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author	deepakjadmin
date	Wed, 20 Jan 2016 12:15:15 -0500
parents	73ae111cf86f
children

rev	line source
0 73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1 <html>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	2 <head>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	3 <title>MayaChemTools:Code:ExtractFromPDBFiles.pl</title>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	6 </head>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	8 <br/>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	9 <center>
73ae111cf86f 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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	11 </center>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	12 <br/>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	13 <pre>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	14 1 #!/usr/bin/perl -w
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	15 2 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	16 3 <span class="c"># $RCSfile: ExtractFromPDBFiles.pl,v $</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	17 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	18 5 <span class="c"># $Revision: 1.39 $</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	19 6 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	21 8 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	23 10 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	24 11 <span class="c"># This file is part of MayaChemTools.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	25 12 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
73ae111cf86f 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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	29 16 <span class="c"># later version.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	30 17 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	34 21 <span class="c"># details.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	35 22 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	40 27 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	41 28
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
73ae111cf86f 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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	50 37 <span class="k">use</span> <span class="w">PDBFileUtil</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	51 38 <span class="k">use</span> <span class="w">AminoAcids</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	52 39 <span class="k">use</span> <span class="w">SequenceFileUtil</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	53 40
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	54 41 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	55 42
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	56 43 <span class="c"># Autoflush STDOUT</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	57 44 <span class="i">$\|</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	58 45
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	59 46 <span class="c"># Starting message...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	60 47 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	61 48 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	62 49 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	63 50
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	64 51 <span class="c"># Get the options and setup script...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	65 52 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	66 53 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	67 54 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	68 55 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	69 56
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	70 57 <span class="k">my</span><span class="s">(</span><span class="i">@PDBFilesList</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	71 58 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	72 59
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	73 60 <span class="c"># Process options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	74 61 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	75 62 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	76 63 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	77 64
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	78 65 <span class="c"># Setup information about input files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	79 66 <span class="k">print</span> <span class="q">"Checking input PDB file(s)...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	80 67 <span class="k">my</span><span class="s">(</span><span class="i">%PDBFilesInfo</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	81 68 <span class="i">RetrievePDBFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	82 69
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	83 70 <span class="c"># Process input files..</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	84 71 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	85 72 <span class="k">if</span> <span class="s">(</span><span class="i">@PDBFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	86 73 <span class="k">print</span> <span class="q">"\nProcessing PDB files...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	87 74 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	88 75 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	89 76 <span class="k">if</span> <span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	90 77 <span class="k">print</span> <span class="q">"\nProcessing file $PDBFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	91 78 <span class="i">ExtractFromPDBFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	92 79 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	93 80 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	94 81 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	95 82
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	96 83 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	97 84 <span class="i">$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>
73ae111cf86f 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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	99 86
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	100 87 <span class="c">###############################################################################</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	101 88
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	102 89 <span class="c"># Extract appropriate information...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	103 <a name="ExtractFromPDBFiles-"></a> 90 <span class="k">sub </span><span class="m">ExtractFromPDBFiles</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	104 91 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f 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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	106 93
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	107 94 <span class="c"># Get PDB data...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	108 95 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	109 96 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	110 97
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	111 98 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/Chains/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	112 99 <span class="i">ExtractChains</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	113 100 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	114 101 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/Sequences/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	115 102 <span class="i">ExtractSequences</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	116 103 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	117 104 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(Atoms\|CAlphas\|AtomNums\|AtomsRange\|AtomNames)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	118 105 <span class="i">ExtractByAtoms</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	119 106 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	120 107 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(ResidueNums\|ResiduesRange\|ResidueNames)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	121 108 <span class="i">ExtractByResidues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	122 109 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	123 110 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/Distance/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	124 111 <span class="i">ExtractByDistance</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	125 112 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	126 113 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/NonWater/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	127 114 <span class="i">ExtractNonWaterRecords</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	128 115 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	129 116 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/NonHydrogens/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	130 117 <span class="i">ExtractNonHydrogenRecords</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	131 118 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	132 119 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	133 120
