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+<title>MayaChemTools:Code:InfoPDBFiles.pl</title>
+<meta http-equiv="content-type" content="text/html;charset=utf-8">
+<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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+<br/>
+<center>
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+<pre>
+1 #!/usr/bin/perl -w
+2 <span class="c">#</span>
+3 <span class="c"># $RCSfile: InfoPDBFiles.pl,v $</span>
+4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
+5 <span class="c"># $Revision: 1.36 $</span>
+6 <span class="c">#</span>
+7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+8 <span class="c">#</span>
+9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+10 <span class="c">#</span>
+11 <span class="c"># This file is part of MayaChemTools.</span>
+12 <span class="c">#</span>
+13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+16 <span class="c"># later version.</span>
+17 <span class="c">#</span>
+18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+21 <span class="c"># details.</span>
+22 <span class="c">#</span>
+23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+27 <span class="c">#</span>
+28
+29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$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">Text::ParseWords</span><span class="sc">;</span>
+34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
+35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
+36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
+37 <span class="k">use</span> <span class="w">PDBFileUtil</span><span class="sc">;</span>
+38
+39 <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>
+40
+41 <span class="c"># Autoflush STDOUT</span>
+42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+43
+44 <span class="c"># Starting message...</span>
+45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
+46 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
+47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+48
+49 <span class="c"># Get the options and setup script...</span>
+50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+51 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+52   <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>
+53 <span class="s">}</span>
+54
+55 <span class="k">my</span><span class="s">(</span><span class="i">@PDBFilesList</span><span class="s">)</span><span class="sc">;</span>
+56 <span class="i">@PDBFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">&quot;pdb&quot;</span><span class="s">)</span><span class="sc">;</span>
+57
+58 <span class="c"># Process options...</span>
+59 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+60 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+62
+63 <span class="c"># Setup information about input files...</span>
+64 <span class="k">my</span><span class="s">(</span><span class="i">%PDBFilesInfo</span><span class="s">)</span><span class="sc">;</span>
+65 <span class="k">print</span> <span class="q">&quot;Checking input PDB file(s)...\n&quot;</span><span class="sc">;</span>
+66 <span class="i">RetrievePDBFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+67
+68 <span class="c"># Process input files..</span>
+69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+70 <span class="k">if</span> <span class="s">(</span><span class="i">@PDBFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+71   <span class="k">print</span> <span class="q">&quot;\nProcessing PDB files...\n&quot;</span><span class="sc">;</span>
+72 <span class="s">}</span>
+73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
+74   <span class="k">if</span> <span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+75     <span class="k">print</span> <span class="q">&quot;\nProcessing file $PDBFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+76     <span class="i">ListPDBFileInfo</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+77   <span class="s">}</span>
+78 <span class="s">}</span>
+79 <span class="i">ListTotalSizeOfFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+80
+81 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+82
+83 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+84 <span class="i">$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>
+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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+86
+87 <span class="c">###############################################################################</span>
+88
+89 <span class="c"># List appropriate information...</span>
+<a name="ListPDBFileInfo-"></a>  90 <span class="k">sub </span><span class="m">ListPDBFileInfo</span> <span class="s">{</span>
+91   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+92   <span class="k">my</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+93
+94   <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+95   <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
+96
+97   <span class="c"># Header informaton...</span>
+98   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListHeaderInfo</span>}<span class="s">)</span> <span class="s">{</span>
+99     <span class="i">ListHeaderInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+100   <span class="s">}</span>
+101
+102   <span class="c"># Experiment informaton...</span>
+103   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListExperimentalTechniqueInfo</span>}<span class="s">)</span> <span class="s">{</span>
+104     <span class="i">ListExperimentalTechniqueInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+105   <span class="s">}</span>
+106
+107   <span class="c"># Total number of records...</span>
+108   <span class="k">my</span><span class="s">(</span><span class="i">$TotalRecordsCount</span><span class="s">)</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="sc">;</span>
+109   <span class="k">print</span> <span class="q">&quot;\nTotal number of records: $TotalRecordsCount\n&quot;</span><span class="sc">;</span>
+110
+111   <span class="c"># List record type count information...</span>
+112   <span class="i">ListRecordTypesInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+113
+114   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountChains</span>} || <span class="i">$OptionsInfo</span>{<span class="w">CountResiduesInChains</span>} || <span class="i">$OptionsInfo</span>{<span class="w">ResiduesFrequencyInChains</span>}<span class="s">)</span> <span class="s">{</span>
+115     <span class="i">ListChainsAndResiduesInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+116   <span class="s">}</span>
+117   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountResiduesAll</span>} || <span class="i">$OptionsInfo</span>{<span class="w">ResiduesFrequencyAll</span>}<span class="s">)</span> <span class="s">{</span>
+118     <span class="i">ListAllResiduesInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+119   <span class="s">}</span>
+120   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ResidueNumbersInfo</span>}<span class="s">)</span> <span class="s">{</span>
+121     <span class="i">ListResidueNumbersInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+122   <span class="s">}</span>
+123   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CalculateBoundingBox</span>}<span class="s">)</span> <span class="s">{</span>
+124     <span class="i">ListBoundingBox</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+125   <span class="s">}</span>
+126
+127   <span class="c"># File size and modification information...</span>
+128   <span class="k">print</span> <span class="q">&quot;\nFile size: &quot;</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="s">)</span><span class="cm">,</span> <span class="q">&quot; \n&quot;</span><span class="sc">;</span>
+129   <span class="k">print</span> <span class="q">&quot;Last modified: &quot;</span><span class="cm">,</span> <span class="i">$PDBFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>]<span class="cm">,</span> <span class="q">&quot; \n&quot;</span><span class="sc">;</span>
+130 <span class="s">}</span>
+131
+<a name="ListHeaderInfo-"></a> 132 <span class="k">sub </span><span class="m">ListHeaderInfo</span> <span class="s">{</span>
+133   <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+134   <span class="k">my</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="cm">,</span> <span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span><span class="sc">;</span>
+135
+136   <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
+137   <span class="i">$HeaderRecordLine</span> = <span class="i">$PDBRecordLinesRef</span>-&gt;[<span class="n">0</span>]<span class="sc">;</span>
+138   <span class="k">if</span> <span class="s">(</span><span class="i">IsHeaderRecordType</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+139     <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="i">ParseHeaderRecordLine</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="sc">;</span>
+140   <span class="s">}</span>
+141
+142   <span class="i">$Classification</span> = <span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Classification</span><span class="s">)</span> ? <span class="q">&#39;Not available&#39;</span> <span class="co">:</span> <span class="i">$Classification</span><span class="sc">;</span>
+143   <span class="i">$DepositionDate</span> = <span class="i">IsEmpty</span><span class="s">(</span><span class="i">$DepositionDate</span><span class="s">)</span> ? <span class="q">&#39;Not available&#39;</span> <span class="co">:</span> <span class="i">$DepositionDate</span><span class="sc">;</span>
+144   <span class="i">$IDCode</span> = <span class="i">IsEmpty</span><span class="s">(</span><span class="i">$IDCode</span><span class="s">)</span> ? <span class="q">&#39;Not available&#39;</span> <span class="co">:</span> <span class="i">$IDCode</span><span class="sc">;</span>
+145
+146   <span class="k">print</span> <span class="q">&quot;\nClassification: $Classification\nID: $IDCode\nDeposition date: $DepositionDate\n&quot;</span><span class="sc">;</span>
+147 <span class="s">}</span>
+148
+149 <span class="c"># List experimental technique information info...</span>
+<a name="ListExperimentalTechniqueInfo-"></a> 150 <span class="k">sub </span><span class="m">ListExperimentalTechniqueInfo</span> <span class="s">{</span>
+151   <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+152   <span class="k">my</span><span class="s">(</span><span class="i">$ExperimentalTechnique</span><span class="cm">,</span> <span class="i">$Resolution</span><span class="cm">,</span> <span class="i">$ResolutionUnits</span><span class="s">)</span><span class="sc">;</span>
+153
+154   <span class="i">$ExperimentalTechnique</span> = <span class="i">GetExperimentalTechnique</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+155   <span class="k">print</span> <span class="q">&quot;\nExperimental technique: &quot;</span> . <span class="s">(</span><span class="i">$ExperimentalTechnique</span> ? <span class="i">$ExperimentalTechnique</span> <span class="co">:</span> <span class="q">&quot;Not available&quot;</span><span class="s">)</span> . <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+156
