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diff docs/scripts/html/code/InfoPDBFiles.html @ 0:4816e4a8ae95 draft default tip
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| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/code/InfoPDBFiles.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,820 @@ +<html> +<head> +<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"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<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 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</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">$0</span><span class="s">)</span><span class="sc">;</span> + 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</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> < <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">"$FindBin::Bin/$ScriptName"</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">"pdb"</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">"Processing options...\n"</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">"Checking input PDB file(s)...\n"</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">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 70 <span class="k">if</span> <span class="s">(</span><span class="i">@PDBFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 71 <span class="k">print</span> <span class="q">"\nProcessing PDB files...\n"</span><span class="sc">;</span> + 72 <span class="s">}</span> + 73 <span class="k">for</span> <span class="i">$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">"\nProcessing file $PDBFilesList[$FileIndex]...\n"</span><span class="sc">;</span> + 76 <span class="i">ListPDBFileInfo</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 77 <span class="s">}</span> + 78 <span class="s">}</span> + 79 <span class="i">ListTotalSizeOfFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 80 + 81 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</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">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 86 + 87 <span class="c">###############################################################################</span> + 88 + 89 <span class="c"># List appropriate information...</span> +<a name="ListPDBFileInfo-"></a> 90 <span class="k">sub </span><span class="m">ListPDBFileInfo</span> <span class="s">{</span> + 91 <span class="k">my</span><span class="s">(</span><span class="i">$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">"\nTotal number of records: $TotalRecordsCount\n"</span><span class="sc">;</span> + 110 + 111 <span class="c"># List record type count information...</span> + 112 <span class="i">ListRecordTypesInfo</span><span class="s">(</span><span class="i">$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">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 125 <span class="s">}</span> + 126 + 127 <span class="c"># File size and modification information...</span> + 128 <span class="k">print</span> <span class="q">"\nFile size: "</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="s">)</span><span class="cm">,</span> <span class="q">" \n"</span><span class="sc">;</span> + 129 <span class="k">print</span> <span class="q">"Last modified: "</span><span class="cm">,</span> <span class="i">$PDBFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>]<span class="cm">,</span> <span class="q">" \n"</span><span class="sc">;</span> + 130 <span class="s">}</span> + 131 +<a name="ListHeaderInfo-"></a> 132 <span class="k">sub </span><span class="m">ListHeaderInfo</span> <span class="s">{</span> + 133 <span class="k">my</span><span class="s">(</span><span class="i">$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">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="sc">;</span> + 138 <span class="k">if</span> <span class="s">(</span><span class="i">IsHeaderRecordType</span><span class="s">(</span><span class="i">$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">'Not available'</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">$DepositionDate</span><span class="s">)</span> ? <span class="q">'Not available'</span> <span class="co">:</span> <span class="i">$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">'Not available'</span> <span class="co">:</span> <span class="i">$IDCode</span><span class="sc">;</span> + 145 + 146 <span class="k">print</span> <span class="q">"\nClassification: $Classification\nID: $IDCode\nDeposition date: $DepositionDate\n"</span><span class="sc">;</span> + 147 <span class="s">}</span> + 148 + 149 <span class="c"># List experimental technique information info...</span> +<a name="ListExperimentalTechniqueInfo-"></a> 150 <span class="k">sub </span><span class="m">ListExperimentalTechniqueInfo</span> <span class="s">{</span> + 151 <span class="k">my</span><span class="s">(</span><span class="i">$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">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 155 <span class="k">print</span> <span class="q">"\nExperimental technique: "</span> . <span class="s">(</span><span class="i">$ExperimentalTechnique</span> ? <span class="i">$ExperimentalTechnique</span> <span class="co">:</span> <span class="q">"Not available"</span><span class="s">)</span> . <span class="q">"\n"</span><span class="sc">;</span> + 156 + 157 <span class="s">(</span><span class="i">$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">"Resolution: "</span> . <span class="s">(</span><span class="i">$Resolution</span> ? <span class="q">"$Resolution $ResolutionUnits"</span> <span class="co">:</span> <span class="q">"Not available"</span><span class="s">)</span> . <span class="q">"\n"</span><span class="sc">;</span> + 159 + 160 <span class="s">}</span> + 161 + 162 <span class="c"># List record type info...