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author	deepakjadmin
date	Wed, 20 Jan 2016 09:23:18 -0500
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0 4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1 <html>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	2 <head>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	3 <title>MayaChemTools:Code:InfoPDBFiles.pl</title>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	6 </head>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	8 <br/>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	9 <center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	11 </center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	12 <br/>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	13 <pre>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	14 1 #!/usr/bin/perl -w
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	15 2 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	16 3 <span class="c"># $RCSfile: InfoPDBFiles.pl,v $</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	17 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	18 5 <span class="c"># $Revision: 1.36 $</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	19 6 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	21 8 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	23 10 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	24 11 <span class="c"># This file is part of MayaChemTools.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	25 12 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	29 16 <span class="c"># later version.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	30 17 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	34 21 <span class="c"># details.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	35 22 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	40 27 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	41 28
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	43 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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	50 37 <span class="k">use</span> <span class="w">PDBFileUtil</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	51 38
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	52 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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	53 40
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	54 41 <span class="c"># Autoflush STDOUT</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	55 42 <span class="i">$\|</span> = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	56 43
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	57 44 <span class="c"># Starting message...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	58 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	59 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	60 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	61 48
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	62 49 <span class="c"># Get the options and setup script...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	63 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	64 51 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	65 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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	66 53 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	67 54
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	68 55 <span class="k">my</span><span class="s">(</span><span class="i">@PDBFilesList</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	69 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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	70 57
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	71 58 <span class="c"># Process options...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	72 59 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	73 60 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	74 61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	75 62
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	76 63 <span class="c"># Setup information about input files...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	77 64 <span class="k">my</span><span class="s">(</span><span class="i">%PDBFilesInfo</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	78 65 <span class="k">print</span> <span class="q">"Checking input PDB file(s)...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	79 66 <span class="i">RetrievePDBFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	80 67
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	81 68 <span class="c"># Process input files..</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	82 69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	83 70 <span class="k">if</span> <span class="s">(</span><span class="i">@PDBFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	84 71 <span class="k">print</span> <span class="q">"\nProcessing PDB files...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	85 72 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	86 73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	87 74 <span class="k">if</span> <span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	88 75 <span class="k">print</span> <span class="q">"\nProcessing file $PDBFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	89 76 <span class="i">ListPDBFileInfo</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	90 77 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	91 78 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	92 79 <span class="i">ListTotalSizeOfFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	93 80
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	94 81 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	95 82
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	96 83 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	97 84 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	98 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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	99 86
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	100 87 <span class="c">###############################################################################</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	101 88
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	102 89 <span class="c"># List appropriate information...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	103 <a name="ListPDBFileInfo-"></a> 90 <span class="k">sub </span><span class="m">ListPDBFileInfo</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	104 91 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	105 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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	106 93
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	107 94 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	108 95 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	109 96
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	110 97 <span class="c"># Header informaton...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	111 98 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListHeaderInfo</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	112 99 <span class="i">ListHeaderInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	113 100 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	114 101
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	115 102 <span class="c"># Experiment informaton...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	116 103 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListExperimentalTechniqueInfo</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	117 104 <span class="i">ListExperimentalTechniqueInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	118 105 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	119 106
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	120 107 <span class="c"># Total number of records...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	121 108 <span class="k">my</span><span class="s">(</span><span class="i">$TotalRecordsCount</span><span class="s">)</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	122 109 <span class="k">print</span> <span class="q">"\nTotal number of records: $TotalRecordsCount\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	123 110
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	124 111 <span class="c"># List record type count information...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	125 112 <span class="i">ListRecordTypesInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	126 113
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	127 114 <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">$OptionsInfo</span>{<span class="w">ResiduesFrequencyInChains</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	128 115 <span class="i">ListChainsAndResiduesInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	129 116 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	130 117 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	131 118 <span class="i">ListAllResiduesInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	132 119 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	133 120 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ResidueNumbersInfo</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	134 121 <span class="i">ListResidueNumbersInfo</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	135 122 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	136 123 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CalculateBoundingBox</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	137 124 <span class="i">ListBoundingBox</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	138 125 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	139 126