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	134 121 <span class="c"># Extract chains and generate new PDB files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	135 122 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	136 <a name="ExtractChains-"></a> 123 <span class="k">sub </span><span class="m">ExtractChains</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	137 124 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	138 125 <span class="k">my</span><span class="s">(</span><span class="i">$ChainIndex</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="cm">,</span> <span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$AtomChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%ChainAtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	139 126
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	140 127 <span class="c"># Get chains and residues data...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	141 128 <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="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	142 129
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	143 130 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	144 131 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	145 132 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	146 133
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	147 134 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	148 135
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	149 136 <span class="c"># Write out header and other older recors...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	150 137 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	151 138 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	152 139
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	153 140 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	154 141 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	155 142 <span class="i">$ChainLabel</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	156 143
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	157 144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	158 145 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	159 146 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	160 147
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	161 148 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	162 149
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	163 150 <span class="c"># Write out header and other older recors...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	164 151 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	165 152 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	166 153
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	167 154 <span class="c"># Write out ATOM/HETATM line for chain and collect all ATOM/HETATM serial numbers</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	168 155 <span class="c"># for writing out appropriate CONECT records...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	169 156 <span class="i">%ChainAtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	170 157 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Lines</span>}{<span class="i">$ChainID</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	171 158 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	172 159 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$AtomChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	173 160 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	174 161 <span class="i">$ChainAtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	175 162 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	176 163 <span class="c"># Write out TER record using information from last chain record...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	177 164 <span class="i">$AtomNumber</span> += <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	178 165 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$AtomChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	179 166
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	180 167 <span class="c"># Write out CONECT records...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	181 168 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%ChainAtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	182 169
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	183 170 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	184 171 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	185 172 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	186 173
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	187 174 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	188 175 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	189 176 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	190 177
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	191 178 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	192 179 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	193 180 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	194 181
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	195 182 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	196 183 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	197 184 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	198 185
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	199 186 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	200 187 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	201 188
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	202 189 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	203 190
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	204 191 <span class="c"># Extract sequences for individual chains or combine all the chains...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	205 <a name="ExtractSequences-"></a> 192 <span class="k">sub </span><span class="m">ExtractSequences</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	206 193 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	207 194 <span class="k">my</span><span class="s">(</span><span class="i">$ChainIndex</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="cm">,</span> <span class="i">$SequenceFileName</span><span class="cm">,</span> <span class="i">$Residue</span><span class="cm">,</span> <span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="cm">,</span> <span class="i">$ChainSequence</span><span class="cm">,</span> <span class="i">$WrappedChainSequence</span><span class="cm">,</span> <span class="i">$ChainSequenceID</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$ChainResiduesRef</span><span class="cm">,</span> <span class="i">%ChainSequencesDataMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	208 195
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	209 196 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} =~ <span class="q">/^SeqRes$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	210 197 <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">'SeqRes'</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	211 198 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	212 199 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	213 200 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	214 201 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	215 202
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	216 203 <span class="c"># Generate sequence data for all the chains...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	217 204 <span class="i">%ChainSequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	218 205 <span class="i">@</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	219 206 <span class="i">%</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	220 207 <span class="i">%</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	221 208
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	222 209 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	223 210 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	224 211 <span class="i">$ChainLabel</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	225 212
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	226 213 <span class="c"># Setup sequence ID...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	227 214 <span class="i">$ChainSequenceID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	228 215 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ChainSequenceID</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	229 216 <span class="i">$ChainSequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$ChainID</span>} = <span class="i">$ChainSequenceID</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	230 217