+157   <span class="s">(</span><span class="i">$Resolution</span><span class="cm">,</span> <span class="i">$ResolutionUnits</span><span class="s">)</span> = <span class="i">GetExperimentalTechniqueResolution</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+158   <span class="k">print</span> <span class="q">&quot;Resolution: &quot;</span> . <span class="s">(</span><span class="i">$Resolution</span> ? <span class="q">&quot;$Resolution $ResolutionUnits&quot;</span> <span class="co">:</span> <span class="q">&quot;Not available&quot;</span><span class="s">)</span> . <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+159
+160 <span class="s">}</span>
+161
+162 <span class="c"># List record type info...</span>
+<a name="ListRecordTypesInfo-"></a> 163 <span class="k">sub </span><span class="m">ListRecordTypesInfo</span> <span class="s">{</span>
+164   <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+165   <span class="k">my</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$RecordCount</span><span class="cm">,</span> <span class="i">$RecordTypesCountRef</span><span class="cm">,</span> <span class="i">@RecordTypeCountInfo</span><span class="s">)</span><span class="sc">;</span>
+166
+167   <span class="i">$RecordTypesCountRef</span> = <span class="i">GetRecordTypesCount</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+168
+169   <span class="i">@RecordTypeCountInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+170   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountRecordType</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+171     <span class="k">for</span> <span class="i">$RecordType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">RecordTypes</span>}}<span class="s">)</span> <span class="s">{</span>
+172       <span class="i">$RecordCount</span> = <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="i">$RecordType</span>}<span class="sc">;</span>
+173       <span class="k">push</span> <span class="i">@RecordTypeCountInfo</span><span class="cm">,</span> <span class="q">&quot;$RecordType - $RecordCount&quot;</span><span class="sc">;</span>
+174     <span class="s">}</span>
+175   <span class="s">}</span>
+176   <span class="k">else</span> <span class="s">{</span>
+177     <span class="k">for</span> <span class="i">$RecordType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRecordTypes</span>}}<span class="s">)</span> <span class="s">{</span>
+178       <span class="i">$RecordCount</span> = <span class="s">(</span><span class="k">exists</span> <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="i">$RecordType</span>}<span class="s">)</span> ? <span class="s">(</span><span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="i">$RecordType</span>}<span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+179       <span class="k">push</span> <span class="i">@RecordTypeCountInfo</span><span class="cm">,</span> <span class="q">&quot;$RecordType - $RecordCount&quot;</span><span class="sc">;</span>
+180     <span class="s">}</span>
+181   <span class="s">}</span>
+182   <span class="k">print</span> <span class="q">&quot;Number of individual records: &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@RecordTypeCountInfo</span><span class="cm">,</span> <span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+183
+184   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckMasterRecord</span>}<span class="s">)</span> <span class="s">{</span>
+185     <span class="i">CheckMasterRecord</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+186   <span class="s">}</span>
+187 <span class="s">}</span>
+188
+189 <span class="c"># List information about residues and chains...</span>
+<a name="ListChainsAndResiduesInfo-"></a> 190 <span class="k">sub </span><span class="m">ListChainsAndResiduesInfo</span> <span class="s">{</span>
+191   <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+192   <span class="k">my</span><span class="s">(</span><span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ResidueCount</span><span class="cm">,</span> <span class="i">$ChainCount</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$CollectChainResiduesBeyondTER</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="s">)</span><span class="sc">;</span>
+193
+194   <span class="i">$CollectChainResiduesBeyondTER</span> = <span class="n">1</span><span class="sc">;</span>
+195   <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="q">&#39;AtomAndHetatm&#39;</span><span class="cm">,</span> <span class="i">$CollectChainResiduesBeyondTER</span><span class="s">)</span><span class="sc">;</span>
+196   <span class="i">$ChainCount</span> = <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}}<span class="sc">;</span>
+197   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountChains</span>}<span class="s">)</span> <span class="s">{</span>
+198     <span class="k">print</span> <span class="q">&quot;\nNumber of chains: $ChainCount \n&quot;</span><span class="sc">;</span>
+199     <span class="k">my</span><span class="s">(</span><span class="i">$ChainID</span><span class="cm">,</span> <span class="i">@ChainIDsList</span><span class="s">)</span><span class="sc">;</span>
+200     <span class="i">@ChainIDsList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+201     <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+202       <span class="k">push</span> <span class="i">@ChainIDsList</span><span class="cm">,</span> <span class="i">CleanupChainID</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="sc">;</span>
+203     <span class="s">}</span>
+204     <span class="k">print</span> <span class="q">&quot;Chain IDs: &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ChainIDsList</span><span class="cm">,</span> <span class="q">&#39;, &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+205   <span class="s">}</span>
+206
+207   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountResiduesInChains</span>}<span class="s">)</span> <span class="s">{</span>
+208     <span class="k">my</span><span class="s">(</span><span class="i">$TotalResiduesCount</span><span class="cm">,</span> <span class="i">$ResidueCountInfo</span><span class="cm">,</span> <span class="i">@ResiduesCountInfo</span><span class="s">)</span><span class="sc">;</span>
+209     <span class="i">@ResiduesCountInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+210     <span class="i">$TotalResiduesCount</span> = <span class="n">0</span><span class="sc">;</span>
+211     <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+212       <span class="i">$ResidueCount</span> = <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="sc">;</span>
+213       <span class="i">$TotalResiduesCount</span> += <span class="i">$ResidueCount</span><span class="sc">;</span>
+214       <span class="i">$ResidueCountInfo</span> =  <span class="q">&quot;Chain ${ChainID} - ${ResidueCount}&quot;</span><span class="sc">;</span>
+215       <span class="k">push</span> <span class="i">@ResiduesCountInfo</span><span class="cm">,</span> <span class="i">$ResidueCountInfo</span><span class="sc">;</span>
+216     <span class="s">}</span>
+217     <span class="k">print</span> <span class="q">&quot;\nNumber of residues in chain(s): &quot;</span><span class="sc">;</span>
+218     <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+219       <span class="k">print</span> <span class="q">&quot;Total - $TotalResiduesCount; &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ResiduesCountInfo</span><span class="cm">,</span> <span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+220     <span class="s">}</span>
+221     <span class="k">else</span> <span class="s">{</span>
+222       <span class="k">print</span> <span class="q">&quot;$TotalResiduesCount\n&quot;</span><span class="sc">;</span>
+223     <span class="s">}</span>
+224
+225     <span class="c"># List of residues in each chain...</span>
+226     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
+227       <span class="k">print</span> <span class="q">&quot;List of residues in chain(s): \n&quot;</span><span class="sc">;</span>
+228       <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+229         <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+230           <span class="k">print</span> <span class="q">&quot;Chain &quot;</span><span class="cm">,</span> <span class="i">CleanupChainID</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;: &quot;</span><span class="sc">;</span>
+231         <span class="s">}</span>
+232         <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="cm">,</span> <span class="q">&#39;, &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+233       <span class="s">}</span>
+234     <span class="s">}</span>
+235   <span class="s">}</span>
+236   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ResiduesFrequencyInChains</span>}<span class="s">)</span> <span class="s">{</span>
+237     <span class="c"># Setup a hash using residue count as key for sorting the values...</span>
+238     <span class="k">my</span><span class="s">(</span><span class="i">%ResiduesCountToNameMap</span><span class="s">)</span><span class="sc">;</span>
+239     <span class="i">%ResiduesCountToNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+240     <span class="i">@</span>{<span class="i">$ResiduesCountToNameMap</span>{<span class="w">ChainIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+241     <span class="i">%</span>{<span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+242
+243     <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+244       <span class="k">push</span> <span class="i">@</span>{<span class="i">$ResiduesCountToNameMap</span>{<span class="w">ChainIDs</span>}}<span class="cm">,</span> <span class="i">$ChainID</span><span class="sc">;</span>
+245       <span class="i">%</span>{<span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ChainID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+246
+247       <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ResidueCount</span>}{<span class="i">$ChainID</span>}}<span class="s">)</span> <span class="s">{</span>
+248         <span class="i">$ResidueCount</span> = <span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ResidueCount</span>}{<span class="i">$ChainID</span>}{<span class="i">$ResidueName</span>}<span class="sc">;</span>
+249         <span class="c"># Setup count value for each chain...</span>
+250         <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ChainID</span>}{<span class="i">$ResidueCount</span>}<span class="s">)</span> <span class="s">{</span>
+251           <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ChainID</span>}{<span class="i">$ResidueCount</span>} .= <span class="q">&quot;~${ResidueName}&quot;</span><span class="sc">;</span>
+252         <span class="s">}</span>
+253         <span class="k">else</span> <span class="s">{</span>