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	140 127 <span class="c"># File size and modification information...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	141 128 <span class="k">print</span> <span class="q">"\nFile size: "</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="s">)</span><span class="cm">,</span> <span class="q">" \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	142 129 <span class="k">print</span> <span class="q">"Last modified: "</span><span class="cm">,</span> <span class="i">$PDBFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>]<span class="cm">,</span> <span class="q">" \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	143 130 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	144 131
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	145 <a name="ListHeaderInfo-"></a> 132 <span class="k">sub </span><span class="m">ListHeaderInfo</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	146 133 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	147 134 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	148 135
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	149 136 <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">$IDCode</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	150 137 <span class="i">$HeaderRecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	151 138 <span class="k">if</span> <span class="s">(</span><span class="i">IsHeaderRecordType</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	152 139 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	153 140 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	154 141
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	155 142 <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">$Classification</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	156 143 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	157 144 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	158 145
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	159 146 <span class="k">print</span> <span class="q">"\nClassification: $Classification\nID: $IDCode\nDeposition date: $DepositionDate\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	160 147 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	161 148
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	162 149 <span class="c"># List experimental technique information info...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	163 <a name="ListExperimentalTechniqueInfo-"></a> 150 <span class="k">sub </span><span class="m">ListExperimentalTechniqueInfo</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	164 151 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	165 152 <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">$ResolutionUnits</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	166 153
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	167 154 <span class="i">$ExperimentalTechnique</span> = <span class="i">GetExperimentalTechnique</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	168 155 <span class="k">print</span> <span class="q">"\nExperimental technique: "</span> . <span class="s">(</span><span class="i">$ExperimentalTechnique</span> ? <span class="i">$ExperimentalTechnique</span> <span class="co">:</span> <span class="q">"Not available"</span><span class="s">)</span> . <span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	169 156
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	170 157 <span class="s">(</span><span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	171 158 <span class="k">print</span> <span class="q">"Resolution: "</span> . <span class="s">(</span><span class="i">$Resolution</span> ? <span class="q">"$Resolution $ResolutionUnits"</span> <span class="co">:</span> <span class="q">"Not available"</span><span class="s">)</span> . <span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	172 159
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	173 160 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	174 161
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	175 162 <span class="c"># List record type info...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	176 <a name="ListRecordTypesInfo-"></a> 163 <span class="k">sub </span><span class="m">ListRecordTypesInfo</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	177 164 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	178 165 <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">$RecordTypesCountRef</span><span class="cm">,</span> <span class="i">@RecordTypeCountInfo</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	179 166
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	180 167 <span class="i">$RecordTypesCountRef</span> = <span class="i">GetRecordTypesCount</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	181 168
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	182 169 <span class="i">@RecordTypeCountInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	183 170 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountRecordType</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	184 171 <span class="k">for</span> <span class="i">$RecordType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RecordTypesCountRef</span>->{<span class="w">RecordTypes</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	185 172 <span class="i">$RecordCount</span> = <span class="i">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="i">$RecordType</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	186 173 <span class="k">push</span> <span class="i">@RecordTypeCountInfo</span><span class="cm">,</span> <span class="q">"$RecordType - $RecordCount"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	187 174 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	188 175 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	189 176 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	190 177 <span class="k">for</span> <span class="i">$RecordType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRecordTypes</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	191 178 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	192 179 <span class="k">push</span> <span class="i">@RecordTypeCountInfo</span><span class="cm">,</span> <span class="q">"$RecordType - $RecordCount"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	193 180 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	194 181 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	195 182 <span class="k">print</span> <span class="q">"Number of individual records: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@RecordTypeCountInfo</span><span class="cm">,</span> <span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	196 183
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	197 184 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckMasterRecord</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	198 185 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	199 186 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	200 187 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	201 188
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	202 189 <span class="c"># List information about residues and chains...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	203 <a name="ListChainsAndResiduesInfo-"></a> 190 <span class="k">sub </span><span class="m">ListChainsAndResiduesInfo</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	204 191 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	205 192 <span class="k">my</span><span class="s">(</span><span class="i">$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">$ChainsAndResiduesInfoRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	206 193
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	207 194 <span class="i">$CollectChainResiduesBeyondTER</span> = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	208 195 <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">$CollectChainResiduesBeyondTER</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	209 196 <span class="i">$ChainCount</span> = <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	210 197 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountChains</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	211 198 <span class="k">print</span> <span class="q">"\nNumber of chains: $ChainCount \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	212 199 <span class="k">my</span><span class="s">(</span><span class="i">$ChainID</span><span class="cm">,</span> <span class="i">@ChainIDsList</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	213 200 <span class="i">@ChainIDsList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	214 201 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	215 202 <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">$ChainID</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	216 203 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	217 204 <span class="k">print</span> <span class="q">"Chain IDs: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ChainIDsList</span><span class="cm">,</span> <span class="q">', '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	218 205 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	219 206
