span>} &gt;= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
230 217 <span class="k">if</span> <span class="s">(</span><span class="i">$ProblematicCmpdData</span><span class="s">)</span> <span class="s">{</span>
231 218 <span class="k">print</span> <span class="q">&quot;\nCompound data:\n$CmpdString\n\n&quot;</span><span class="sc">;</span>
232 219 <span class="s">}</span>
233 220 <span class="s">}</span>
234 221 <span class="s">}</span>
235 222 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} &lt;= <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">$PrintCmpdCounterHeader</span><span class="s">)</span> <span class="s">{</span>
237 224 <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
238 225 <span class="s">}</span>
239 226 <span class="s">}</span>
240 227 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
241 228
242 229 <span class="i">$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">&quot;\nNumber of compounds: $CmpdCount\n&quot;</span><span class="sc">;</span>
245 232
246 233 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Number of empty atom/bond blocks: $EmptyCtabBlocksCount\n&quot;</span><span class="sc">;</span>
248 235 <span class="s">}</span>
249 236 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Number of mismatched atom/bond blocks: $MismatchCtabBlockCount\n&quot;</span><span class="sc">;</span>
251 238 <span class="s">}</span>
252 239 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Number of atom blocks with unknown atom labels: $UnknownAtomsCtabBlockCount\n&quot;</span><span class="sc">;</span>
254 241 <span class="s">}</span>
255 242 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Number of bond blocks and atom property blocks with invalid atom numbers: $InvalidAtomNumbersCtabBlockCount\n&quot;</span><span class="sc">;</span>
257 244 <span class="s">}</span>
258 245 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Number of atom blocks containing salts: $SaltsCtabBlockCount\n&quot;</span><span class="sc">;</span>
260 247 <span class="s">}</span>
261 248 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Number of chiral atom/bond blocks: $ChiralCtabBlockCount\n&quot;</span><span class="sc">;</span>
263 250 <span class="s">}</span>
264 251 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;PresentInSome&quot;</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 &#39;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">&quot;PresentInSome&quot;</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 &#39;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">$Label</span>}<span class="s">)</span> <span class="s">{</span>
307 294 <span class="c"># It&#39;s a new label...</span>
308 295 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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">$Label</span>} = <span class="q">&quot;PresentInSome&quot;</span><span class="sc">;</span>
310 297 <span class="s">}</span>
311 298 <span class="s">}</span>
312 299 <span class="s">}</span>
313 300 <span class="k">else</span> <span class="s">{</span>
314 301 <span class="c"># Get the initial label set and set up a map...</span>
315 302 <span class="i">@</span>{<span class="i">$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">$Label</span>} = <span class="q">&quot;PresentInAll&quot;</span><span class="sc">;</span>
318 305 <span class="s">}</span>
319 306 <span class="s">}</span>
320 307 <span class="k">if</span> <span class="s">(</span><span class="i">$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>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
338 325 <span class="k">print</span> <span class="q">&quot;Compound record $CmpdCount: Empty data field &lt;$Label&gt;\n&quot;</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">&quot;\nNumber of data fields: &quot;</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
380 367 <span class="k">print</span> <span class="q">&quot;All data field labels: &quot;</span><span class="sc">;</span>
381 368 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabelsMap</span>}}<span class="s">)</span> <span class="s">{</span>
382 369 <span class="k">print</span> <span class="q">&quot;&lt;$Label&gt; &quot;</span><span class="sc">;</span>
383 370 <span class="s">}</span>
384 371 <span class="k">print</span> <span class="q">&quot;\n&quot;</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">&quot;PresentInAll&quot;</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">&quot;Data field labels present in all compounds: &quot;</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">&quot;PresentInAll&quot;</span><span class="s">)</span> <span class="s">{</span>
395 382 <span class="k">print</span> <span class="q">&quot;&lt;$Label&gt; &quot;</span><span class="sc">;</span>
396 383 <span class="s">}</span>
397 384 <span class="s">}</span>
398 385 <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
399 386 <span class="k">print</span> <span class="q">&quot;Data field labels present in some compounds: &quot;</span><span class="sc">;</span>
400 387 <span class="k">for</span> <span class="i">$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">$Label</span>} <span class="k">eq</span> <span class="q">&quot;PresentInSome&quot;</span><span class="s">)</span> <span class="s">{</span>