+254           <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ChainID</span>}{<span class="i">$ResidueCount</span>} = <span class="i">$ResidueName</span><span class="sc">;</span>
+255         <span class="s">}</span>
+256       <span class="s">}</span>
+257     <span class="s">}</span>
+258     <span class="c"># Collect data for all the residues in all the chains...</span>
+259     <span class="k">my</span><span class="s">(</span><span class="i">%AllResiduesNameToCountMap</span><span class="cm">,</span> <span class="i">%AllResiduesCountToNameMap</span><span class="s">)</span><span class="sc">;</span>
+260     <span class="i">%AllResiduesNameToCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+261     <span class="i">%AllResiduesCountToNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+262     <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+263       <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+264         <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ResidueCount</span>}{<span class="i">$ChainID</span>}}<span class="s">)</span> <span class="s">{</span>
+265           <span class="i">$ResidueCount</span> = <span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ResidueCount</span>}{<span class="i">$ChainID</span>}{<span class="i">$ResidueName</span>}<span class="sc">;</span>
+266           <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AllResiduesNameToCountMap</span>{<span class="i">$ResidueName</span>}<span class="s">)</span> <span class="s">{</span>
+267             <span class="i">$AllResiduesNameToCountMap</span>{<span class="i">$ResidueName</span>} += <span class="i">$ResidueCount</span><span class="sc">;</span>
+268           <span class="s">}</span>
+269           <span class="k">else</span> <span class="s">{</span>
+270             <span class="i">$AllResiduesNameToCountMap</span>{<span class="i">$ResidueName</span>} = <span class="i">$ResidueCount</span><span class="sc">;</span>
+271           <span class="s">}</span>
+272         <span class="s">}</span>
+273       <span class="s">}</span>
+274       <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AllResiduesNameToCountMap</span><span class="s">)</span> <span class="s">{</span>
+275         <span class="i">$ResidueCount</span> = <span class="i">$AllResiduesNameToCountMap</span>{<span class="i">$ResidueName</span>}<span class="sc">;</span>
+276         <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AllResiduesCountToNameMap</span>{<span class="i">$ResidueCount</span>}<span class="s">)</span> <span class="s">{</span>
+277           <span class="i">$AllResiduesCountToNameMap</span>{<span class="i">$ResidueCount</span>} .= <span class="q">&quot;~${ResidueName}&quot;</span><span class="sc">;</span>
+278         <span class="s">}</span>
+279         <span class="k">else</span> <span class="s">{</span>
+280           <span class="i">$AllResiduesCountToNameMap</span>{<span class="i">$ResidueCount</span>} = <span class="i">$ResidueName</span><span class="sc">;</span>
+281         <span class="s">}</span>
+282       <span class="s">}</span>
+283     <span class="s">}</span>
+284
+285     <span class="c"># Setup distribution data for individual chains and the grand total as well...</span>
+286     <span class="k">my</span><span class="s">(</span><span class="i">$ChainResidueCount</span><span class="cm">,</span> <span class="i">$PercentResidueCount</span><span class="cm">,</span> <span class="i">$TotalResidueCount</span><span class="cm">,</span> <span class="i">$ResidueNames</span><span class="cm">,</span> <span class="i">@ResidueNamesList</span><span class="cm">,</span> <span class="i">%ResiduesFrequencyInfoMap</span><span class="s">)</span><span class="sc">;</span>
+287     <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">ChainIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+288     <span class="i">%</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">Frequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+289     <span class="i">%</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">PercentFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+290
+291     <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+292     <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsPercentFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+293
+294     <span class="i">$TotalResidueCount</span> = <span class="n">0</span><span class="sc">;</span>
+295
+296     <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ResiduesCountToNameMap</span>{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+297       <span class="k">push</span> <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">ChainIDs</span>}}<span class="cm">,</span> <span class="i">$ChainID</span><span class="sc">;</span>
+298       <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">Frequency</span>}{<span class="i">$ChainID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+299       <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">PercentFrequency</span>}{<span class="i">$ChainID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+300
+301       <span class="i">$ChainResidueCount</span> = <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="sc">;</span>
+302       <span class="i">$TotalResidueCount</span> += <span class="i">$ChainResidueCount</span><span class="sc">;</span>
+303
+304       <span class="k">for</span> <span class="i">$ResidueCount</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span><span class="i">$b</span> &lt;=&gt; <span class="i">$a</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ChainID</span>}}<span class="s">)</span> <span class="s">{</span>
+305         <span class="i">$ResidueNames</span> = <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ChainID</span>}{<span class="i">$ResidueCount</span>}<span class="sc">;</span>
+306         <span class="i">@ResidueNamesList</span> = <span class="k">split</span> <span class="q">/~/</span><span class="cm">,</span> <span class="i">$ResidueNames</span><span class="sc">;</span>
+307         <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@ResidueNamesList</span><span class="s">)</span> <span class="s">{</span>
+308           <span class="k">push</span> <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">Frequency</span>}{<span class="i">$ChainID</span>}}<span class="cm">,</span> <span class="q">&quot;${ResidueName} - ${ResidueCount}&quot;</span><span class="sc">;</span>
+309           <span class="i">$PercentResidueCount</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.1f&quot;</span><span class="cm">,</span> <span class="s">(</span><span class="s">(</span><span class="i">$ResidueCount</span>/<span class="i">$ChainResidueCount</span><span class="s">)</span>*<span class="n">100</span><span class="s">)</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+310           <span class="k">push</span> <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">PercentFrequency</span>}{<span class="i">$ChainID</span>}}<span class="cm">,</span> <span class="q">&quot;${ResidueName} - ${PercentResidueCount}%&quot;</span><span class="sc">;</span>
+311         <span class="s">}</span>
+312       <span class="s">}</span>
+313     <span class="s">}</span>
+314     <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+315       <span class="k">for</span> <span class="i">$ResidueCount</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span><span class="i">$b</span> &lt;=&gt; <span class="i">$a</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%AllResiduesCountToNameMap</span><span class="s">)</span> <span class="s">{</span>
+316         <span class="i">$ResidueNames</span> = <span class="i">$AllResiduesCountToNameMap</span>{<span class="i">$ResidueCount</span>}<span class="sc">;</span>
+317         <span class="i">@ResidueNamesList</span> = <span class="k">split</span> <span class="q">/~/</span><span class="cm">,</span> <span class="i">$ResidueNames</span><span class="sc">;</span>
+318         <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@ResidueNamesList</span><span class="s">)</span> <span class="s">{</span>
+319           <span class="k">push</span> <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsFrequency</span>}}<span class="cm">,</span> <span class="q">&quot;${ResidueName} - ${ResidueCount}&quot;</span><span class="sc">;</span>
+320           <span class="i">$PercentResidueCount</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.1f&quot;</span><span class="cm">,</span> <span class="s">(</span><span class="s">(</span><span class="i">$ResidueCount</span>/<span class="i">$TotalResidueCount</span><span class="s">)</span>*<span class="n">100</span><span class="s">)</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+321           <span class="k">push</span> <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsPercentFrequency</span>}}<span class="cm">,</span> <span class="q">&quot;${ResidueName} - ${PercentResidueCount}%&quot;</span><span class="sc">;</span>
+322         <span class="s">}</span>
+323       <span class="s">}</span>
+324     <span class="s">}</span>
+325
+326     <span class="c"># List distribution of residues</span>
+327     <span class="k">print</span> <span class="q">&quot;\nDistribution of residues in chain(s): \n&quot;</span><span class="sc">;</span>
+328     <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+329       <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+330         <span class="k">print</span> <span class="q">&quot;Chain &quot;</span><span class="cm">,</span> <span class="i">CleanupChainID</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;: &quot;</span><span class="sc">;</span>
+331       <span class="s">}</span>
+332       <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">Frequency</span>}{<span class="i">$ChainID</span>}}<span class="cm">,</span> <span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+333     <span class="s">}</span>
+334     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+335       <span class="k">print</span> <span class="q">&quot;\nPercent distribution of residues in chain(s): \n&quot;</span><span class="sc">;</span>
+336       <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+337         <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+338           <span class="k">print</span> <span class="q">&quot;Chain &quot;</span><span class="cm">,</span> <span class="i">CleanupChainID</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;: &quot;</span><span class="sc">;</span>
+339         <span class="s">}</span>
+340         <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">PercentFrequency</span>}{<span class="i">$ChainID</span>}}<span class="cm">,</span> <span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+341       <span class="s">}</span>
+342     <span class="s">}</span>
+343     <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+344       <span class="k">print</span> <span class="q">&quot;\nDistribution of residues across all chains: \n&quot;</span><span class="sc">;</span>