</span> +<a name="ListRecordTypesInfo-"></a> 163 <span class="k">sub </span><span class="m">ListRecordTypesInfo</span> <span class="s">{</span> + 164 <span class="k">my</span><span class="s">(</span><span class="i">$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">$RecordTypesCountRef</span>->{<span class="w">RecordTypes</span>}}<span class="s">)</span> <span class="s">{</span> + 172 <span class="i">$RecordCount</span> = <span class="i">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="i">$RecordType</span>}<span class="sc">;</span> + 173 <span class="k">push</span> <span class="i">@RecordTypeCountInfo</span><span class="cm">,</span> <span class="q">"$RecordType - $RecordCount"</span><span class="sc">;</span> + 174 <span class="s">}</span> + 175 <span class="s">}</span> + 176 <span class="k">else</span> <span class="s">{</span> + 177 <span class="k">for</span> <span class="i">$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">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="i">$RecordType</span>}<span class="s">)</span> ? <span class="s">(</span><span class="i">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="i">$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">"$RecordType - $RecordCount"</span><span class="sc">;</span> + 180 <span class="s">}</span> + 181 <span class="s">}</span> + 182 <span class="k">print</span> <span class="q">"Number of individual records: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@RecordTypeCountInfo</span><span class="cm">,</span> <span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 183 + 184 <span class="k">if</span> <span class="s">(</span><span class="i">$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">'AtomAndHetatm'</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">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="sc">;</span> + 197 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountChains</span>}<span class="s">)</span> <span class="s">{</span> + 198 <span class="k">print</span> <span class="q">"\nNumber of chains: $ChainCount \n"</span><span class="sc">;</span> + 199 <span class="k">my</span><span class="s">(</span><span class="i">$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>->{<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">$ChainID</span><span class="s">)</span><span class="sc">;</span> + 203 <span class="s">}</span> + 204 <span class="k">print</span> <span class="q">"Chain IDs: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ChainIDsList</span><span class="cm">,</span> <span class="q">', '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">"\n"</span><span class="sc">;</span> + 205 <span class="s">}</span> + 206 + 207 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span> + 212 <span class="i">$ResidueCount</span> = <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$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">"Chain ${ChainID} - ${ResidueCount}"</span><span class="sc">;</span> + 215 <span class="k">push</span> <span class="i">@ResiduesCountInfo</span><span class="cm">,</span> <span class="i">$ResidueCountInfo</span><span class="sc">;</span> + 216 <span class="s">}</span> + 217 <span class="k">print</span> <span class="q">"\nNumber of residues in chain(s): "</span><span class="sc">;</span> + 218 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 219 <span class="k">print</span> <span class="q">"Total - $TotalResiduesCount; "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ResiduesCountInfo</span><span class="cm">,</span> <span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">"\n"</span><span class="sc">;</span> + 220 <span class="s">}</span> + 221 <span class="k">else</span> <span class="s">{</span> + 222 <span class="k">print</span> <span class="q">"$TotalResiduesCount\n"</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">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span> + 227 <span class="k">print</span> <span class="q">"List of residues in chain(s): \n"</span><span class="sc">;</span> + 228 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span> + 229 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 230 <span class="k">print</span> <span class="q">"Chain "</span><span class="cm">,</span> <span class="i">CleanupChainID</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">": "</span><span class="sc">;</span> + 231 <span class="s">}</span> + 232 <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="cm">,</span> <span class="q">', '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">"\n"</span><span class="sc">;</span> + 233 <span class="s">}</span> + 234 <span class="s">}</span> + 235 <span class="s">}</span> + 236 <span class="k">if</span> <span class="s">(</span><span class="i">$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>->{<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>->{<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">$ChainsAndResiduesInfoRef</span>->{<span class="w">ResidueCount</span>}{<span class="i">$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">$ResidueCount</span>} .