402 389 <span class="k">print</span> <span class="q">&quot;&lt;$Label&gt; &quot;</span><span class="sc">;</span>
403 390 <span class="k">push</span> <span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> <span class="i">$Label</span><span class="sc">;</span>
404 391 <span class="s">}</span>
405 392 <span class="s">}</span>
406 393 <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
407 394 <span class="s">}</span>
408 395 <span class="c"># List empty data field values count...</span>
409 396 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;\n&quot;</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">&quot;Number of non-empty values for data field(s)&quot;</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">&quot;Number of empty values for data field(s)&quot;</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">&quot;Number of non-empty values for data field(s) present in all compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
417 404 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of empty values for data field(s) present in all compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$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">&quot;Number of non-empty values for data field(s) present in some compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonEmptyFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
419 406 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of empty values for data field(s) present in some compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$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">&quot;\n&quot;</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">$OptionsInfo</span>{<span class="w">CheckData</span>}<span class="s">)</span> <span class="s">{</span>
425 412 <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
426 413 <span class="k">if</span> <span class="s">(</span><span class="i">$PresentInAllCount</span> == <span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="s">)</span> <span class="s">{</span>
427 414 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of non-numerical values for data field(s)&quot;</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NonNumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
428 415 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of numerical values for data field(s)&quot;</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">FieldLabels</span>}}<span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
429 416 <span class="s">}</span>
430 417 <span class="k">else</span> <span class="s">{</span>
431 418 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of non-numerical values for data field(s) present in all compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$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">&quot;Number of numerical values for data field(s) present in all compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInAll</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
433 420 <span class="i">PrintDataInformation</span><span class="s">(</span><span class="q">&quot;Number of non-numerical values for data field(s) present in some compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$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">&quot;Number of numerical values for data field(s) present in some compounds&quot;</span><span class="cm">,</span> \<span class="i">@FieldLabelsPresentInSome</span><span class="cm">,</span> \<span class="i">%</span>{<span class="i">$SDCmpdsInfo</span>{<span class="w">NumericalFieldValuesCountMap</span>}}<span class="s">)</span><span class="sc">;</span>
435 422 <span class="s">}</span>
436 423 <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
437 424 <span class="s">}</span>
438 425 <span class="s">}</span>
439 426 <span class="k">else</span> <span class="s">{</span>
440 427 <span class="k">print</span> <span class="q">&quot;\nNumber of data fields: 0\n&quot;</span><span class="sc">;</span>
441 428 <span class="s">}</span>
442 429 <span class="s">}</span>
443 430 <span class="c"># List data information...</span>
444 <a name="PrintDataInformation-"></a> 431 <span class="k">sub </span><span class="m">PrintDataInformation</span> <span class="s">{</span>
445 432 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Line</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
449 436 <span class="k">for</span> <span class="i">$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">&quot; &lt;$Label&gt; - &quot;</span> . <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$DataLabelToValueMapRef</span>-&gt;{<span class="i">$Label</span>}<span class="s">)</span> ? <span class="i">$DataLabelToValueMapRef</span>-&gt;{<span class="i">$Label</span>} <span class="co">:</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;,&quot;</span><span class="sc">;</span>
451 438 <span class="s">}</span>
452 439 <span class="i">$Line</span> =~ <span class="q">s/\,$//g</span><span class="sc">;</span>
453 440 <span class="k">print</span> <span class="q">&quot;$InfoLabel: $Line\n&quot;</span><span class="sc">;</span>
454 441 <span class="s">}</span>
455 442
456 443 <span class="c"># Total size of all the files...</span>
457 <a name="ListTotalSizeOfFiles-"></a> 444 <span class="k">sub </span><span class="m">ListTotalSizeOfFiles</span> <span class="s">{</span>