+345       <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsFrequency</span>}}<span class="cm">,</span> <span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+346
+347       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+348         <span class="k">print</span> <span class="q">&quot;\nPercent distribution of residues across all chains: \n&quot;</span><span class="sc">;</span>
+349         <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsPercentFrequency</span>}}<span class="cm">,</span> <span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+350       <span class="s">}</span>
+351     <span class="s">}</span>
+352   <span class="s">}</span>
+353 <span class="s">}</span>
+354
+355 <span class="c"># List information about all the residues...</span>
+<a name="ListAllResiduesInfo-"></a> 356 <span class="k">sub </span><span class="m">ListAllResiduesInfo</span> <span class="s">{</span>
+357   <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+358   <span class="k">my</span><span class="s">(</span><span class="i">$TotalResidueCount</span><span class="cm">,</span> <span class="i">$AtomResiduesCount</span><span class="cm">,</span> <span class="i">$HetatmResiduesCount</span><span class="cm">,</span> <span class="i">$ResiduesInfoRef</span><span class="s">)</span><span class="sc">;</span>
+359
+360   <span class="i">$ResiduesInfoRef</span> = <span class="i">GetAllResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+361   <span class="i">$TotalResidueCount</span> = <span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>-&gt;{<span class="w">ResidueNames</span>}}<span class="sc">;</span>
+362   <span class="i">$AtomResiduesCount</span> = <span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>-&gt;{<span class="w">AtomResidueNames</span>}}<span class="sc">;</span>
+363   <span class="i">$HetatmResiduesCount</span> = <span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>-&gt;{<span class="w">HetatmResidueNames</span>}}<span class="sc">;</span>
+364
+365   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountResiduesAll</span>}<span class="s">)</span> <span class="s">{</span>
+366     <span class="k">print</span> <span class="q">&quot;\nTotal number of residues: Total - $TotalResidueCount; ATOM residues - $AtomResiduesCount; HETATM residues - $HetatmResiduesCount\n&quot;</span><span class="sc">;</span>
+367
+368     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
+369       <span class="k">print</span> <span class="q">&quot;List of residues: \n&quot;</span><span class="sc">;</span>
+370       <span class="k">if</span> <span class="s">(</span><span class="i">$AtomResiduesCount</span><span class="s">)</span> <span class="s">{</span>
+371         <span class="k">print</span> <span class="q">&quot;ATOM residues: &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>-&gt;{<span class="w">AtomResidueNames</span>}}<span class="cm">,</span> <span class="q">&#39;, &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+372       <span class="s">}</span>
+373       <span class="k">if</span> <span class="s">(</span><span class="i">$HetatmResiduesCount</span><span class="s">)</span> <span class="s">{</span>
+374         <span class="k">print</span> <span class="q">&quot;HETATM residues: &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>-&gt;{<span class="w">HetatmResidueNames</span>}}<span class="cm">,</span> <span class="q">&#39;, &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+375       <span class="s">}</span>
+376     <span class="s">}</span>
+377   <span class="s">}</span>
+378
+379   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ResiduesFrequencyAll</span>}<span class="s">)</span> <span class="s">{</span>
+380     <span class="k">my</span><span class="s">(</span><span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ResidueCount</span><span class="s">)</span><span class="sc">;</span>
+381
+382     <span class="c"># Setup a hash using residue count as key for sorting the values...</span>
+383     <span class="k">my</span><span class="s">(</span><span class="i">%ResiduesCountToNameMap</span><span class="cm">,</span> <span class="i">%AtomResiduesCountToNameMap</span><span class="cm">,</span> <span class="i">%HetatmResiduesCountToNameMap</span><span class="s">)</span><span class="sc">;</span>
+384     <span class="i">%ResiduesCountToNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+385     <span class="i">%</span>{<span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+386
+387     <span class="i">%AtomResiduesCountToNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+388     <span class="i">%</span>{<span class="i">$AtomResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+389
+390     <span class="i">%HetatmResiduesCountToNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+391     <span class="i">%</span>{<span class="i">$HetatmResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+392
+393     <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$ResiduesInfoRef</span>-&gt;{<span class="w">ResidueCount</span>}}<span class="s">)</span> <span class="s">{</span>
+394       <span class="i">$ResidueCount</span> = <span class="i">$ResiduesInfoRef</span>-&gt;{<span class="w">ResidueCount</span>}{<span class="i">$ResidueName</span>}<span class="sc">;</span>
+395       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>}<span class="s">)</span> <span class="s">{</span>
+396         <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} .= <span class="q">&quot;~${ResidueName}&quot;</span><span class="sc">;</span>
+397       <span class="s">}</span>
+398       <span class="k">else</span> <span class="s">{</span>
+399         <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} = <span class="i">$ResidueName</span><span class="sc">;</span>
+400       <span class="s">}</span>
+401     <span class="s">}</span>
+402
+403     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+404       <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$ResiduesInfoRef</span>-&gt;{<span class="w">AtomResidueCount</span>}}<span class="s">)</span> <span class="s">{</span>
+405         <span class="i">$ResidueCount</span> = <span class="i">$ResiduesInfoRef</span>-&gt;{<span class="w">AtomResidueCount</span>}{<span class="i">$ResidueName</span>}<span class="sc">;</span>
+406         <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>}<span class="s">)</span> <span class="s">{</span>
+407           <span class="i">$AtomResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} .= <span class="q">&quot;~${ResidueName}&quot;</span><span class="sc">;</span>
+408         <span class="s">}</span>
+409         <span class="k">else</span> <span class="s">{</span>
+410           <span class="i">$AtomResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} = <span class="i">$ResidueName</span><span class="sc">;</span>
+411         <span class="s">}</span>
+412       <span class="s">}</span>
+413       <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$ResiduesInfoRef</span>-&gt;{<span class="w">HetatmResidueCount</span>}}<span class="s">)</span> <span class="s">{</span>
+414         <span class="i">$ResidueCount</span> = <span class="i">$ResiduesInfoRef</span>-&gt;{<span class="w">HetatmResidueCount</span>}{<span class="i">$ResidueName</span>}<span class="sc">;</span>
+415         <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$HetatmResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>}<span class="s">)</span> <span class="s">{</span>
+416           <span class="i">$HetatmResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} .= <span class="q">&quot;~${ResidueName}&quot;</span><span class="sc">;</span>
+417         <span class="s">}</span>
+418         <span class="k">else</span> <span class="s">{</span>
+419           <span class="i">$HetatmResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} = <span class="i">$ResidueName</span><span class="sc">;</span>
+420         <span class="s">}</span>
+421       <span class="s">}</span>
+422     <span class="s">}</span>
+423
+424     <span class="c"># Setup distribution of residues info...</span>
+425     <span class="k">my</span><span class="s">(</span><span class="i">$ResidueNames</span><span class="cm">,</span> <span class="i">$PercentResidueCount</span><span class="cm">,</span> <span class="i">@ResidueNamesList</span><span class="cm">,</span> <span class="i">%ResiduesCountInfoMap</span><span class="cm">,</span> <span class="i">%AtomResiduesCountInfoMap</span><span class="cm">,</span> <span class="i">%HetatmResiduesCountInfoMap</span><span class="s">)</span><span class="sc">;</span>
+426
+427     <span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">Frequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+428     <span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+429     <span class="k">for</span> <span class="i">$ResidueCount</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span><span class="i">$b</span> &lt;=&gt; <span class="i">$a</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}}<span class="s">)</span> <span class="s">{</span>
+430       <span class="i">$PercentResidueCount</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.1f&quot;</span><span class="cm">,</span> <span class="s">(</span><span class="s">(</span><span class="i">$ResidueCount</span>/<span class="i">$TotalResidueCount</span><span class="s">)</span>*<span class="n">100</span><span class="s">)</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+431       <span class="i">$ResidueNames</span> = <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>}<span class="sc">;</span>
+432       <span class="i">@ResidueNamesList</span> = <span class="k">split</span> <span class="q">/~/</span><span class="cm">,</span> <span class="i">$ResidueNames</span><span class="sc">;</span>
+433       <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@ResidueNamesList</span><span class="s">)</span> <span class="s">{</span>
+434         <span class="k">push</span> <span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span> <span class="q">&quot;${ResidueName} - ${ResidueCount}&quot;</span><span class="sc">;</span>
+435         <span class="k">push</span> <span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span> <span class="q">&quot;${ResidueName} - ${PercentResidueCount}&quot;</span><span class="sc">;</span>
+436       <span class="s">}</span>
+437     <span class="s">}</span>
+438     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+439       <span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">Frequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+440       <span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+441       <span class="k">for</span> <span class="i">$ResidueCount</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span><span class="i">$b</span> &lt;=&gt; <span class="i">$a</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$AtomResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}}<span class="s">)</span> <span class="s">{</span>