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	231 218 <span class="c"># Collect sequence data for the chain...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	232 219 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} =~ <span class="q">/^SeqRes/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	233 220 <span class="i">$ChainResiduesRef</span> = \<span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	234 221 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	235 222 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	236 223 <span class="i">$ChainResiduesRef</span> = \<span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	237 224 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	238 225 <span class="c"># Setup sequence data...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	239 226 <span class="i">$ChainSequence</span> = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	240 227 <span class="j">RESIDUE:</span> <span class="k">for</span> <span class="i">$Residue</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainResiduesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	241 228 <span class="s">(</span><span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="s">)</span> = <span class="i">GetResidueCode</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	242 229 <span class="k">if</span> <span class="s">(</span>!<span class="i">$StandardResidue</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	243 230 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepNonStandardSequences</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	244 231 <span class="i">$ResidueCode</span> = <span class="i">$OptionsInfo</span>{<span class="w">NonStandardSequenceCode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	245 232 <span class="k">warn</span> <span class="q">"Warning: Keeping nonstandard residue $Residue in $ChainLabel...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	246 233 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	247 234 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	248 235 <span class="k">warn</span> <span class="q">"Warning: Ignoring nonstandard residue $Residue in $ChainLabel...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	249 236 <span class="k">next</span> <span class="j">RESIDUE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	250 237 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	251 238 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	252 239 <span class="i">$ChainSequence</span> .= <span class="i">$ResidueCode</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	253 240 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	254 241 <span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ChainID</span>} = <span class="i">$ChainSequence</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	255 242
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	256 243 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	257 244
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	258 245 <span class="c"># Write out the sequence files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	259 246 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceID</span><span class="cm">,</span> <span class="i">$SequenceDescription</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">%SequencesDataMap</span> <span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	260 247 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChainSequences</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	261 248 <span class="c"># Combine all the chain sequences...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	262 249 <span class="i">$Sequence</span> = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	263 250 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	264 251 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	265 252
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	266 253 <span class="i">$Sequence</span> .= <span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ChainID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	267 254 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	268 255 <span class="i">$SequenceID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>] . <span class="q">"_CombinedChains\|PDB"</span><span class="sc">;</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	269 256 <span class="i">$SequenceDescription</span> = <span class="i">$SequenceID</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	270 257 <span class="i">$SequenceFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	271 258
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	272 259 <span class="k">print</span> <span class="q">"Generating sequence file $SequenceFileName...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	273 260 <span class="i">%SequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	274 261 <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	275 262 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	276 263 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	277 264
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	278 265 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$SequenceID</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	279 266 <span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$SequenceID</span>} = <span class="i">$SequenceDescription</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	280 267 <span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$SequenceID</span>} = <span class="i">$Sequence</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	281 268
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	282 269 <span class="i">WritePearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFileName</span><span class="cm">,</span> \<span class="i">%SequencesDataMap</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	283 270 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	284 271 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	285 272 <span class="c"># For each specifed chain, write out the sequences...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	286 273 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	287 274 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	288 275
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	289 276 <span class="i">$SequenceFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	290 277
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	291 278 <span class="i">$SequenceID</span> = <span class="i">$ChainSequencesDataMap</span>{<span class="w">IDs</span>}[<span class="i">$ChainIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	292 279 <span class="i">$SequenceDescription</span> = <span class="i">$ChainSequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$ChainID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	293 280 <span class="i">$Sequence</span> = <span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ChainID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	294 281
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	295 282 <span class="k">print</span> <span class="q">"Generating sequence file $SequenceFileName...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	296 283 <span class="i">%SequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	297 284 <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	298 285 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	299 286 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	300 287
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	301 288 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$SequenceID</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	302 289 <span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$SequenceID</span>} = <span class="i">$SequenceDescription</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	303 290 <span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$SequenceID</span>} = <span class="i">$Sequence</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	304 291
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	305 292 <span class="i">WritePearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFileName</span><span class="cm">,</span> \<span class="i">%SequencesDataMap</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	306 293 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	307 294 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	308 295 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	309 296
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	310 297 <span class="c"># Extract atoms...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	311 <a name="ExtractByAtoms-"></a> 298 <span class="k">sub </span><span class="m">ExtractByAtoms</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	312 299 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	313 300 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$IgnoreRecord</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	314 301
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	315 302 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	316 303 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	317 304 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	318 305
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	319 306 <span class="c"># Write out header and other older recors...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	320 307 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	321 308
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	322 309 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	323 310 <span class="c"># chains and multiple models..</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	324 311 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	325 312 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	326 313 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	327 314 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	328 315 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	329 316