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	220 207 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountResiduesInChains</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	221 208 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	222 209 <span class="i">@ResiduesCountInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	223 210 <span class="i">$TotalResiduesCount</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	224 211 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	225 212 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	226 213 <span class="i">$TotalResiduesCount</span> += <span class="i">$ResidueCount</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	227 214 <span class="i">$ResidueCountInfo</span> = <span class="q">"Chain ${ChainID} - ${ResidueCount}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	228 215 <span class="k">push</span> <span class="i">@ResiduesCountInfo</span><span class="cm">,</span> <span class="i">$ResidueCountInfo</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	229 216 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	230 217 <span class="k">print</span> <span class="q">"\nNumber of residues in chain(s): "</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	231 218 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	232 219 <span class="k">print</span> <span class="q">"Total - $TotalResiduesCount; "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ResiduesCountInfo</span><span class="cm">,</span> <span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	233 220 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	234 221 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	235 222 <span class="k">print</span> <span class="q">"$TotalResiduesCount\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	236 223 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	237 224
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	238 225 <span class="c"># List of residues in each chain...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	239 226 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	240 227 <span class="k">print</span> <span class="q">"List of residues in chain(s): \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	241 228 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	242 229 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	243 230 <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">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">": "</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	244 231 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	245 232 <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="cm">,</span> <span class="q">', '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	246 233 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	247 234 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	248 235 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	249 236 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ResiduesFrequencyInChains</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	250 237 <span class="c"># Setup a hash using residue count as key for sorting the values...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	251 238 <span class="k">my</span><span class="s">(</span><span class="i">%ResiduesCountToNameMap</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	252 239 <span class="i">%ResiduesCountToNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	253 240 <span class="i">@</span>{<span class="i">$ResiduesCountToNameMap</span>{<span class="w">ChainIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	254 241 <span class="i">%</span>{<span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	255 242
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	256 243 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	257 244 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	258 245 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	259 246
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	260 247 <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">$ChainID</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	261 248 <span class="i">$ResidueCount</span> = <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ResidueCount</span>}{<span class="i">$ChainID</span>}{<span class="i">$ResidueName</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	262 249 <span class="c"># Setup count value for each chain...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	263 250 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	264 251 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	265 252 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	266 253 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	267 254 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	268 255 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	269 256 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	270 257 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	271 258 <span class="c"># Collect data for all the residues in all the chains...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	272 259 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	273 260 <span class="i">%AllResiduesNameToCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	274 261 <span class="i">%AllResiduesCountToNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	275 262 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	276 263 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	277 264 <span class="k">for</span> <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	278 265 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	279 266 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	280 267 <span class="i">$AllResiduesNameToCountMap</span>{<span class="i">$ResidueName</span>} += <span class="i">$ResidueCount</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	281 268 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	282 269 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	283 270 <span class="i">$AllResiduesNameToCountMap</span>{<span class="i">$ResidueName</span>} = <span class="i">$ResidueCount</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	284 271 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	285 272 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	286 273 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	287 274 <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AllResiduesNameToCountMap</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	288 275 <span class="i">$ResidueCount</span> = <span class="i">$AllResiduesNameToCountMap</span>{<span class="i">$ResidueName</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	289 276 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	290 277 <span class="i">$AllResiduesCountToNameMap</span>{<span class="i">$ResidueCount</span>} .= <span class="q">"~${ResidueName}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	291 278 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	292 279 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	293 280 <span class="i">$AllResiduesCountToNameMap</span>{<span class="i">$ResidueCount</span>} = <span class="i">$ResidueName</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	294 281 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	295 282 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	296 283 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	297 284
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	298 285 <span class="c"># Setup distribution data for individual chains and the grand total as well...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	299 286 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	300 287 <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">ChainIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	301 288 <span class="i">%</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">Frequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	302 289 <span class="i">%</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">PercentFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	303 290
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	304 291 <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	305 292 <span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">AllChainsPercentFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	306 293
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	307 294 <span class="i">$TotalResidueCount</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	308 295
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	309 296 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	310 297 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	311 298 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	312 299 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	313 300
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	314 301 <span class="i">$ChainResidueCount</span> = <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	315 302 <span class="i">$TotalResidueCount</span> += <span class="i">$ChainResidueCount</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	316 303
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	317 304 <span class="k">for</span> <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	318 305 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	319 306 <span class="i">@ResidueNamesList</span> = <span class="k">split</span> <span class="q">/~/</span><span class="cm">,</span> <span class="i">$ResidueNames</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	320 307 <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@ResidueNamesList</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	321 308 <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} - ${ResidueCount}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	322 309 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	323 310 <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} - ${PercentResidueCount}%"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	324 311 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	325 312 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	326 313 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	327 314 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	328 315 <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">$a</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%AllResiduesCountToNameMap</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	329 316 <span class="i">$ResidueNames</span> = <span class="i">$AllResiduesCountToNameMap</span>{<span class="i">$ResidueCount</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	330 317 <span class="i">@ResidueNamesList</span> = <span class="k">split</span> <span class="q">/~/</span><span class="cm">,</span> <span class="i">$ResidueNames</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	331 318 <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@ResidueNamesList</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	332 319 <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} - ${ResidueCount}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	333 320 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	334 321 <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} - ${PercentResidueCount}%"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	335 322 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	336 323 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	337 324 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	338 325