+442         <span class="i">$PercentResidueCount</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.1f&quot;</span><span class="cm">,</span> <span class="s">(</span><span class="s">(</span><span class="i">$ResidueCount</span>/<span class="i">$TotalResidueCount</span><span class="s">)</span>*<span class="n">100</span><span class="s">)</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+443         <span class="i">$ResidueNames</span> = <span class="i">$AtomResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>}<span class="sc">;</span>
+444         <span class="i">@ResidueNamesList</span> = <span class="k">split</span> <span class="q">/~/</span><span class="cm">,</span> <span class="i">$ResidueNames</span><span class="sc">;</span>
+445         <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@ResidueNamesList</span><span class="s">)</span> <span class="s">{</span>
+446           <span class="k">push</span> <span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span> <span class="q">&quot;${ResidueName} - ${ResidueCount}&quot;</span><span class="sc">;</span>
+447           <span class="k">push</span> <span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span> <span class="q">&quot;${ResidueName} - ${PercentResidueCount}&quot;</span><span class="sc">;</span>
+448         <span class="s">}</span>
+449       <span class="s">}</span>
+450       <span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">Frequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+451       <span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+452       <span class="k">for</span> <span class="i">$ResidueCount</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span><span class="i">$b</span> &lt;=&gt; <span class="i">$a</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$HetatmResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}}<span class="s">)</span> <span class="s">{</span>
+453         <span class="i">$PercentResidueCount</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.1f&quot;</span><span class="cm">,</span> <span class="s">(</span><span class="s">(</span><span class="i">$ResidueCount</span>/<span class="i">$TotalResidueCount</span><span class="s">)</span>*<span class="n">100</span><span class="s">)</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+454         <span class="i">$ResidueNames</span> = <span class="i">$HetatmResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>}<span class="sc">;</span>
+455         <span class="i">@ResidueNamesList</span> = <span class="k">split</span> <span class="q">/~/</span><span class="cm">,</span> <span class="i">$ResidueNames</span><span class="sc">;</span>
+456         <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@ResidueNamesList</span><span class="s">)</span> <span class="s">{</span>
+457           <span class="k">push</span> <span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span> <span class="q">&quot;${ResidueName} - ${ResidueCount}&quot;</span><span class="sc">;</span>
+458           <span class="k">push</span> <span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span> <span class="q">&quot;${ResidueName} - ${PercentResidueCount}&quot;</span><span class="sc">;</span>
+459         <span class="s">}</span>
+460       <span class="s">}</span>
+461     <span class="s">}</span>
+462
+463     <span class="c"># List distribution of residues</span>
+464     <span class="k">print</span> <span class="q">&quot;\nDistribution of residues: &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span><span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+465     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+466       <span class="k">print</span> <span class="q">&quot;\nPercent distribution of residues: &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span><span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+467     <span class="s">}</span>
+468
+469     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+470       <span class="k">print</span> <span class="q">&quot;\nDistribution of ATOM residues: &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span><span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+471       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+472         <span class="k">print</span> <span class="q">&quot;\nPercent distribution of ATOM residues: &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span><span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+473       <span class="s">}</span>
+474
+475       <span class="k">print</span> <span class="q">&quot;\nDistribution of HETATM residues: &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span><span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+476       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+477         <span class="k">print</span> <span class="q">&quot;\nPercent distribution of HETATM residues: &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span><span class="q">&#39;; &#39;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+478       <span class="s">}</span>
+479     <span class="s">}</span>
+480   <span class="s">}</span>
+481 <span class="s">}</span>
+482
+483 <span class="c"># List information about residue numbers for each chain...</span>
+<a name="ListResidueNumbersInfo-"></a> 484 <span class="k">sub </span><span class="m">ListResidueNumbersInfo</span> <span class="s">{</span>
+485   <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+486   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ResidueCount</span><span class="cm">,</span> <span class="i">$StartResidueNum</span><span class="cm">,</span> <span class="i">$EndResidueNum</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$CollectChainResiduesBeyondTER</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$ResidueNum</span><span class="cm">,</span> <span class="i">$PreviousResidueNum</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$PreviousResidueName</span><span class="cm">,</span> <span class="i">$GapResiduePairsCount</span><span class="cm">,</span> <span class="i">$GapLength</span><span class="cm">,</span> <span class="i">$DescendingOrderResiduePairsCount</span><span class="cm">,</span> <span class="i">@DescendingOrderResiduePairs</span><span class="cm">,</span> <span class="i">@GapResiduePairs</span><span class="s">)</span><span class="sc">;</span>
+487
+488   <span class="i">$CollectChainResiduesBeyondTER</span> = <span class="n">0</span><span class="sc">;</span>
+489   <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="q">&#39;AtomAndHetatm&#39;</span><span class="cm">,</span> <span class="i">$CollectChainResiduesBeyondTER</span><span class="s">)</span><span class="sc">;</span>
+490
+491   <span class="k">print</span> <span class="q">&quot;\nATOM/HETATM residue numbers information for chains:\n&quot;</span><span class="sc">;</span>
+492
+493   <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+494     <span class="k">print</span> <span class="q">&quot;\nChain ID - &quot;</span><span class="cm">,</span>  <span class="i">CleanupChainID</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;&quot;</span><span class="sc">;</span>
+495
+496     <span class="i">$ResidueCount</span> = <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ResidueNumbers</span>}{<span class="i">$ChainID</span>}}<span class="sc">;</span>
+497
+498     <span class="c"># Start and end residue numbers...</span>
+499     <span class="i">$StartResidueNum</span> = <span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ResidueNumbers</span>}{<span class="i">$ChainID</span>}[<span class="n">0</span>]<span class="sc">;</span>
+500     <span class="i">$EndResidueNum</span> = <span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ResidueNumbers</span>}{<span class="i">$ChainID</span>}[<span class="i">$ResidueCount</span> - <span class="n">1</span>]<span class="sc">;</span>
+501     <span class="k">print</span> <span class="q">&quot;; Number of residues: $ResidueCount; Start residue number - $StartResidueNum; End residue number - $EndResidueNum\n&quot;</span><span class="sc">;</span>
+502
+503     <span class="c"># Identify any gaps in residue numbers or non-ascending order residue numbers...</span>
+504     <span class="i">$GapResiduePairsCount</span> = <span class="n">0</span><span class="sc">;</span>
+505     <span class="i">$DescendingOrderResiduePairsCount</span> = <span class="n">0</span><span class="sc">;</span>
+506
+507     <span class="i">@DescendingOrderResiduePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+508     <span class="i">@GapResiduePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+509
+510     <span class="j">RESIDUE:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="s">(</span><span class="i">$ResidueCount</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+511       <span class="i">$ResidueNum</span> = <span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ResidueNumbers</span>}{<span class="i">$ChainID</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
+512       <span class="i">$PreviousResidueNum</span> = <span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ResidueNumbers</span>}{<span class="i">$ChainID</span>}[<span class="i">$Index</span> - <span class="n">1</span>]<span class="sc">;</span>
+513
+514       <span class="i">$ResidueName</span> = <span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
+515       <span class="i">$PreviousResidueName</span> = <span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}[<span class="i">$Index</span> - <span class="n">1</span>]<span class="sc">;</span>
+516
+517       <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueNum</span> == <span class="s">(</span><span class="i">$PreviousResidueNum</span> + <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+518         <span class="c"># All is good...</span>
+519         <span class="k">next</span> <span class="j">RESIDUE</span><span class="sc">;</span>
+520       <span class="s">}</span>
+521
+522       <span class="c"># Are residue in descending order?</span>
+523       <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueNum</span> &lt; <span class="i">$PreviousResidueNum</span><span class="s">)</span> <span class="s">{</span>
+524         <span class="i">$DescendingOrderResiduePairsCount</span>++<span class="sc">;</span>
+525         <span class="k">push</span> <span class="i">@DescendingOrderResiduePairs</span><span class="cm">,</span> <span class="q">&quot;&lt;${PreviousResidueName}${PreviousResidueNum} - ${ResidueName}${ResidueNum}&gt;&quot;</span><span class="sc">;</span>
+526       <span class="s">}</span>
+527
+528       <span class="c"># Track gaps in residue pairs...</span>
+529       <span class="i">$GapResiduePairsCount</span>++<span class="sc">;</span>
+530       <span class="i">$GapLength</span> = <span class="k">abs</span><span class="s">(</span><span class="i">$ResidueNum</span> - <span class="i">$PreviousResidueNum</span><span class="s">)</span> - <span class="n">1</span><span class="sc">;</span>