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	330 317 <span class="c"># Check atoms...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	331 318 <span class="i">$IgnoreRecord</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	332 319 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Atoms$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	333 320 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	334 321 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	335 322 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(CAlphas\|AtomNames)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	336 323 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesMap</span>}{<span class="k">lc</span> <span class="i">$AtomName</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	337 324 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	338 325 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	339 326 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	340 327 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomNums$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	341 328 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsMap</span>}{<span class="i">$AtomNumber</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	342 329 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	343 330 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	344 331 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	345 332 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomsRange$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	346 333 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNumber</span> >= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartAtomNum</span>} && <span class="i">$AtomNumber</span> <= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndAtomNum</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	347 334 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	348 335 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	349 336 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	350 337
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	351 338 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IgnoreRecord</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	352 339 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	353 340 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	354 341
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	355 342 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	356 343 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	357 344 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	358 345 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	359 346 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	360 347 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	361 348 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	362 349 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	363 350 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	364 351 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	365 352 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> \|\| <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	366 353 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	367 354 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	368 355 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	369 356
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	370 357 <span class="c"># Write out appropriate CONECT records...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	371 358 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	372 359 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	373 360 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	374 361 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	375 362
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	376 363 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	377 364 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	378 365
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	379 366 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	380 367 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	381 368
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	382 369 <span class="c"># Extract residues...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	383 <a name="ExtractByResidues-"></a> 370 <span class="k">sub </span><span class="m">ExtractByResidues</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	384 371 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	385 372 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$IgnoreRecord</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	386 373
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	387 374 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	388 375 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	389 376 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	390 377
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	391 378 <span class="c"># Write out header and other older recors...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	392 379 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	393 380
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	394 381 <span class="c"># Write out all ATOM records for specified residues with TER and model records to indicate</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	395 382 <span class="c"># chains and multiple models...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	396 383 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	397 384 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	398 385 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	399 386 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	400 387 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	401 388
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	402 389 <span class="c"># Check residues...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	403 390 <span class="i">$IgnoreRecord</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	404 391 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResidueNums$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	405 392 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsMap</span>}{<span class="i">$ResidueNumber</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	406 393 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	407 394 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	408 395 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	409 396 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResiduesRange$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	410 397 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueNumber</span> >= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartResidueNum</span>} && <span class="i">$ResidueNumber</span> <= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndResidueNum</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	411 398 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	412 399 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	413 400 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	414 401 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResidueNames$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	415 402 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesMap</span>}{<span class="k">lc</span> <span class="i">$ResidueName</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	416 403 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	417 404 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	418 405 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	419 406 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IgnoreRecord</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	420 407 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	421 408 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	422 409 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	423 410 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	424 411 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	425 412 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	426 413 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	427 414 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	428 415 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	429 416 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	430 417 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	431 418 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	432 419 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> \|\| <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	433 420 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	434 421 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	435 422 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	436 423
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	437 424 <span class="c"># Write out appropriate CONECT records...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	438 425 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	439 426 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	440 427 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	441 428 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	442 429 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	443 430 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	444 431
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	445 432 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	446 433 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	447 434
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	448 435 <span class="c"># Extract non water records...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	449 <a name="ExtractNonWaterRecords-"></a> 436 <span class="k">sub </span><span class="m">ExtractNonWaterRecords</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	450 437 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	451 438 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	452 439
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	453 440 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	454 441 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	455 442 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	456 443