458 445 <span class="k">my</span><span class="s">(</span><span class="i">$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>
459 446
460 447 <span class="i">$FileOkayCount</span> = <span class="n">0</span><span class="sc">;</span>
461 448 <span class="i">$TotalSize</span> = <span class="n">0</span><span class="sc">;</span>
462 449
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>
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>
465 452 <span class="i">$FileOkayCount</span>++<span class="sc">;</span>
466 453 <span class="i">$TotalSize</span> += <span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
467 454 <span class="s">}</span>
468 455 <span class="s">}</span>
469 456 <span class="k">if</span> <span class="s">(</span><span class="i">$FileOkayCount</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
470 457 <span class="k">print</span> <span class="q">&quot;\nTotal number of compounds in $FileOkayCount SD files: $SDCmpdsInfo{TotalCmpdCount}\n&quot;</span><span class="sc">;</span>
471 458 <span class="k">print</span> <span class="q">&quot;\nTotal size of $FileOkayCount SD files: &quot;</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$TotalSize</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
472 459 <span class="s">}</span>
473 460
474 461 <span class="s">}</span>
475 462
476 463 <span class="c"># Retrieve information about SD files...</span>
477 <a name="RetrieveSDFilesInfo-"></a> 464 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
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>
479 466
480 467 <span class="i">%SDCmpdsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
481 468
482 469 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
483 470 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
484 471 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileSize</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
485 472 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileLastModified</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
486 473
487 474 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$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">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
491 478
492 479 <span class="i">$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">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
495 482 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
496 483 <span class="s">}</span>
497 484 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">&quot;sdf sd&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
498 485 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
499 486 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
500 487 <span class="s">}</span>
501 488 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span><span class="s">)</span> <span class="s">{</span>
502 489 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
503 490 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
504 491 <span class="s">}</span>
505 492 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
506 493
507 494 <span class="i">$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">$Index</span>] = <span class="q">&quot;$ModifiedTimeString; $ModifiedDateString&quot;</span><span class="sc">;</span>
511 498 <span class="s">}</span>
512 499 <span class="s">}</span>
513 500
514 501 <span class="c"># Process option values...</span>
515 <a name="ProcessOptions-"></a> 502 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
516 503 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
517 504
518 505 <span class="i">$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">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
545 532 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;all|a&quot;</span><span class="cm">,</span> <span class="q">&quot;count|c&quot;</span><span class="cm">,</span> <span class="q">&quot;chiral&quot;</span><span class="cm">,</span> <span class="q">&quot;datacheck&quot;</span><span class="cm">,</span> <span class="q">&quot;detail|d:i&quot;</span><span class="cm">,</span> <span class="q">&quot;empty|e&quot;</span><span class="cm">,</span> <span class="q">&quot;fields|f&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;invalidatomnumbers|i&quot;</span><span class="cm">,</span> <span class="q">&quot;mismatch|m&quot;</span><span class="cm">,</span> <span class="q">&quot;salts|s&quot;</span><span class="cm">,</span> <span class="q">&quot;unknownatoms|u&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
546 533 <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
547 534 <span class="s">}</span>
548 535 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
551 538 <span class="s">}</span>
552 539 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
553 540 <span class="s">}</span>
554 541 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>} &lt;= <span class="n">0</span> || <span class="i">$Options</span>{<span class="w">detail</span>} &gt; <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
555 542 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{detail}, for option \&quot;-d --detail\&quot; is not valid. Possible values: 1 to 3\n&quot;</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>&nbsp;</p>
561 <br />
562 <center>
563 <img src="../../../images/h2o2.png">
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