+531
+532       <span class="k">push</span> <span class="i">@GapResiduePairs</span><span class="cm">,</span> <span class="q">&quot;&lt;${PreviousResidueName}${PreviousResidueNum} - ${ResidueName}${ResidueNum}; $GapLength&gt;&quot;</span><span class="sc">;</span>
+533     <span class="s">}</span>
+534
+535     <span class="c"># Print gaps information...</span>
+536     <span class="k">print</span> <span class="q">&quot;Gaps in residue numbers: &quot;</span><span class="cm">,</span> <span class="i">$GapResiduePairsCount</span> ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;None&quot;</span><span class="sc">;</span>
+537     <span class="k">if</span> <span class="s">(</span><span class="i">$GapResiduePairsCount</span><span class="s">)</span> <span class="s">{</span>
+538       <span class="k">print</span> <span class="q">&quot;; Number of gap residue number pairs: $GapResiduePairsCount; Gap residue pairs: &lt;StartRes-EndRes; GapLength&gt; - &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@GapResiduePairs</span><span class="cm">,</span> <span class="q">&quot;; &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
+539     <span class="s">}</span>
+540     <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+541
+542     <span class="c"># Print descending residue order information...</span>
+543     <span class="k">print</span> <span class="q">&quot;Residue numbers in descending order: &quot;</span><span class="cm">,</span> <span class="i">$DescendingOrderResiduePairsCount</span> ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;None&quot;</span><span class="sc">;</span>
+544     <span class="k">if</span> <span class="s">(</span><span class="i">$DescendingOrderResiduePairsCount</span><span class="s">)</span> <span class="s">{</span>
+545       <span class="k">print</span> <span class="q">&quot;; Number of descending residue number pairs: $DescendingOrderResiduePairsCount; Descending residue number pairs: &lt;StartRes-EndRes&gt; &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@DescendingOrderResiduePairs</span><span class="cm">,</span> <span class="q">&quot;; &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
+546     <span class="s">}</span>
+547     <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+548   <span class="s">}</span>
+549 <span class="s">}</span>
+550
+551 <span class="c"># List min/max XYZ coordinates for ATOM/HETATM records...</span>
+<a name="ListBoundingBox-"></a> 552 <span class="k">sub </span><span class="m">ListBoundingBox</span> <span class="s">{</span>
+553   <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+554   <span class="k">my</span><span class="s">(</span><span class="i">$XMin</span><span class="cm">,</span> <span class="i">$YMin</span><span class="cm">,</span> <span class="i">$ZMin</span><span class="cm">,</span> <span class="i">$XMax</span><span class="cm">,</span> <span class="i">$YMax</span><span class="cm">,</span> <span class="i">$ZMax</span><span class="cm">,</span> <span class="i">$XSize</span><span class="cm">,</span> <span class="i">$YSize</span><span class="cm">,</span> <span class="i">$ZSize</span><span class="s">)</span><span class="sc">;</span>
+555
+556   <span class="s">(</span><span class="i">$XMin</span><span class="cm">,</span> <span class="i">$YMin</span><span class="cm">,</span> <span class="i">$ZMin</span><span class="cm">,</span> <span class="i">$XMax</span><span class="cm">,</span> <span class="i">$YMax</span><span class="cm">,</span> <span class="i">$ZMax</span><span class="s">)</span> = <span class="i">GetMinMaxCoords</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+557   <span class="i">$XSize</span> = <span class="k">abs</span><span class="s">(</span><span class="i">$XMax</span> - <span class="i">$XMin</span><span class="s">)</span><span class="sc">;</span>
+558   <span class="i">$YSize</span> = <span class="k">abs</span><span class="s">(</span><span class="i">$YMax</span> - <span class="i">$YMin</span><span class="s">)</span><span class="sc">;</span>
+559   <span class="i">$ZSize</span> = <span class="k">abs</span><span class="s">(</span><span class="i">$ZMax</span> - <span class="i">$ZMin</span><span class="s">)</span><span class="sc">;</span>
+560
+561   <span class="i">$XMin</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.3f&quot;</span><span class="cm">,</span> <span class="i">$XMin</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> <span class="i">$XMax</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.3f&quot;</span><span class="cm">,</span> <span class="i">$XMax</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+562   <span class="i">$YMin</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.3f&quot;</span><span class="cm">,</span> <span class="i">$YMin</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> <span class="i">$YMax</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.3f&quot;</span><span class="cm">,</span> <span class="i">$YMax</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+563   <span class="i">$ZMin</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.3f&quot;</span><span class="cm">,</span> <span class="i">$ZMin</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> <span class="i">$ZMax</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.3f&quot;</span><span class="cm">,</span> <span class="i">$ZMax</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+564
+565   <span class="i">$XSize</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.3f&quot;</span><span class="cm">,</span> <span class="i">$XSize</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+566   <span class="i">$YSize</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.3f&quot;</span><span class="cm">,</span> <span class="i">$YSize</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+567   <span class="i">$ZSize</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.3f&quot;</span><span class="cm">,</span> <span class="i">$ZSize</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+568
+569   <span class="k">print</span> <span class="q">&quot;\nBounding box coordinates: &lt;XMin, XMax&gt; - &lt;$XMin, $XMax&gt;; &lt;YMin, YMax&gt; - &lt;$YMin, $YMax&gt;; &lt;ZMin, ZMax&gt; - &lt;$ZMin, $ZMax&gt;;\n&quot;</span><span class="sc">;</span>
+570   <span class="k">print</span> <span class="q">&quot;Bounding box size in angstroms: XSize - $XSize; YSize - $YSize; ZSize - $ZSize\n&quot;</span><span class="sc">;</span>
+571
+572 <span class="s">}</span>
+573
+574 <span class="c"># Check master record counts against actual record counts...</span>
+<a name="CheckMasterRecord-"></a> 575 <span class="k">sub </span><span class="m">CheckMasterRecord</span> <span class="s">{</span>
+576   <span class="k">my</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+577
+578   <span class="c"># Get master record information...</span>
+579   <span class="k">my</span><span class="s">(</span><span class="i">$NumOfRemarkRecords</span><span class="cm">,</span> <span class="i">$NumOfHetRecords</span><span class="cm">,</span> <span class="i">$NumOfHelixRecords</span><span class="cm">,</span> <span class="i">$NumOfSheetRecords</span><span class="cm">,</span> <span class="i">$NumOfTurnRecords</span><span class="cm">,</span> <span class="i">$NumOfSiteRecords</span><span class="cm">,</span> <span class="i">$NumOfTransformationsRecords</span><span class="cm">,</span> <span class="i">$NumOfAtomAndHetatmRecords</span><span class="cm">,</span> <span class="i">$NumOfTerRecords</span><span class="cm">,</span> <span class="i">$NumOfConectRecords</span><span class="cm">,</span> <span class="i">$NumOfSeqresRecords</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">11</span><span class="sc">;</span>
+580   <span class="k">my</span><span class="s">(</span><span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$MasterRecordFound</span><span class="s">)</span><span class="sc">;</span>
+581   <span class="i">$MasterRecordFound</span> = <span class="n">0</span><span class="sc">;</span>
+582
+583   <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+584       <span class="k">if</span> <span class="s">(</span><span class="i">IsMasterRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+585         <span class="s">(</span><span class="i">$NumOfRemarkRecords</span><span class="cm">,</span> <span class="i">$NumOfHetRecords</span><span class="cm">,</span> <span class="i">$NumOfHelixRecords</span><span class="cm">,</span> <span class="i">$NumOfSheetRecords</span><span class="cm">,</span> <span class="i">$NumOfTurnRecords</span><span class="cm">,</span> <span class="i">$NumOfSiteRecords</span><span class="cm">,</span> <span class="i">$NumOfTransformationsRecords</span><span class="cm">,</span> <span class="i">$NumOfAtomAndHetatmRecords</span><span class="cm">,</span> <span class="i">$NumOfTerRecords</span><span class="cm">,</span> <span class="i">$NumOfConectRecords</span><span class="cm">,</span> <span class="i">$NumOfSeqresRecords</span><span class="s">)</span> = <span class="i">ParseMasterRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+586         <span class="i">$MasterRecordFound</span> = <span class="n">1</span><span class="sc">;</span>
+587         <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span>
+588       <span class="s">}</span>
+589   <span class="s">}</span>
+590   <span class="k">if</span> <span class="s">(</span>!<span class="i">$MasterRecordFound</span><span class="s">)</span> <span class="s">{</span>
+591     <span class="k">print</span> <span class="q">&quot;\nWarning: MASTER record is missing.\n&quot;</span><span class="sc">;</span>
+592     <span class="k">return</span><span class="sc">;</span>
+593   <span class="s">}</span>
+594   <span class="k">my</span><span class="s">(</span><span class="i">@MasterRecordValidationInfo</span><span class="s">)</span><span class="sc">;</span>
+595   <span class="i">@MasterRecordValidationInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+596   <span class="i">$NumOfRemarkRecords</span> += <span class="n">0</span><span class="sc">;</span>
+597   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">REMARK</span>}<span class="s">)</span> &amp;&amp; <span class="i">$NumOfRemarkRecords</span> != <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">REMARK</span>}<span class="s">)</span> <span class="s">{</span>
+598     <span class="k">push</span> <span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;Number of REMARK records, $NumOfRemarkRecords, specified in MASTER record doen&#39;t match its explict count, $RecordTypesCountRef-&gt;{Count}{REMARK}.&quot;</span><span class="sc">;</span>
+599   <span class="s">}</span>
+600   <span class="i">$NumOfHetRecords</span> += <span class="n">0</span><span class="sc">;</span>
+601   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">HET</span>}<span class="s">)</span> &amp;&amp; <span class="i">$NumOfHetRecords</span> != <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">HET</span>}<span class="s">)</span> <span class="s">{</span>