= <span class="q">"~${ResidueName}"</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">$ChainCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 263 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span> + 264 <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ResidueCount</span>}{<span class="i">$ChainID</span>}}<span class="s">)</span> <span class="s">{</span> + 265 <span class="i">$ResidueCount</span> = <span class="i">$ChainsAndResiduesInfoRef</span>->{<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">"~${ResidueName}"</span><span class="sc">;</span> + 278 <span class="s">}</span> + 279 <span class="k">else</span> <span class="s">{</span> + 280 <span class="i">$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>->{<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">$b</span> <=> <span class="i">$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">"${ResidueName} - ${ResidueCount}"</span><span class="sc">;</span> + 309 <span class="i">$PercentResidueCount</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.1f"</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">"${ResidueName} - ${PercentResidueCount}%"</span><span class="sc">;</span> + 311 <span class="s">}</span> + 312 <span class="s">}</span> + 313 <span class="s">}</span> + 314 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> > <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> <=> <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">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsFrequency</span>}}<span class="cm">,</span> <span class="q">"${ResidueName} - ${ResidueCount}"</span><span class="sc">;</span> + 320 <span class="i">$PercentResidueCount</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.1f"</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">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsPercentFrequency</span>}}<span class="cm">,</span> <span class="q">"${ResidueName} - ${PercentResidueCount}%"</span><span class="sc">;</span> + 322 <span class="s">}</span> + 323 <span class="s">}</span> + 324 <span class="s">}</span> + 325 + 326 <span class="c"># List distribution of residues</span> + 327 <span class="k">print</span> <span class="q">"\nDistribution of residues in chain(s): \n"</span><span class="sc">;</span> + 328 <span class="k">for</span> <span class="i">$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> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 330 <span class="k">print</span> <span class="q">"Chain "</span><span class="cm">,</span> <span class="i">CleanupChainID</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">": "</span><span class="sc">;</span> + 331 <span class="s">}</span> + 332 <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">Frequency</span>}{<span class="i">$ChainID</span>}}<span class="cm">,</span> <span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 333 <span class="s">}</span> + 334 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 335 <span class="k">print</span> <span class="q">"\nPercent distribution of residues in chain(s): \n"</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">$ChainCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 338 <span class="k">print</span> <span class="q">"Chain "</span><span class="cm">,</span> <span class="i">CleanupChainID</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">": "</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">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</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">$ChainCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 344 <span class="k">print</span> <span class="q">"\nDistribution of residues across all chains: \n"</span><span class="sc">;</span> + 345 <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsFrequency</span>}}<span class="cm">,</span> <span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 346 + 347 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 348 <span class="k">print</span> <span class="q">"\nPercent distribution of residues across all chains: \n"</span><span class="sc">;</span> + 349 <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsPercentFrequency</span>}}<span class="cm">,</span> <span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</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">$ResiduesInfoRef</span>->{<span class="w">ResidueNames</span>}}<span class="sc">;</span> + 362 <span class="i">$AtomResiduesCount</span> = <span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>->{<span class="w">AtomResidueNames</span>}}<span class="sc">;</span> + 363 <span class="i">$HetatmResiduesCount</span> = <span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>->{<span class="w">HetatmResidueNames</span>}}<span class="sc">;</span> + 364 + 365 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountResiduesAll</span>}<span class="s">)</span> <span class="s">{</span> + 366 <span class="k">print</span> <span class="q">"\nTotal number of residues: Total - $TotalResidueCount; ATOM residues - $AtomResiduesCount; HETATM residues - $HetatmResiduesCount\n"</span><span class="sc">;</span> + 367 + 368 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span> + 369 <span class="k">print</span> <span class="q">"List of residues: \n"</span><span class="sc">;</span> + 370 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomResiduesCount</span><span class="s">)</span> <span class="s">{</span> + 371 <span class="k">print</span> <span class="q">"ATOM residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>->{<span class="w">AtomResidueNames</span>}}<span class="cm">,</span> <span class="q">', '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 372 <span class="s">}</span> + 373 <span class="k">if</span> <span class="s">(</span><span class="i">$HetatmResiduesCount</span><span class="s">)</span> <span class="s">{</span> + 374 <span class="k">print</span> <span class="q">"HETATM residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>->{<span class="w">HetatmResidueNames</span>}}<span class="cm">,</span> <span class="q">', '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</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>->{<span class="w">ResidueCount</span>}}<span class="s">)</span> <span class="s">{</span> + 394 <span class="i">$ResidueCount</span> = <span class="i">$ResiduesInfoRef</span>->{<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">$ResidueCount</span>} .