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	457 444 <span class="c"># Write out header and other older recors...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	458 445 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	459 446
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	460 447 <span class="c"># Write out all ATOM/HETATM non water records along with TER and model records to indicate</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	461 448 <span class="c"># chains and multiple models..</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	462 449 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	463 450 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	464 451 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	465 452 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	466 453 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	467 454 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$ResidueName</span>} <span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	468 455 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	469 456 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	470 457 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	471 458 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	472 459 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	473 460 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	474 461 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	475 462 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	476 463 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	477 464 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	478 465 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	479 466 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	480 467 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> \|\| <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	481 468 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	482 469 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	483 470 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	484 471
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	485 472 <span class="c"># Write out appropriate CONECT records...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	486 473 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	487 474 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	488 475 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	489 476 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	490 477 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	491 478 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	492 479
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	493 480 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	494 481 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	495 482
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	496 483 <span class="c"># Extract non hydrogen records...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	497 <a name="ExtractNonHydrogenRecords-"></a> 484 <span class="k">sub </span><span class="m">ExtractNonHydrogenRecords</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	498 485 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	499 486 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	500 487
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	501 488 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	502 489 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	503 490 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	504 491
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	505 492 <span class="c"># Write out header and other older recors...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	506 493 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	507 494
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	508 495 <span class="c"># Write out all ATOM/HETATM non hydrogen records along with TER and model records to indicate</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	509 496 <span class="c"># chains and multiple models..</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	510 497 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	511 498 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	512 499 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	513 500 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	514 501 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	515 502 <span class="k">if</span> <span class="s">(</span><span class="i">$ElementSymbol</span> !~ <span class="q">/^H$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	516 503 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	517 504 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	518 505 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	519 506 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	520 507 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	521 508 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	522 509 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	523 510 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	524 511 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	525 512 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	526 513 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	527 514 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	528 515 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> \|\| <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	529 516 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	530 517 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	531 518 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	532 519
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	533 520 <span class="c"># Write out appropriate CONECT records...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	534 521 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	535 522 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	536 523 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	537 524 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	538 525 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	539 526 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	540 527
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	541 528 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	542 529 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	543 530
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	544 531 <span class="c"># Extract ATOM/HETATM records by distance...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	545 <a name="ExtractByDistance-"></a> 532 <span class="k">sub </span><span class="m">ExtractByDistance</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	546 533 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	547 534 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$RecordLineNum</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$IgnoreRecord</span><span class="cm">,</span> <span class="i">$ResidueID</span><span class="cm">,</span> <span class="i">@OriginCoords</span><span class="cm">,</span> <span class="i">@Coords</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="cm">,</span> <span class="i">%ResiduesDataMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	548 535
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	549 536 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	550 537 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	551 538 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	552 539
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	553 540 <span class="c"># Write out header and other older recors...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	554 541 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	555 542
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	556 543 <span class="c"># Setup coordinates of origin to calculate distance...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	557 544 <span class="i">@OriginCoords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	558 545 <span class="k">push</span> <span class="i">@OriginCoords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	559 546
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	560 547 <span class="c"># Write out all ATOM records for which meet specified criteria along with TER and model records to indicate</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	561 548 <span class="c"># chains and multiple models...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	562 549 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	563 550
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	564 551 <span class="i">%ResiduesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	565 552 <span class="i">%</span>{<span class="i">$ResiduesDataMap</span>{<span class="w">ID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	566 553 <span class="i">%</span>{<span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	567 554
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	568 555 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	569 556 <span class="i">$RecordLineNum</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	570 557
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	571 558 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	572 559 <span class="i">$RecordLineNum</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	573 560 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	574 561 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	575 562 <span class="i">@Coords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">push</span> <span class="i">@Coords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	576 563