+602     <span class="k">push</span> <span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;Number of HET records, $NumOfHetRecords, specified in MASTER record doen&#39;t match its explict count, $RecordTypesCountRef-&gt;{Count}{HET}.&quot;</span><span class="sc">;</span>
+603   <span class="s">}</span>
+604   <span class="i">$NumOfHelixRecords</span> += <span class="n">0</span><span class="sc">;</span>
+605   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">HELIX</span>}<span class="s">)</span> &amp;&amp; <span class="i">$NumOfHelixRecords</span> != <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">HELIX</span>}<span class="s">)</span> <span class="s">{</span>
+606     <span class="k">push</span> <span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;Number of HELIX records, $NumOfHelixRecords, specified in MASTER record doen&#39;t match its explict count, $RecordTypesCountRef-&gt;{Count}{HELIX}.&quot;</span><span class="sc">;</span>
+607   <span class="s">}</span>
+608   <span class="i">$NumOfSheetRecords</span> += <span class="n">0</span><span class="sc">;</span>
+609   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">SHEET</span>}<span class="s">)</span> &amp;&amp; <span class="i">$NumOfSheetRecords</span> != <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">SHEET</span>}<span class="s">)</span> <span class="s">{</span>
+610     <span class="k">push</span> <span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;Number of SHEET records, $NumOfSheetRecords, specified in MASTER record doen&#39;t match its explict count, $RecordTypesCountRef-&gt;{Count}{SHEET}.&quot;</span><span class="sc">;</span>
+611   <span class="s">}</span>
+612   <span class="i">$NumOfTurnRecords</span> += <span class="n">0</span><span class="sc">;</span>
+613   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">TURN</span>}<span class="s">)</span> &amp;&amp; <span class="i">$NumOfTurnRecords</span> != <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">TURN</span>}<span class="s">)</span> <span class="s">{</span>
+614     <span class="k">push</span> <span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;Number of TURN records, $NumOfTurnRecords, specified in MASTER record doen&#39;t match its explict count, $RecordTypesCountRef-&gt;{Count}{REMARK}.&quot;</span><span class="sc">;</span>
+615   <span class="s">}</span>
+616   <span class="i">$NumOfSiteRecords</span> += <span class="n">0</span><span class="sc">;</span>
+617   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">SITE</span>}<span class="s">)</span> &amp;&amp; <span class="i">$NumOfSiteRecords</span> != <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">SITE</span>}<span class="s">)</span> <span class="s">{</span>
+618     <span class="k">push</span> <span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;Number of SITE records, $NumOfSiteRecords, specified in MASTER record doen&#39;t match its explict count, $RecordTypesCountRef-&gt;{Count}{SITE}.&quot;</span><span class="sc">;</span>
+619   <span class="s">}</span>
+620
+621   <span class="i">$NumOfTransformationsRecords</span> += <span class="n">0</span><span class="sc">;</span>
+622   <span class="k">my</span><span class="s">(</span><span class="i">$RecordsCount</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$RecordID</span><span class="cm">,</span> <span class="i">$RecordLabel</span><span class="s">)</span><span class="sc">;</span>
+623   <span class="i">$RecordsCount</span> = <span class="n">0</span><span class="sc">;</span>
+624   <span class="k">for</span> <span class="i">$RecordLabel</span> <span class="s">(</span><span class="q">&#39;ORIGX&#39;</span><span class="cm">,</span> <span class="q">&#39;SCALE&#39;</span><span class="cm">,</span> <span class="q">&#39;MTRIX&#39;</span><span class="s">)</span> <span class="s">{</span>
+625     <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="n">1</span> .. <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
+626       <span class="i">$RecordID</span> = <span class="q">&quot;${RecordLabel}${ID}&quot;</span><span class="sc">;</span>
+627       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="i">$RecordID</span>}<span class="s">)</span> <span class="s">{</span>
+628         <span class="i">$RecordsCount</span> += <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="i">$RecordID</span>}<span class="sc">;</span>
+629       <span class="s">}</span>
+630     <span class="s">}</span>
+631   <span class="s">}</span>
+632   <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfTransformationsRecords</span> != <span class="i">$RecordsCount</span><span class="s">)</span> <span class="s">{</span>
+633     <span class="k">push</span> <span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;Number of transformation records (ORIGXn+SCALEn+MTRIXn), $NumOfTransformationsRecords, specified in MASTER record doen&#39;t match its explict count, $RecordsCount.&quot;</span><span class="sc">;</span>
+634   <span class="s">}</span>
+635
+636   <span class="i">$RecordsCount</span> = <span class="n">0</span><span class="sc">;</span>
+637   <span class="k">for</span> <span class="i">$RecordLabel</span> <span class="s">(</span><span class="q">&#39;ATOM&#39;</span><span class="cm">,</span> <span class="q">&#39;HETATM&#39;</span><span class="s">)</span> <span class="s">{</span>
+638       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="i">$RecordLabel</span>}<span class="s">)</span> <span class="s">{</span>
+639         <span class="i">$RecordsCount</span> += <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="i">$RecordLabel</span>}<span class="sc">;</span>
+640       <span class="s">}</span>
+641   <span class="s">}</span>
+642   <span class="i">$NumOfAtomAndHetatmRecords</span> += <span class="n">0</span><span class="sc">;</span>
+643   <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfAtomAndHetatmRecords</span> != <span class="i">$RecordsCount</span><span class="s">)</span> <span class="s">{</span>
+644     <span class="k">push</span> <span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;Number of ATOM + HETATM records, $NumOfAtomAndHetatmRecords, specified in MASTER record doen&#39;t match its explict count, $RecordsCount.&quot;</span><span class="sc">;</span>
+645   <span class="s">}</span>
+646   <span class="i">$NumOfTerRecords</span> += <span class="n">0</span><span class="sc">;</span>
+647   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">TER</span>}<span class="s">)</span> &amp;&amp; <span class="i">$NumOfTerRecords</span> != <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">TER</span>}<span class="s">)</span> <span class="s">{</span>
+648     <span class="k">push</span> <span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;Number of TER records, $NumOfTerRecords, specified in MASTER record doen&#39;t match its explict count, $RecordTypesCountRef-&gt;{Count}{TER}.&quot;</span><span class="sc">;</span>
+649   <span class="s">}</span>
+650   <span class="i">$NumOfConectRecords</span> += <span class="n">0</span><span class="sc">;</span>
+651   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">CONECT</span>}<span class="s">)</span> &amp;&amp; <span class="i">$NumOfConectRecords</span> != <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">CONECT</span>}<span class="s">)</span> <span class="s">{</span>
+652     <span class="k">push</span> <span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;Number of CONECT records, $NumOfConectRecords, specified in MASTER record doen&#39;t match its explict count, $RecordTypesCountRef-&gt;{Count}{CONECT}.&quot;</span><span class="sc">;</span>
+653   <span class="s">}</span>
+654   <span class="i">$NumOfSeqresRecords</span> += <span class="n">0</span><span class="sc">;</span>
+655   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">SEQRES</span>}<span class="s">)</span> &amp;&amp; <span class="i">$NumOfSeqresRecords</span> != <span class="i">$RecordTypesCountRef</span>-&gt;{<span class="w">Count</span>}{<span class="w">SEQRES</span>}<span class="s">)</span> <span class="s">{</span>
+656     <span class="k">push</span> <span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;Number of SITE records, $NumOfSeqresRecords, specified in MASTER record doen&#39;t match its explict count, $RecordTypesCountRef-&gt;{Count}{SEQRES}.&quot;</span><span class="sc">;</span>
+657   <span class="s">}</span>
+658
+659   <span class="k">if</span> <span class="s">(</span><span class="i">@MasterRecordValidationInfo</span><span class="s">)</span> <span class="s">{</span>
+660     <span class="k">print</span> <span class="q">&quot;\nMASTER record validation: Count mismatches found:\n&quot;</span><span class="sc">;</span>
+661     <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+662   <span class="s">}</span>
+663   <span class="k">else</span> <span class="s">{</span>
+664     <span class="k">print</span> <span class="q">&quot;\nMASTER record validation: Count values match with the explicit count of the corresponding records.\n&quot;</span><span class="sc">;</span>
+665   <span class="s">}</span>
+666 <span class="s">}</span>
+667
+668 <span class="c"># Total size of all the files...</span>
+<a name="ListTotalSizeOfFiles-"></a> 669 <span class="k">sub </span><span class="m">ListTotalSizeOfFiles</span> <span class="s">{</span>
+670   <span class="k">my</span><span class="s">(</span><span class="i">$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>
+671
+672   <span class="i">$FileOkayCount</span> = <span class="n">0</span><span class="sc">;</span>
+673   <span class="i">$TotalSize</span> = <span class="n">0</span><span class="sc">;</span>
+674
+675   <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
+676     <span class="k">if</span> <span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span>
+677       <span class="i">$FileOkayCount</span>++<span class="sc">;</span>
+678       <span class="i">$TotalSize</span> += <span class="i">$PDBFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
+679     <span class="s">}</span>
+680   <span class="s">}</span>
+681   <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>
+682     <span class="k">print</span> <span class="q">&quot;\nTotal size of $FileOkayCount files: &quot;</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$TotalSize</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+683   <span class="s">}</span>
+684
+685 <span class="s">}</span>
+686
+687 <span class="c"># Empty chain IDs are replaced with &quot;None[1-9]&quot;. But for displaying purposes, take out any</span>
+688 <span class="c"># numbers from label...</span>
+<a name="CleanupChainID-"></a> 689 <span class="k">sub </span><span class="m">CleanupChainID</span> <span class="s">{</span>
+690   <span class="k">my</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+691
+692   <span class="k">if</span> <span class="s">(</span><span class="i">$ChainID</span> =~ <span class="q">/^None/i</span><span class="s">)</span> <span class="s">{</span>
+693     <span class="k">return</span> <span class="q">&#39;None&#39;</span><span class="sc">;</span>