= <span class="q">"~${ResidueName}"</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>} >= <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>->{<span class="w">AtomResidueCount</span>}}<span class="s">)</span> <span class="s">{</span> + 405 <span class="i">$ResidueCount</span> = <span class="i">$ResiduesInfoRef</span>->{<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">$ResidueCount</span>} .= <span class="q">"~${ResidueName}"</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">$ResiduesInfoRef</span>->{<span class="w">HetatmResidueCount</span>}}<span class="s">)</span> <span class="s">{</span> + 414 <span class="i">$ResidueCount</span> = <span class="i">$ResiduesInfoRef</span>->{<span class="w">HetatmResidueCount</span>}{<span class="i">$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">"~${ResidueName}"</span><span class="sc">;</span> + 417 <span class="s">}</span> + 418 <span class="k">else</span> <span class="s">{</span> + 419 <span class="i">$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> <=> <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">$PercentResidueCount</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.1f"</span><span class="cm">,</span> <span class="s">(</span><span class="s">(</span><span class="i">$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">$ResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span> <span class="q">"${ResidueName} - ${ResidueCount}"</span><span class="sc">;</span> + 435 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span> <span class="q">"${ResidueName} - ${PercentResidueCount}"</span><span class="sc">;</span> + 436 <span class="s">}</span> + 437 <span class="s">}</span> + 438 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <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> <=> <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">$PercentResidueCount</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.1f"</span><span class="cm">,</span> <span class="s">(</span><span class="s">(</span><span class="i">$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">$AtomResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span> <span class="q">"${ResidueName} - ${ResidueCount}"</span><span class="sc">;</span> + 447 <span class="k">push</span> <span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span> <span class="q">"${ResidueName} - ${PercentResidueCount}"</span><span class="sc">;</span> + 448 <span class="s">}</span> + 449 <span class="s">}</span> + 450 <span class="i">@</span>{<span class="i">$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">$b</span> <=> <span class="i">$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">"%.1f"</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">"${ResidueName} - ${ResidueCount}"</span><span class="sc">;</span> + 458 <span class="k">push</span> <span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span> <span class="q">"${ResidueName} - ${PercentResidueCount}"</span><span class="sc">;</span> + 459 <span class="s">}</span> + 460 <span class="s">}</span> + 461 <span class="s">}</span> + 462 + 463 <span class="c"># List distribution of residues</span> + 464 <span class="k">print</span> <span class="q">"\nDistribution of residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span><span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 465 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 466 <span class="k">print</span> <span class="q">"\nPercent distribution of residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span><span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 467 <span class="s">}</span> + 468 + 469 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 470 <span class="k">print</span> <span class="q">"\nDistribution of ATOM residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span><span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 471 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 472 <span class="k">print</span> <span class="q">"\nPercent distribution of ATOM residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span><span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 473 <span class="s">}</span> + 474 + 475 <span class="k">print</span> <span class="q">"\nDistribution of HETATM residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span><span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 476 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 477 <span class="k">print</span> <span class="q">"\nPercent distribution of HETATM residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span><span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 478 <span class="s">}</span> + 479 <span class="s">}</span> + 480 <span class="s">}</span> + 481 <span class="s">}</span> + 482 + 483 <span class="c"># List information about residue numbers for each chain...