Mercurial > repos > deepakjadmin > mayatool3_test2
view docs/scripts/html/code/InfoPDBFiles.html @ 0:4816e4a8ae95 draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
| parents | |
| children |
line wrap: on
line source
<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>