+694   <span class="s">}</span>
+695   <span class="k">return</span> <span class="i">$ChainID</span><span class="sc">;</span>
+696 <span class="s">}</span>
+697
+698 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 699 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+700   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+701
+702   <span class="c"># Setup record types to count...</span>
+703   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">count</span>}<span class="s">)</span> <span class="s">{</span>
+704     <span class="i">$OptionsInfo</span>{<span class="w">CountRecordType</span>} = <span class="i">$Options</span>{<span class="w">count</span>}<span class="sc">;</span>
+705   <span class="s">}</span>
+706   <span class="k">else</span> <span class="s">{</span>
+707     <span class="i">$OptionsInfo</span>{<span class="w">CountRecordType</span>} = <span class="i">$Options</span>{<span class="w">all</span>} ? <span class="q">&#39;All&#39;</span> <span class="co">:</span> <span class="q">&#39;ATOM,HETATM&#39;</span><span class="sc">;</span>
+708   <span class="s">}</span>
+709   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRecordTypes</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+710   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountRecordType</span>} !~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+711     <span class="k">my</span><span class="s">(</span><span class="i">@RecordTypes</span><span class="s">)</span><span class="sc">;</span>
+712     <span class="i">@RecordTypes</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CountRecordType</span>}<span class="sc">;</span>
+713     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRecordTypes</span>}}<span class="cm">,</span> <span class="i">@RecordTypes</span><span class="sc">;</span>
+714   <span class="s">}</span>
+715   <span class="i">$OptionsInfo</span>{<span class="w">CountChains</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">chains</span>} || <span class="i">$Options</span>{<span class="w">all</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+716   <span class="i">$OptionsInfo</span>{<span class="w">CheckMasterRecord</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">mastercheck</span>} || <span class="i">$Options</span>{<span class="w">all</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+717
+718   <span class="c"># Residue count is the default. So $Options{residues} is simply ignored.</span>
+719   <span class="k">my</span><span class="s">(</span><span class="i">$CountResidues</span><span class="s">)</span> = <span class="n">1</span><span class="sc">;</span>
+720   <span class="i">$OptionsInfo</span>{<span class="w">CountResiduesInChains</span>} = <span class="s">(</span><span class="s">(</span><span class="i">$CountResidues</span> || <span class="i">$Options</span>{<span class="w">all</span>}<span class="s">)</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">residuesmode</span>} =~ <span class="q">/^(InChains|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+721   <span class="i">$OptionsInfo</span>{<span class="w">CountResiduesAll</span>} = <span class="s">(</span><span class="s">(</span><span class="i">$CountResidues</span> || <span class="i">$Options</span>{<span class="w">all</span>}<span class="s">)</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">residuesmode</span>} =~ <span class="q">/^(All|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+722
+723   <span class="i">$OptionsInfo</span>{<span class="w">ResiduesFrequencyInChains</span>} = <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">frequency</span>} || <span class="i">$Options</span>{<span class="w">all</span>}<span class="s">)</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">residuesmode</span>} =~ <span class="q">/^(InChains|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+724   <span class="i">$OptionsInfo</span>{<span class="w">ResiduesFrequencyAll</span>} = <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">frequency</span>} || <span class="i">$Options</span>{<span class="w">all</span>}<span class="s">)</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">residuesmode</span>} =~ <span class="q">/^(All|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+725
+726   <span class="i">$OptionsInfo</span>{<span class="w">ResidueNumbersInfo</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumbers</span>} || <span class="i">$Options</span>{<span class="w">all</span>}<span class="s">)</span>  ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+727
+728   <span class="i">$OptionsInfo</span>{<span class="w">CalculateBoundingBox</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">boundingbox</span>} || <span class="i">$Options</span>{<span class="w">all</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+729
+730   <span class="i">$OptionsInfo</span>{<span class="w">ListHeaderInfo</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">header</span>} || <span class="i">$Options</span>{<span class="w">all</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+731   <span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span>
+732
+733   <span class="i">$OptionsInfo</span>{<span class="w">ListExperimentalTechniqueInfo</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">experiment</span>} || <span class="i">$Options</span>{<span class="w">all</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+734
+735 <span class="s">}</span>
+736
+737 <span class="c"># Retrieve information about PDB files...</span>
+<a name="RetrievePDBFilesInfo-"></a> 738 <span class="k">sub </span><span class="m">RetrievePDBFilesInfo</span> <span class="s">{</span>
+739   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$PDBFile</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>
+740
+741   <span class="i">%PDBFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+742   <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+743   <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileSize</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+744   <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileLastModified</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+745
+746   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
+747     <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+748     <span class="i">$PDBFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+749     <span class="i">$PDBFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+750
+751     <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+752     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$PDBFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+753       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+754       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+755     <span class="s">}</span>
+756     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="q">&quot;pdb&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+757       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: It&#39;s not a PDB file\n&quot;</span><span class="sc">;</span>
+758       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+759     <span class="s">}</span>
+760     <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">PDBFILE</span><span class="cm">,</span> <span class="q">&quot;$PDBFile&quot;</span><span class="s">)</span> <span class="s">{</span>
+761       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+762       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+763     <span class="s">}</span>
+764     <span class="k">close</span> <span class="w">PDBFILE</span><span class="sc">;</span>
+765
+766     <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+767     <span class="i">$PDBFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>] = <span class="i">FileSize</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
+768     <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">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
+769     <span class="i">$PDBFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">&quot;$ModifiedTimeString; $ModifiedDateString&quot;</span><span class="sc">;</span>
+770   <span class="s">}</span>
+771 <span class="s">}</span>
+772
+773
+774 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 775 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+776
+777   <span class="c"># Retrieve all the options...</span>
+778   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+779   <span class="i">$Options</span>{<span class="w">count</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+780   <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
+781   <span class="i">$Options</span>{<span class="w">residuesmode</span>} = <span class="q">&#39;Both&#39;</span><span class="sc">;</span>
+782
+783   <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;boundingbox|b&quot;</span><span class="cm">,</span> <span class="q">&quot;count|c=s&quot;</span><span class="cm">,</span> <span class="q">&quot;chains&quot;</span><span class="cm">,</span> <span class="q">&quot;detail|d=i&quot;</span><span class="cm">,</span> <span class="q">&quot;experiment|e&quot;</span><span class="cm">,</span> <span class="q">&quot;frequency|f&quot;</span><span class="cm">,</span> <span class="q">&quot;mastercheck|m&quot;</span><span class="cm">,</span> <span class="q">&quot;header&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;residues&quot;</span><span class="cm">,</span> <span class="q">&quot;residuesmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;residuenumbers&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>
+784     <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 $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+785   <span class="s">}</span>
+786   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+787     <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>
+788       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+789     <span class="s">}</span>
+790     <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
+791   <span class="s">}</span>
+792   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+793     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{detail}, for option \&quot;-d --detail\&quot; is not valid. Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
+794   <span class="s">}</span>
+795   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">residuesmode</span>} !~ <span class="q">/^(InChains|All|Both)$/i</span><span class="s">)</span> <span class="s">{</span>
+796     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{residuesmode}, for option \&quot;--ResiduesMode\&quot; is not valid. Allowed values: InChains, All, or Both\n&quot;</span><span class="sc">;</span>
+797   <span class="s">}</span>
+798 <span class="s">}</span>
+799
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>

Mercurial > repos > deepakjadmin > mayatool3_test2

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