</span> +<a name="ListResidueNumbersInfo-"></a> 484 <span class="k">sub </span><span class="m">ListResidueNumbersInfo</span> <span class="s">{</span> + 485 <span class="k">my</span><span class="s">(</span><span class="i">$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">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="q">'AtomAndHetatm'</span><span class="cm">,</span> <span class="i">$CollectChainResiduesBeyondTER</span><span class="s">)</span><span class="sc">;</span> + 490 + 491 <span class="k">print</span> <span class="q">"\nATOM/HETATM residue numbers information for chains:\n"</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>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span> + 494 <span class="k">print</span> <span class="q">"\nChain ID - "</span><span class="cm">,</span> <span class="i">CleanupChainID</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">""</span><span class="sc">;</span> + 495 + 496 <span class="i">$ResidueCount</span> = <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ResidueNumbers</span>}{<span class="i">$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>->{<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">$ChainsAndResiduesInfoRef</span>->{<span class="w">ResidueNumbers</span>}{<span class="i">$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">"; Number of residues: $ResidueCount; Start residue number - $StartResidueNum; End residue number - $EndResidueNum\n"</span><span class="sc">;</span> + 502 + 503 <span class="c"># Identify any gaps in residue numbers or non-ascending order residue numbers...</span> + 504 <span class="i">$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">$ChainsAndResiduesInfoRef</span>->{<span class="w">ResidueNumbers</span>}{<span class="i">$ChainID</span>}[<span class="i">$Index</span>]<span class="sc">;</span> + 512 <span class="i">$PreviousResidueNum</span> = <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ResidueNumbers</span>}{<span class="i">$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">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}[<span class="i">$Index</span>]<span class="sc">;</span> + 515 <span class="i">$PreviousResidueName</span> = <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$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> < <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">"<${PreviousResidueName}${PreviousResidueNum} - ${ResidueName}${ResidueNum}>"</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">"<${PreviousResidueName}${PreviousResidueNum} - ${ResidueName}${ResidueNum}; $GapLength>"</span><span class="sc">;</span> + 533 <span class="s">}</span> + 534 + 535 <span class="c"># Print gaps information...</span> + 536 <span class="k">print</span> <span class="q">"Gaps in residue numbers: "</span><span class="cm">,</span> <span class="i">$GapResiduePairsCount</span> ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"None"</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">"; Number of gap residue number pairs: $GapResiduePairsCount; Gap residue pairs: <StartRes-EndRes; GapLength> - "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@GapResiduePairs</span><span class="cm">,</span> <span class="q">"; "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> + 539 <span class="s">}</span> + 540 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span> + 541 + 542 <span class="c"># Print descending residue order information...</span> + 543 <span class="k">print</span> <span class="q">"Residue numbers in descending order: "</span><span class="cm">,</span> <span class="i">$DescendingOrderResiduePairsCount</span> ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"None"</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">"; Number of descending residue number pairs: $DescendingOrderResiduePairsCount; Descending residue number pairs: <StartRes-EndRes> "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@DescendingOrderResiduePairs</span><span class="cm">,</span> <span class="q">"; "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> + 546 <span class="s">}</span> + 547 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span> + 548 <span class="s">}</span> + 549 <span class="s">}</span> + 550 + 551 <span class="c"># List min/max XYZ coordinates for ATOM/HETATM records...</span> +<a name="ListBoundingBox-"></a> 552 <span class="k">sub </span><span class="m">ListBoundingBox</span> <span class="s">{</span> + 553 <span class="k">my</span><span class="s">(</span><span class="i">$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">"%.3f"</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">"%.3f"</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">"%.3f"</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">"%.3f"</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">"%.3f"</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">"%.3f"</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">"%.3f"</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">"%.3f"</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">"%.3f"</span><span class="cm">,</span> <span class="i">$ZSize</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> + 568 + 569 <span class="k">print</span> <span class="q">"\nBounding box coordinates: <XMin, XMax> - <$XMin, $XMax>; <YMin, YMax> - <$YMin, $YMax>; <ZMin, ZMax> - <$ZMin, $ZMax>;\n"</span><span class="sc">;</span> + 570 <span class="k">print</span> <span class="q">"Bounding box size in angstroms: XSize - $XSize; YSize - $YSize; ZSize - $ZSize\n"</span><span class="sc">;</span> + 571 + 572 <span class="s">}</span> + 573 + 574 <span class="c"># Check master record counts against actual record counts...</span> +<a name="CheckMasterRecord-"></a> 575 <span class="k">sub </span><span class="m">CheckMasterRecord</span> <span class="s">{</span> + 576 <span class="k">my</span><span class="s">(</span><span class="i">$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">"\nWarning: MASTER record is missing.\n"</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>->{<span class="w">Count</span>}{<span class="w">REMARK</span>}<span class="s">)</span> && <span class="i">$NumOfRemarkRecords</span> != <span class="i">$RecordTypesCountRef</span>->{<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">"Number of REMARK records, $NumOfRemarkRecords, specified in MASTER record doen't match its explict count, $RecordTypesCountRef->{Count}{REMARK}."