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	339 326 <span class="c"># List distribution of residues</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	340 327 <span class="k">print</span> <span class="q">"\nDistribution of residues in chain(s): \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	341 328 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	342 329 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	343 330 <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">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">": "</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	344 331 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	345 332 <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$ResiduesFrequencyInfoMap</span>{<span class="w">Frequency</span>}{<span class="i">$ChainID</span>}}<span class="cm">,</span> <span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	346 333 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	347 334 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	348 335 <span class="k">print</span> <span class="q">"\nPercent distribution of residues in chain(s): \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	349 336 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	350 337 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	351 338 <span class="k">print</span> <span class="q">"Chain "</span><span class="cm">,</span> <span class="i">CleanupChainID</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">": "</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	352 339 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	353 340 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	354 341 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	355 342 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	356 343 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	357 344 <span class="k">print</span> <span class="q">"\nDistribution of residues across all chains: \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	358 345 <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	359 346
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	360 347 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	361 348 <span class="k">print</span> <span class="q">"\nPercent distribution of residues across all chains: \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	362 349 <span class="k">print</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	363 350 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	364 351 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	365 352 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	366 353 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	367 354
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	368 355 <span class="c"># List information about all the residues...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	369 <a name="ListAllResiduesInfo-"></a> 356 <span class="k">sub </span><span class="m">ListAllResiduesInfo</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	370 357 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	371 358 <span class="k">my</span><span class="s">(</span><span class="i">$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">$ResiduesInfoRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	372 359
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	373 360 <span class="i">$ResiduesInfoRef</span> = <span class="i">GetAllResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	374 361 <span class="i">$TotalResidueCount</span> = <span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>->{<span class="w">ResidueNames</span>}}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	375 362 <span class="i">$AtomResiduesCount</span> = <span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>->{<span class="w">AtomResidueNames</span>}}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	376 363 <span class="i">$HetatmResiduesCount</span> = <span class="i">@</span>{<span class="i">$ResiduesInfoRef</span>->{<span class="w">HetatmResidueNames</span>}}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	377 364
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	378 365 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountResiduesAll</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	379 366 <span class="k">print</span> <span class="q">"\nTotal number of residues: Total - $TotalResidueCount; ATOM residues - $AtomResiduesCount; HETATM residues - $HetatmResiduesCount\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	380 367
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	381 368 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	382 369 <span class="k">print</span> <span class="q">"List of residues: \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	383 370 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomResiduesCount</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	384 371 <span class="k">print</span> <span class="q">"ATOM residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	385 372 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	386 373 <span class="k">if</span> <span class="s">(</span><span class="i">$HetatmResiduesCount</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	387 374 <span class="k">print</span> <span class="q">"HETATM residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	388 375 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	389 376 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	390 377 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	391 378
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	392 379 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ResiduesFrequencyAll</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	393 380 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ResidueCount</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	394 381
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	395 382 <span class="c"># Setup a hash using residue count as key for sorting the values...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	396 383 <span class="k">my</span><span class="s">(</span><span class="i">%ResiduesCountToNameMap</span><span class="cm">,</span> <span class="i">%AtomResiduesCountToNameMap</span><span class="cm">,</span> <span class="i">%HetatmResiduesCountToNameMap</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	397 384 <span class="i">%ResiduesCountToNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	398 385 <span class="i">%</span>{<span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	399 386
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	400 387 <span class="i">%AtomResiduesCountToNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	401 388 <span class="i">%</span>{<span class="i">$AtomResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	402 389
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	403 390 <span class="i">%HetatmResiduesCountToNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	404 391 <span class="i">%</span>{<span class="i">$HetatmResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	405 392
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	406 393 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	407 394 <span class="i">$ResidueCount</span> = <span class="i">$ResiduesInfoRef</span>->{<span class="w">ResidueCount</span>}{<span class="i">$ResidueName</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	408 395 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	409 396 <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} .= <span class="q">"~${ResidueName}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	410 397 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	411 398 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	412 399 <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} = <span class="i">$ResidueName</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	413 400 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	414 401 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	415 402
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	416 403 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	417 404 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	418 405 <span class="i">$ResidueCount</span> = <span class="i">$ResiduesInfoRef</span>->{<span class="w">AtomResidueCount</span>}{<span class="i">$ResidueName</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	419 406 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	420 407 <span class="i">$AtomResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} .= <span class="q">"~${ResidueName}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	421 408 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	422 409 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	423 410 <span class="i">$AtomResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} = <span class="i">$ResidueName</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	424 411 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	425 412 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	426 413 <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$ResiduesInfoRef</span>->{<span class="w">HetatmResidueCount</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	427 414 <span class="i">$ResidueCount</span> = <span class="i">$ResiduesInfoRef</span>->{<span class="w">HetatmResidueCount</span>}{<span class="i">$ResidueName</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	428 415 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	429 416 <span class="i">$HetatmResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} .= <span class="q">"~${ResidueName}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	430 417 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	431 418 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	432 419 <span class="i">$HetatmResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>} = <span class="i">$ResidueName</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	433 420 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	434 421 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	435 422 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	436 423
