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+++ b/docs/scripts/html/code/JoinSDFiles.html	Wed Jan 20 09:23:18 2016 -0500
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+<html>
+<head>
+<title>MayaChemTools:Code:JoinSDFiles.pl</title>
+<meta http-equiv="content-type" content="text/html;charset=utf-8">
+<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
+</head>
+<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
+<br/>
+<center>
+<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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+<br/>
+<pre>
+   1 #!/usr/bin/perl -w
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: JoinSDFiles.pl,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
+   5 <span class="c"># $Revision: 1.35 $</span>
+   6 <span class="c">#</span>
+   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+   8 <span class="c">#</span>
+   9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+  10 <span class="c">#</span>
+  11 <span class="c"># This file is part of MayaChemTools.</span>
+  12 <span class="c">#</span>
+  13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+  14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+  15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+  16 <span class="c"># later version.</span>
+  17 <span class="c">#</span>
+  18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+  19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+  20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+  21 <span class="c"># details.</span>
+  22 <span class="c">#</span>
+  23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+  24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+  25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+  26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+  27 <span class="c">#</span>
+  28 
+  29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+  30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</span><span class="sc">;</span>
+  31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
+  32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
+  33 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  34 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span>
+  35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
+  36 
+  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>
+  38 
+  39 <span class="c"># Autoflush STDOUT</span>
+  40 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+  41 
+  42 <span class="c"># Starting message...</span>
+  43 <span class="i">$ScriptName</span> = <span class="w">basename</span> <span class="i">$0</span><span class="sc">;</span>
+  44 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Starting...\n\n&quot;</span><span class="sc">;</span>
+  45 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  46 
+  47 <span class="c"># Get the options and setup script...</span>
+  48 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  49 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+  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>
+  51 <span class="s">}</span>
+  52 
+  53 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
+  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>
+  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>
+  56   <span class="k">die</span> <span class="q">&quot;Error: Specify more than one SD file.\n&quot;</span><span class="sc">;</span>
+  57 <span class="s">}</span>
+  58 
+  59 <span class="c"># Process options...</span>
+  60 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+  61 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+  62 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  63 
+  64 <span class="c"># Setup information about input files...</span>
+  65 <span class="k">print</span> <span class="q">&quot;Checking input SD files...\n&quot;</span><span class="sc">;</span>
+  66 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
+  67 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  68 
+  69 <span class="c"># Join files...</span>
+  70 <span class="k">print</span> <span class="q">&quot;\nGenerating new SD file $OptionsInfo{NewSDFile}...\n&quot;</span><span class="sc">;</span>
+  71 <span class="i">JoinSDFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  72 
+  73 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+  74 
+  75 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  76 <span class="i">$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>
+  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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+  78 
+  79 <span class="c">###############################################################################</span>
+  80 
+  81 <span class="c"># Join all valid SD files...</span>
+<a name="JoinSDFiles-"></a>  82 <span class="k">sub </span><span class="m">JoinSDFiles</span> <span class="s">{</span>
+  83   <span class="k">my</span><span class="s">(</span><span class="i">$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>
+  84 
+  85   <span class="i">$NewSDFile</span> = <span class="i">$OptionsInfo</span>{<span class="w">NewSDFile</span>}<span class="sc">;</span>
+  86 
+  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: $! \n&quot;</span><span class="sc">;</span>
+  88   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+  89     <span class="k">if</span> <span class="s">(</span>!<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+  90       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+  91     <span class="s">}</span>
+  92     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+  93     <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFile...\n&quot;</span><span class="sc">;</span>
+  94 
+  95     <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
+  96     <span class="k">while</span> <span class="s">(</span><span class="q">&lt;SDFILE&gt;</span><span class="s">)</span> <span class="s">{</span>
+  97       <span class="q">s/(\r\n)|(\r)/\n/g</span><span class="sc">;</span>
+  98       <span class="k">print</span> <span class="i">NEWSDFILE</span><span class="sc">;</span>
