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   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 
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