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	437 424 <span class="c"># Setup distribution of residues info...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	438 425 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	439 426
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	440 427 <span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">Frequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	441 428 <span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	442 429 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	443 430 <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">$TotalResidueCount</span><span class="s">)</span>*<span class="n">100</span><span class="s">)</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	444 431 <span class="i">$ResidueNames</span> = <span class="i">$ResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	445 432 <span class="i">@ResidueNamesList</span> = <span class="k">split</span> <span class="q">/~/</span><span class="cm">,</span> <span class="i">$ResidueNames</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	446 433 <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@ResidueNamesList</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	447 434 <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} - ${ResidueCount}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	448 435 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span> <span class="q">"${ResidueName} - ${PercentResidueCount}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	449 436 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	450 437 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	451 438 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	452 439 <span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">Frequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	453 440 <span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	454 441 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	455 442 <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">$TotalResidueCount</span><span class="s">)</span>*<span class="n">100</span><span class="s">)</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	456 443 <span class="i">$ResidueNames</span> = <span class="i">$AtomResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	457 444 <span class="i">@ResidueNamesList</span> = <span class="k">split</span> <span class="q">/~/</span><span class="cm">,</span> <span class="i">$ResidueNames</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	458 445 <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@ResidueNamesList</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	459 446 <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} - ${ResidueCount}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	460 447 <span class="k">push</span> <span class="i">@</span>{<span class="i">$AtomResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span> <span class="q">"${ResidueName} - ${PercentResidueCount}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	461 448 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	462 449 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	463 450 <span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">Frequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	464 451 <span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	465 452 <span class="k">for</span> <span class="i">$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">$HetatmResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	466 453 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	467 454 <span class="i">$ResidueNames</span> = <span class="i">$HetatmResiduesCountToNameMap</span>{<span class="w">ResidueNames</span>}{<span class="i">$ResidueCount</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	468 455 <span class="i">@ResidueNamesList</span> = <span class="k">split</span> <span class="q">/~/</span><span class="cm">,</span> <span class="i">$ResidueNames</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	469 456 <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@ResidueNamesList</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	470 457 <span class="k">push</span> <span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span> <span class="q">"${ResidueName} - ${ResidueCount}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	471 458 <span class="k">push</span> <span class="i">@</span>{<span class="i">$HetatmResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span> <span class="q">"${ResidueName} - ${PercentResidueCount}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	472 459 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	473 460 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	474 461 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	475 462
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	476 463 <span class="c"># List distribution of residues</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	477 464 <span class="k">print</span> <span class="q">"\nDistribution of residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	478 465 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	479 466 <span class="k">print</span> <span class="q">"\nPercent distribution of residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	480 467 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	481 468
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	482 469 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	483 470 <span class="k">print</span> <span class="q">"\nDistribution of ATOM residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	484 471 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	485 472 <span class="k">print</span> <span class="q">"\nPercent distribution of ATOM residues: "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	486 473 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	487 474
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	488 475 <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">$HetatmResiduesCountInfoMap</span>{<span class="w">Frequency</span>}}<span class="cm">,</span><span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	489 476 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	490 477 <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">$HetatmResiduesCountInfoMap</span>{<span class="w">PercentFrequency</span>}}<span class="cm">,</span><span class="q">'; '</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	491 478 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	492 479 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	493 480 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	494 481 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	495 482
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	496 483 <span class="c"># List information about residue numbers for each chain...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	497 <a name="ListResidueNumbersInfo-"></a> 484 <span class="k">sub </span><span class="m">ListResidueNumbersInfo</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	498 485 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	499 486 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	500 487
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	501 488 <span class="i">$CollectChainResiduesBeyondTER</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	502 489 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	503 490
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	504 491 <span class="k">print</span> <span class="q">"\nATOM/HETATM residue numbers information for chains:\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	505 492
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	506 493 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	507 494 <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">$ChainID</span><span class="s">)</span><span class="cm">,</span> <span class="q">""</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	508 495
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	509 496 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	510 497
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	511 498 <span class="c"># Start and end residue numbers...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	512 499 <span class="i">$StartResidueNum</span> = <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ResidueNumbers</span>}{<span class="i">$ChainID</span>}[<span class="n">0</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	513 500 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	514 501 <span class="k">print</span> <span class="q">"; Number of residues: $ResidueCount; Start residue number - $StartResidueNum; End residue number - $EndResidueNum\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	515 502