</span><span class="sc">;</span> + 599 <span class="s">}</span> + 600 <span class="i">$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">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="w">HET</span>}<span class="s">)</span> && <span class="i">$NumOfHetRecords</span> != <span class="i">$RecordTypesCountRef</span>->{<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">"Number of HET records, $NumOfHetRecords, specified in MASTER record doen't match its explict count, $RecordTypesCountRef->{Count}{HET}."</span><span class="sc">;</span> + 603 <span class="s">}</span> + 604 <span class="i">$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">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="w">HELIX</span>}<span class="s">)</span> && <span class="i">$NumOfHelixRecords</span> != <span class="i">$RecordTypesCountRef</span>->{<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">"Number of HELIX records, $NumOfHelixRecords, specified in MASTER record doen't match its explict count, $RecordTypesCountRef->{Count}{HELIX}."</span><span class="sc">;</span> + 607 <span class="s">}</span> + 608 <span class="i">$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">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="w">SHEET</span>}<span class="s">)</span> && <span class="i">$NumOfSheetRecords</span> != <span class="i">$RecordTypesCountRef</span>->{<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">"Number of SHEET records, $NumOfSheetRecords, specified in MASTER record doen't match its explict count, $RecordTypesCountRef->{Count}{SHEET}."</span><span class="sc">;</span> + 611 <span class="s">}</span> + 612 <span class="i">$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">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="w">TURN</span>}<span class="s">)</span> && <span class="i">$NumOfTurnRecords</span> != <span class="i">$RecordTypesCountRef</span>->{<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">"Number of TURN records, $NumOfTurnRecords, specified in MASTER record doen't match its explict count, $RecordTypesCountRef->{Count}{REMARK}."</span><span class="sc">;</span> + 615 <span class="s">}</span> + 616 <span class="i">$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">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="w">SITE</span>}<span class="s">)</span> && <span class="i">$NumOfSiteRecords</span> != <span class="i">$RecordTypesCountRef</span>->{<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">"Number of SITE records, $NumOfSiteRecords, specified in MASTER record doen't match its explict count, $RecordTypesCountRef->{Count}{SITE}."</span><span class="sc">;</span> + 619 <span class="s">}</span> + 620 + 621 <span class="i">$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">'ORIGX'</span><span class="cm">,</span> <span class="q">'SCALE'</span><span class="cm">,</span> <span class="q">'MTRIX'</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">"${RecordLabel}${ID}"</span><span class="sc">;</span> + 627 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="i">$RecordID</span>}<span class="s">)</span> <span class="s">{</span> + 628 <span class="i">$RecordsCount</span> += <span class="i">$RecordTypesCountRef</span>->{<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">"Number of transformation records (ORIGXn+SCALEn+MTRIXn), $NumOfTransformationsRecords, specified in MASTER record doen't match its explict count, $RecordsCount."</span><span class="sc">;</span> + 634 <span class="s">}</span> + 635 + 636 <span class="i">$RecordsCount</span> = <span class="n">0</span><span class="sc">;</span> + 637 <span class="k">for</span> <span class="i">$RecordLabel</span> <span class="s">(</span><span class="q">'ATOM'</span><span class="cm">,</span> <span class="q">'HETATM'</span><span class="s">)</span> <span class="s">{</span> + 638 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$RecordTypesCountRef</span>->{<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">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="i">$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">"Number of ATOM + HETATM records, $NumOfAtomAndHetatmRecords, specified in MASTER record doen't match its explict count, $RecordsCount."</span><span class="sc">;</span> + 645 <span class="s">}</span> + 646 <span class="i">$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">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="w">TER</span>}<span class="s">)</span> && <span class="i">$NumOfTerRecords</span> != <span class="i">$RecordTypesCountRef</span>->{<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">"Number of TER records, $NumOfTerRecords, specified in MASTER record doen't match its explict count, $RecordTypesCountRef->{Count}{TER}."</span><span class="sc">;</span> + 649 <span class="s">}</span> + 650 <span class="i">$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">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="w">CONECT</span>}<span class="s">)</span> && <span class="i">$NumOfConectRecords</span> != <span class="i">$RecordTypesCountRef</span>->{<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">"Number of CONECT records, $NumOfConectRecords, specified in MASTER record doen't match its explict count, $RecordTypesCountRef->{Count}{CONECT}."</span><span class="sc">;</span> + 653 <span class="s">}</span> + 654 <span class="i">$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">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="w">SEQRES</span>}<span class="s">)</span> && <span class="i">$NumOfSeqresRecords</span> != <span class="i">$RecordTypesCountRef</span>->{<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">"Number of SITE records, $NumOfSeqresRecords, specified in MASTER record doen't match its explict count, $RecordTypesCountRef->{Count}{SEQRES}."