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2 <head>
3 <title>MayaChemTools:Code:JoinSDFiles.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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9 <center>
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13 <pre>
14 1 #!/usr/bin/perl -w
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: JoinSDFiles.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">FileUtil</span><span class="sc">;</span>
49 36
50 37 <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>
51 38
52 39 <span class="c"># Autoflush STDOUT</span>
53 40 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
54 41
55 42 <span class="c"># Starting message...</span>
56 43 <span class="i">$ScriptName</span> = <span class="w">basename</span> <span class="i">$0</span><span class="sc">;</span>
57 44 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Starting...\n\n&quot;</span><span class="sc">;</span>
58 45 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
59 46
60 47 <span class="c"># Get the options and setup script...</span>
61 48 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
62 49 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
63 50 <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>
64 51 <span class="s">}</span>
65 52
66 53 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
67 54 <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>
68 55 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
69 56 <span class="k">die</span> <span class="q">&quot;Error: Specify more than one SD file.\n&quot;</span><span class="sc">;</span>
70 57 <span class="s">}</span>
71 58
72 59 <span class="c"># Process options...</span>
73 60 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
74 61 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
75 62 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
76 63
77 64 <span class="c"># Setup information about input files...</span>
78 65 <span class="k">print</span> <span class="q">&quot;Checking input SD files...\n&quot;</span><span class="sc">;</span>
79 66 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
80 67 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
81 68
82 69 <span class="c"># Join files...</span>
83 70 <span class="k">print</span> <span class="q">&quot;\nGenerating new SD file $OptionsInfo{NewSDFile}...\n&quot;</span><span class="sc">;</span>
84 71 <span class="i">JoinSDFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
85 72
86 73 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
87 74
88 75 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
89 76 <span class="i">$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>
90 77 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
91 78
92 79 <span class="c">###############################################################################</span>
93 80
94 81 <span class="c"># Join all valid SD files...</span>
95 <a name="JoinSDFiles-"></a> 82 <span class="k">sub </span><span class="m">JoinSDFiles</span> <span class="s">{</span>
96 83 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$NewSDFile</span><span class="s">)</span><span class="sc">;</span>
97 84
98 85 <span class="i">$NewSDFile</span> = <span class="i">$OptionsInfo</span>{<span class="w">NewSDFile</span>}<span class="sc">;</span>
99 86
100 87 <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewSDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $NewSDFile: $! \n&quot;</span><span class="sc">;</span>
101 88 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
102 89 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
103 90 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
104 91 <span class="s">}</span>
105 92 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
106 93 <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFile...\n&quot;</span><span class="sc">;</span>
107 94
108 95 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
109 96 <span class="k">while</span> <span class="s">(</span><span class="q">&lt;SDFILE&gt;</span><span class="s">)</span> <span class="s">{</span>
110 97 <span class="q">s/(\r\n)|(\r)/\n/g</span><span class="sc">;</span>
111 98 <span class="k">print</span> <span class="i">NEWSDFILE</span><span class="sc">;</span>
112 99 <span class="s">}</span>
113 100 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
114 101 <span class="s">}</span>
115 102
116 103 <span class="k">close</span> <span class="w">NEWSDFILE</span><span class="sc">;</span>
117 104 <span class="s">}</span>
118 105
119 106 <span class="c"># Retrieve information about SD files...</span>
120 <a name="RetrieveSDFilesInfo-"></a> 107 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
121 108 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
122 109
123 110 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
124 111 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
125 112
126 113 <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>
127 114 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
128 115
129 116 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
130 117 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
131 118 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
132 119 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
133 120 <span class="s">}</span>
134 121 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$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>
135 122 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
136 123 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
137 124 <span class="s">}</span>
138 125 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span><span class="s">)</span> <span class="s">{</span>
139 126 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
140 127 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
141 128 <span class="s">}</span>
142 129 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
143 130
144 131 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
145 132 <span class="s">}</span>
146 133 <span class="s">}</span>
147 134
148 135 <span class="c"># Process option values...</span>
149 <a name="ProcessOptions-"></a> 136 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
150 137 <span class="k">my</span><span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$NewSDFile</span><span class="s">)</span><span class="sc">;</span>
151 138
152 139 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
153 140
154 141 <span class="i">$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="k">undef</span><span class="sc">;</span>
155 142 <span class="i">$OptionsInfo</span>{<span class="w">Overwrite</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="i">$Options</span>{<span class="w">overwrite</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
156 143
157 144 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span>
158 145 <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">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
159 146 <span class="s">(</span><span class="i">$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">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span>
160 147 <span class="k">if</span> <span class="s">(</span><span class="i">$FileName</span> &amp;&amp; <span class="i">$FileExt</span><span class="s">)</span> <span class="s">{</span>
161 148 <span class="i">$NewSDFile</span> = <span class="i">$FileName</span> . <span class="q">&quot;.&quot;</span> . <span class="i">$FileExt</span><span class="sc">;</span>
162 149 <span class="s">}</span>
163 150 <span class="k">else</span> <span class="s">{</span>
164 151 <span class="i">$NewSDFile</span> = <span class="i">$Options</span>{<span class="w">root</span>} . <span class="q">&quot;.sdf&quot;</span><span class="sc">;</span>
165 152 <span class="s">}</span>
166 153 <span class="s">}</span>
167 154 <span class="k">else</span> <span class="s">{</span>
168 155 <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">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
169 156 <span class="s">(</span><span class="i">$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">$SDFilesList</span>[<span class="n">0</span>]<span class="s">)</span><span class="sc">;</span>
170 157 <span class="i">$NewSDFile</span> = <span class="i">$FileName</span> . <span class="q">&quot;1To&quot;</span> . <span class="i">@SDFilesList</span> . <span class="q">&quot;Joined.sdf&quot;</span><span class="sc">;</span>
171 158 <span class="s">}</span>
172 159
173 160 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
174 161 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFile</span><span class="s">)</span> <span class="s">{</span>
175 162 <span class="k">die</span> <span class="q">&quot;Error: The file $NewSDFile already exists.\n&quot;</span><span class="sc">;</span>
176 163 <span class="s">}</span>
177 164 <span class="s">}</span>
178 165 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span>
179 166 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
180 167 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
181 168 <span class="k">if</span> <span class="s">(</span><span class="k">lc</span><span class="s">(</span><span class="i">$NewSDFile</span><span class="s">)</span> <span class="k">eq</span> <span class="k">lc</span><span class="s">(</span><span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
182 169 <span class="k">die</span> <span class="q">&quot;Error: Output filename, $NewSDFile, is similar to a input file name.\nSpecify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
183 170 <span class="s">}</span>
184 171 <span class="s">}</span>
185 172 <span class="s">}</span>
186 173 <span class="i">$OptionsInfo</span>{<span class="w">NewSDFile</span>} = <span class="i">$NewSDFile</span><span class="sc">;</span>
187 174
188 175 <span class="s">}</span>
189 176
190 177 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
191 <a name="SetupScriptUsage-"></a> 178 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
192 179
193 180 <span class="c"># Retrieve all the options...</span>
194 181 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
195 182 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
196 183 <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
197 184 <span class="s">}</span>
198 185 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
199 186 <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>
200 187 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
201 188 <span class="s">}</span>
202 189 <span class="k">chdir</span> <span class="i">$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>
203 190 <span class="s">}</span>
204 191 <span class="s">}</span>
205 192
206 <a name="EOF-"></a></pre>
207 <p>&nbsp;</p>
208 <br />
209 <center>
210 <img src="../../../images/h2o2.png">
211 </center>
212 </body>
213 </html>