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	516 503 <span class="c"># Identify any gaps in residue numbers or non-ascending order residue numbers...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	517 504 <span class="i">$GapResiduePairsCount</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	518 505 <span class="i">$DescendingOrderResiduePairsCount</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	519 506
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	520 507 <span class="i">@DescendingOrderResiduePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	521 508 <span class="i">@GapResiduePairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	522 509
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	523 510 <span class="j">RESIDUE:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="s">(</span><span class="i">$ResidueCount</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	524 511 <span class="i">$ResidueNum</span> = <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ResidueNumbers</span>}{<span class="i">$ChainID</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	525 512 <span class="i">$PreviousResidueNum</span> = <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ResidueNumbers</span>}{<span class="i">$ChainID</span>}[<span class="i">$Index</span> - <span class="n">1</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	526 513
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	527 514 <span class="i">$ResidueName</span> = <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	528 515 <span class="i">$PreviousResidueName</span> = <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}[<span class="i">$Index</span> - <span class="n">1</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	529 516
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	530 517 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueNum</span> == <span class="s">(</span><span class="i">$PreviousResidueNum</span> + <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	531 518 <span class="c"># All is good...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	532 519 <span class="k">next</span> <span class="j">RESIDUE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	533 520 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	534 521
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	535 522 <span class="c"># Are residue in descending order?</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	536 523 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueNum</span> < <span class="i">$PreviousResidueNum</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	537 524 <span class="i">$DescendingOrderResiduePairsCount</span>++<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	538 525 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	539 526 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	540 527
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	541 528 <span class="c"># Track gaps in residue pairs...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	542 529 <span class="i">$GapResiduePairsCount</span>++<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	543 530 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	544 531
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	545 532 <span class="k">push</span> <span class="i">@GapResiduePairs</span><span class="cm">,</span> <span class="q">"<${PreviousResidueName}${PreviousResidueNum} - ${ResidueName}${ResidueNum}; $GapLength>"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	546 533 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	547 534
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	548 535 <span class="c"># Print gaps information...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	549 536 <span class="k">print</span> <span class="q">"Gaps in residue numbers: "</span><span class="cm">,</span> <span class="i">$GapResiduePairsCount</span> ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"None"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	550 537 <span class="k">if</span> <span class="s">(</span><span class="i">$GapResiduePairsCount</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	551 538 <span class="k">print</span> <span class="q">"; Number of gap residue number pairs: $GapResiduePairsCount; Gap residue pairs: <StartRes-EndRes; GapLength> - "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@GapResiduePairs</span><span class="cm">,</span> <span class="q">"; "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	552 539 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	553 540 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	554 541
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	555 542 <span class="c"># Print descending residue order information...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	556 543 <span class="k">print</span> <span class="q">"Residue numbers in descending order: "</span><span class="cm">,</span> <span class="i">$DescendingOrderResiduePairsCount</span> ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"None"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	557 544 <span class="k">if</span> <span class="s">(</span><span class="i">$DescendingOrderResiduePairsCount</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	558 545 <span class="k">print</span> <span class="q">"; Number of descending residue number pairs: $DescendingOrderResiduePairsCount; Descending residue number pairs: <StartRes-EndRes> "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@DescendingOrderResiduePairs</span><span class="cm">,</span> <span class="q">"; "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	559 546 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	560 547 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	561 548 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	562 549 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	563 550
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	564 551 <span class="c"># List min/max XYZ coordinates for ATOM/HETATM records...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	565 <a name="ListBoundingBox-"></a> 552 <span class="k">sub </span><span class="m">ListBoundingBox</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	566 553 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	567 554 <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">$ZSize</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	568 555
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	569 556 <span class="s">(</span><span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	570 557 <span class="i">$XSize</span> = <span class="k">abs</span><span class="s">(</span><span class="i">$XMax</span> - <span class="i">$XMin</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	571 558 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	572 559 <span class="i">$ZSize</span> = <span class="k">abs</span><span class="s">(</span><span class="i">$ZMax</span> - <span class="i">$ZMin</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	573 560
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	574 561 <span class="i">$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">$XMax</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	575 562 <span class="i">$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">$YMax</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	576 563 <span class="i">$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">$ZMax</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	577 564
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	578 565 <span class="i">$XSize</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.3f"</span><span class="cm">,</span> <span class="i">$XSize</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	579 566 <span class="i">$YSize</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.3f"</span><span class="cm">,</span> <span class="i">$YSize</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	580 567 <span class="i">$ZSize</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.3f"</span><span class="cm">,</span> <span class="i">$ZSize</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	581 568
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	582 569 <span class="k">print</span> <span class="q">"\nBounding box coordinates: <XMin, XMax> - <$XMin, $XMax>; <YMin, YMax> - <$YMin, $YMax>; <ZMin, ZMax> - <$ZMin, $ZMax>;\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	583 570 <span class="k">print</span> <span class="q">"Bounding box size in angstroms: XSize - $XSize; YSize - $YSize; ZSize - $ZSize\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	584 571
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	585 572 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	586 573
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	587 574 <span class="c"># Check master record counts against actual record counts...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	588 <a name="CheckMasterRecord-"></a> 575 <span class="k">sub </span><span class="m">CheckMasterRecord</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	589 576 <span class="k">my</span><span class="s">(</span><span class="i">$RecordTypesCountRef</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	590 577
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	591 578 <span class="c"># Get master record information...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	592 579 <span class="k">my</span><span class="s">(</span><span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	593 580 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	594 581 <span class="i">$MasterRecordFound</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	595 582