</span><span class="sc">;</span> + 657 <span class="s">}</span> + 658 + 659 <span class="k">if</span> <span class="s">(</span><span class="i">@MasterRecordValidationInfo</span><span class="s">)</span> <span class="s">{</span> + 660 <span class="k">print</span> <span class="q">"\nMASTER record validation: Count mismatches found:\n"</span><span class="sc">;</span> + 661 <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@MasterRecordValidationInfo</span><span class="cm">,</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 662 <span class="s">}</span> + 663 <span class="k">else</span> <span class="s">{</span> + 664 <span class="k">print</span> <span class="q">"\nMASTER record validation: Count values match with the explicit count of the corresponding records.\n"</span><span class="sc">;</span> + 665 <span class="s">}</span> + 666 <span class="s">}</span> + 667 + 668 <span class="c"># Total size of all the files...</span> +<a name="ListTotalSizeOfFiles-"></a> 669 <span class="k">sub </span><span class="m">ListTotalSizeOfFiles</span> <span class="s">{</span> + 670 <span class="k">my</span><span class="s">(</span><span class="i">$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> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 682 <span class="k">print</span> <span class="q">"\nTotal size of $FileOkayCount files: "</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$TotalSize</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</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 "None[1-9]". 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">'None'</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">'All'</span> <span class="co">:</span> <span class="q">'ATOM,HETATM'</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">$Options</span>{<span class="w">all</span>}<span class="s">)</span> && <span class="i">$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> && <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">$Options</span>{<span class="w">all</span>}<span class="s">)</span> && <span class="i">$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> && <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">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 750 + 751 <span class="i">$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">"Warning: Ignoring file $PDBFile: It doesn't exist\n"</span><span class="sc">;</span> + 754 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 755 <span class="s">}</span> + 756 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="q">"pdb"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 757 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It's not a PDB file\n"</span><span class="sc">;</span> + 758 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 759 <span class="s">}</span> + 760 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">PDBFILE</span><span class="cm">,</span> <span class="q">"$PDBFile"</span><span class="s">)</span> <span class="s">{</span> + 761 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: Couldn't open it: $! \n"</span><span class="sc">;</span> + 762 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 763 <span class="s">}</span> + 764 <span class="k">close</span> <span class="w">PDBFILE</span><span class="sc">;</span> + 765 + 766 <span class="i">$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">$Index</span>] = <span class="q">"$ModifiedTimeString; $ModifiedDateString"</span><span class="sc">;</span> + 770 <span class="s">}</span> + 771 <span class="s">}</span> + 772 + 773 + 774 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> +<a name="SetupScriptUsage-"></a> 775 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> + 776 + 777 <span class="c"># Retrieve all the options...</span> + 778 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 779 <span class="i">$Options</span>{<span class="w">count</span>} = <span class="q">''</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">'Both'</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">"all|a"</span><span class="cm">,</span> <span class="q">"boundingbox|b"</span><span class="cm">,</span> <span class="q">"count|c=s"</span><span class="cm">,</span> <span class="q">"chains"</span><span class="cm">,</span> <span class="q">"detail|d=i"</span><span class="cm">,</span> <span class="q">"experiment|e"</span><span class="cm">,</span> <span class="q">"frequency|f"</span><span class="cm">,</span> <span class="q">"mastercheck|m"</span><span class="cm">,</span> <span class="q">"header"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"residues"</span><span class="cm">,</span> <span class="q">"residuesmode=s"</span><span class="cm">,</span> <span class="q">"residuenumbers"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 784 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> + 785 <span class="s">}</span> + 786 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> + 789 <span class="s">}</span> + 790 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span> + 791 <span class="s">}</span> + 792 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n"</span><span class="sc">;</span> + 794 <span class="s">}</span> + 795 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{residuesmode}, for option \"--ResiduesMode\" is not valid. Allowed values: InChains, All, or Both\n"</span><span class="sc">;</span> + 797 <span class="s">}</span> + 798 <span class="s">}</span> + 799 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>