+  99     <span class="s">}</span>
+ 100     <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+ 101   <span class="s">}</span>
+ 102 
+ 103   <span class="k">close</span> <span class="w">NEWSDFILE</span><span class="sc">;</span>
+ 104 <span class="s">}</span>
+ 105 
+ 106 <span class="c"># Retrieve information about SD files...</span>
+<a name="RetrieveSDFilesInfo-"></a> 107 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
+ 108   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
+ 109 
+ 110   <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 111   <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 112 
+ 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>
+ 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>
+ 115 
+ 116     <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 117     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 118       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+ 119       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 120     <span class="s">}</span>
+ 121     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$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>
+ 122       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
+ 123       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 124     <span class="s">}</span>
+ 125     <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span><span class="s">)</span> <span class="s">{</span>
+ 126       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+ 127       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 128     <span class="s">}</span>
+ 129     <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
+ 130 
+ 131     <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+ 132   <span class="s">}</span>
+ 133 <span class="s">}</span>
+ 134 
+ 135 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 136 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+ 137   <span class="k">my</span><span class="s">(</span><span class="i">$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">$NewSDFile</span><span class="s">)</span><span class="sc">;</span>
+ 138 
+ 139   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 140 
+ 141   <span class="i">$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>
+ 142   <span class="i">$OptionsInfo</span>{<span class="w">Overwrite</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="i">$Options</span>{<span class="w">overwrite</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 143 
+ 144   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span>
+ 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">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+ 146     <span class="s">(</span><span class="i">$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">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span>
+ 147     <span class="k">if</span> <span class="s">(</span><span class="i">$FileName</span> &amp;&amp; <span class="i">$FileExt</span><span class="s">)</span> <span class="s">{</span>
+ 148       <span class="i">$NewSDFile</span> = <span class="i">$FileName</span> . <span class="q">&quot;.&quot;</span> . <span class="i">$FileExt</span><span class="sc">;</span>
+ 149     <span class="s">}</span>
+ 150     <span class="k">else</span> <span class="s">{</span>
+ 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>
+ 152     <span class="s">}</span>
+ 153   <span class="s">}</span>
+ 154   <span class="k">else</span> <span class="s">{</span>
+ 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">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+ 156     <span class="s">(</span><span class="i">$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">$SDFilesList</span>[<span class="n">0</span>]<span class="s">)</span><span class="sc">;</span>
+ 157     <span class="i">$NewSDFile</span> = <span class="i">$FileName</span> . <span class="q">&quot;1To&quot;</span> . <span class="i">@SDFilesList</span> . <span class="q">&quot;Joined.sdf&quot;</span><span class="sc">;</span>
+ 158   <span class="s">}</span>
+ 159 
+ 160   <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
+ 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>
+ 162       <span class="k">die</span> <span class="q">&quot;Error: The file $NewSDFile already exists.\n&quot;</span><span class="sc">;</span>
+ 163     <span class="s">}</span>
+ 164   <span class="s">}</span>
+ 165   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span>
+ 166     <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+ 167     <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
+ 168       <span class="k">if</span> <span class="s">(</span><span class="k">lc</span><span class="s">(</span><span class="i">$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>
+ 169         <span class="k">die</span> <span class="q">&quot;Error: Output filename, $NewSDFile, is similar to a input file name.\nSpecify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
+ 170       <span class="s">}</span>
+ 171     <span class="s">}</span>
+ 172   <span class="s">}</span>
+ 173   <span class="i">$OptionsInfo</span>{<span class="w">NewSDFile</span>} = <span class="i">$NewSDFile</span><span class="sc">;</span>
+ 174 
+ 175 <span class="s">}</span>
+ 176 
+ 177 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 178 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+ 179 
+ 180   <span class="c"># Retrieve all the options...</span>
+ 181   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 182   <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 183     <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+ 184   <span class="s">}</span>
+ 185   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+ 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>
+ 187       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+ 188     <span class="s">}</span>
+ 189     <span class="k">chdir</span> <span class="i">$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>
+ 190   <span class="s">}</span>
+ 191 <span class="s">}</span>
+ 192 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>