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	596 583 <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	597 584 <span class="k">if</span> <span class="s">(</span><span class="i">IsMasterRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	598 585 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	599 586 <span class="i">$MasterRecordFound</span> = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	600 587 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	601 588 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	602 589 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	603 590 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MasterRecordFound</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	604 591 <span class="k">print</span> <span class="q">"\nWarning: MASTER record is missing.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	605 592 <span class="k">return</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	606 593 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	607 594 <span class="k">my</span><span class="s">(</span><span class="i">@MasterRecordValidationInfo</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	608 595 <span class="i">@MasterRecordValidationInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	609 596 <span class="i">$NumOfRemarkRecords</span> += <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	610 597 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	611 598 <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, $RecordTypesCountRef->{Count}{REMARK}."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	612 599 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	613 600 <span class="i">$NumOfHetRecords</span> += <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	614 601 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	615 602 <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, $RecordTypesCountRef->{Count}{HET}."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	616 603 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	617 604 <span class="i">$NumOfHelixRecords</span> += <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	618 605 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	619 606 <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, $RecordTypesCountRef->{Count}{HELIX}."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	620 607 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	621 608 <span class="i">$NumOfSheetRecords</span> += <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	622 609 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	623 610 <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, $RecordTypesCountRef->{Count}{SHEET}."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	624 611 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	625 612 <span class="i">$NumOfTurnRecords</span> += <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	626 613 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	627 614 <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, $RecordTypesCountRef->{Count}{REMARK}."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	628 615 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	629 616 <span class="i">$NumOfSiteRecords</span> += <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	630 617 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	631 618 <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, $RecordTypesCountRef->{Count}{SITE}."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	632 619 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	633 620
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	634 621 <span class="i">$NumOfTransformationsRecords</span> += <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	635 622 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	636 623 <span class="i">$RecordsCount</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	637 624 <span class="k">for</span> <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	638 625 <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="n">1</span> .. <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	639 626 <span class="i">$RecordID</span> = <span class="q">"${RecordLabel}${ID}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	640 627 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	641 628 <span class="i">$RecordsCount</span> += <span class="i">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="i">$RecordID</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	642 629 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	643 630 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	644 631 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	645 632 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfTransformationsRecords</span> != <span class="i">$RecordsCount</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	646 633 <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, $RecordsCount."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	647 634 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	648 635
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	649 636 <span class="i">$RecordsCount</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	650 637 <span class="k">for</span> <span class="i">$RecordLabel</span> <span class="s">(</span><span class="q">'ATOM'</span><span class="cm">,</span> <span class="q">'HETATM'</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	651 638 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="i">$RecordLabel</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	652 639 <span class="i">$RecordsCount</span> += <span class="i">$RecordTypesCountRef</span>->{<span class="w">Count</span>}{<span class="i">$RecordLabel</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	653 640 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	654 641 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	655 642 <span class="i">$NumOfAtomAndHetatmRecords</span> += <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	656 643 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfAtomAndHetatmRecords</span> != <span class="i">$RecordsCount</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	657 644 <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, $RecordsCount."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	658 645 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	659 646 <span class="i">$NumOfTerRecords</span> += <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	660 647 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	661 648 <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, $RecordTypesCountRef->{Count}{TER}."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	662 649 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	663 650 <span class="i">$NumOfConectRecords</span> += <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	664 651 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	665 652 <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, $RecordTypesCountRef->{Count}{CONECT}."</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	666 653 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	667 654 <span class="i">$NumOfSeqresRecords</span> += <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	668 655 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	669 656 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	670 657 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	671 658
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	672 659 <span class="k">if</span> <span class="s">(</span><span class="i">@MasterRecordValidationInfo</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	673 660 <span class="k">print</span> <span class="q">"\nMASTER record validation: Count mismatches found:\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	674 661 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	675 662 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	676 663 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	677 664 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	678 665 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	679 666 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	680 667
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	681 668 <span class="c"># Total size of all the files...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	682 <a name="ListTotalSizeOfFiles-"></a> 669 <span class="k">sub </span><span class="m">ListTotalSizeOfFiles</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	683 670 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	684 671
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	685 672 <span class="i">$FileOkayCount</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	686 673 <span class="i">$TotalSize</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	687 674
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	688 675 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	689 676 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	690 677 <span class="i">$FileOkayCount</span>++<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	691 678 <span class="i">$TotalSize</span> += <span class="i">$PDBFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	692 679 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	693 680 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	694 681 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	695 682 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	696 683 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	697 684
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	698 685 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	699 686
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	700 687 <span class="c"># Empty chain IDs are replaced with "None[1-9]". But for displaying purposes, take out any</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	701 688 <span class="c"># numbers from label...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	702 <a name="CleanupChainID-"></a> 689 <span class="k">sub </span><span class="m">CleanupChainID</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	703 690 <span class="k">my</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	704 691
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	705 692 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainID</span> =~ <span class="q">/^None/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	706 693 <span class="k">return</span> <span class="q">'None'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	707 694 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	708 695 <span class="k">return</span> <span class="i">$ChainID</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	709 696 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	710 697
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	711 698 <span class="c"># Process option values...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	712 <a name="ProcessOptions-"></a> 699 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	713 700 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	714 701
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	715 702 <span class="c"># Setup record types to count...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	716 703 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">count</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	717 704 <span class="i">$OptionsInfo</span>{<span class="w">CountRecordType</span>} = <span class="i">$Options</span>{<span class="w">count</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	718 705 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	719 706 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	720 707 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	721 708 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	722 709 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRecordTypes</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	723 710 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CountRecordType</span>} !~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	724 711 <span class="k">my</span><span class="s">(</span><span class="i">@RecordTypes</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	725 712 <span class="i">@RecordTypes</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CountRecordType</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	726 713 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRecordTypes</span>}}<span class="cm">,</span> <span class="i">@RecordTypes</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	727 714 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	728 715 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	729 716 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	730 717
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	731 718 <span class="c"># Residue count is the default. So $Options{residues} is simply ignored.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	732 719 <span class="k">my</span><span class="s">(</span><span class="i">$CountResidues</span><span class="s">)</span> = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	733 720 <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	734 721 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	735 722
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	736 723 <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	737 724 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	738 725
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	739 726 <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">$Options</span>{<span class="w">all</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	740 727
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	741 728 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	742 729
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	743 730 <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">$Options</span>{<span class="w">all</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	744 731 <span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	745 732
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	746 733 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	747 734
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	748 735 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	749 736
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	750 737 <span class="c"># Retrieve information about PDB files...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	751 <a name="RetrievePDBFilesInfo-"></a> 738 <span class="k">sub </span><span class="m">RetrievePDBFilesInfo</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	752 739 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	753 740
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	754 741 <span class="i">%PDBFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	755 742 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	756 743 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileSize</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	757 744 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileLastModified</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	758 745
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	759 746 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	760 747 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	761 748 <span class="i">$PDBFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	762 749 <span class="i">$PDBFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	763 750
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	764 751 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	765 752 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	766 753 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It doesn't exist\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	767 754 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	768 755 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	769 756 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="q">"pdb"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	770 757 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It's not a PDB file\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	771 758 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	772 759 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	773 760 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">PDBFILE</span><span class="cm">,</span> <span class="q">"$PDBFile"</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	774 761 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: Couldn't open it: $! \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	775 762 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	776 763 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	777 764 <span class="k">close</span> <span class="w">PDBFILE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	778 765
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	779 766 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	780 767 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	781 768 <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">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	782 769 <span class="i">$PDBFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">"$ModifiedTimeString; $ModifiedDateString"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	783 770 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	784 771 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	785 772
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	786 773
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	787 774 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	788 <a name="SetupScriptUsage-"></a> 775 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	789 776
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	790 777 <span class="c"># Retrieve all the options...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	791 778 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	792 779 <span class="i">$Options</span>{<span class="w">count</span>} = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	793 780 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	794 781 <span class="i">$Options</span>{<span class="w">residuesmode</span>} = <span class="q">'Both'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	795 782
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	796 783 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	797 784 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	798 785 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	799 786 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	800 787 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	801 788 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	802 789 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	803 790 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	804 791 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	805 792 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	806 793 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	807 794 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	808 795 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">residuesmode</span>} !~ <span class="q">/^(InChains\|All\|Both)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	809 796 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	810 797 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	811 798 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	812 799
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	813 <a name="EOF-"></a></pre>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	814 <p> </p>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	815 <br />
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	816 <center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	817 <img src="../../../images/h2o2.png">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	818 </center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	819 </body>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	820 </html>

Mercurial > repos > deepakjadmin > mayatool3_test2

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