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	577 564 <span class="i">$IgnoreRecord</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	578 565 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DistanceSelectionMode</span>} =~ <span class="q">/^ByResidue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	579 566 <span class="i">$ResidueID</span> = <span class="q">"${ResidueName}_${ResidueNumber}_${ChainID}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	580 567 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ResiduesDataMap</span>{<span class="w">ID</span>}{<span class="i">$ResidueID</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	581 568 <span class="c"># Residue data has been processed; check its selection status...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	582 569 <span class="k">if</span> <span class="s">(</span><span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}{<span class="i">$ResidueID</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	583 570 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	584 571 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	585 572 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	586 573 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	587 574 <span class="c"># Residue hasn't been processed...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	588 575 <span class="i">$ResiduesDataMap</span>{<span class="w">ID</span>}{<span class="i">$ResidueID</span>} = <span class="i">$ResidueID</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	589 576 <span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}{<span class="i">$ResidueID</span>} = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	590 577 <span class="k">if</span> <span class="s">(</span><span class="i">CheckResidueDistance</span><span class="s">(</span><span class="i">$ResidueID</span><span class="cm">,</span> <span class="i">$RecordLineNum</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">@OriginCoords</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	591 578 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	592 579 <span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}{<span class="i">$ResidueID</span>} = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	593 580 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	594 581 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	595 582 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	596 583 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DistanceSelectionMode</span>} =~ <span class="q">/^ByAtom$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	597 584 <span class="k">if</span> <span class="s">(</span><span class="i">CheckDistance</span><span class="s">(</span>\<span class="i">@Coords</span><span class="cm">,</span> \<span class="i">@OriginCoords</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	598 585 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	599 586 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	600 587 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	601 588
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	602 589 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IgnoreRecord</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	603 590 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	604 591 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	605 592 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	606 593 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	607 594 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	608 595 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	609 596 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	610 597 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	611 598 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	612 599 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	613 600 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	614 601 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	615 602 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> \|\| <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	616 603 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	617 604 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	618 605 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	619 606
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	620 607 <span class="c"># Write out appropriate CONECT records...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	621 608 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	622 609 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	623 610 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	624 611 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	625 612
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	626 613 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	627 614 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	628 615
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	629 616 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	630 617 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	631 618
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	632 619 <span class="c"># Does record type correspond to the specified record type?</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	633 <a name="CheckRecordType-"></a> 620 <span class="k">sub </span><span class="m">CheckRecordType</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	634 621 <span class="k">my</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	635 622 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	636 623
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	637 624 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	638 625 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} =~ <span class="q">/^Atom$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	639 626 <span class="i">$Status</span> = <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	640 627 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	641 628 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} =~ <span class="q">/^Hetatm$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	642 629 <span class="i">$Status</span> = <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	643 630 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	644 631 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} =~ <span class="q">/^AtomAndHetatm$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	645 632 <span class="i">$Status</span> = <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> \|\| <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	646 633 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	647 634
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	648 635 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	649 636 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	650 637
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	651 638 <span class="c"># Does record meets distance citerion specified by the user?</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	652 <a name="CheckResidueDistance-"></a> 639 <span class="k">sub </span><span class="m">CheckResidueDistance</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	653 640 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedResidueID</span><span class="cm">,</span> <span class="i">$StartingLineNum</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="i">$OriginCoordsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	654 641 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$RecordLineIndex</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$ResidueID</span><span class="cm">,</span> <span class="i">@Coords</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	655 642
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	656 643 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	657 644
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	658 645 <span class="j">RECORDLINE:</span> <span class="k">for</span> <span class="i">$RecordLineIndex</span> <span class="s">(</span><span class="s">(</span><span class="i">$StartingLineNum</span> - <span class="n">1</span><span class="s">)</span> .. <span class="i">$#</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	659 646 <span class="i">$RecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="i">$RecordLineIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	660 647 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	661 648 <span class="k">next</span> <span class="j">RECORDLINE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	662 649 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	663 650 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	664 651 <span class="i">$ResidueID</span> = <span class="q">"${ResidueName}_${ResidueNumber}_${ChainID}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	665 652
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	666 653 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueID</span> !~ <span class="q">/^$SpecifiedResidueID$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	667 654 <span class="c"># It's a new residue line...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	668 655 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	669 656 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	670 657
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	671 658 <span class="c"># Check distance...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	672 659 <span class="i">@Coords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">push</span> <span class="i">@Coords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	673 660 <span class="k">if</span> <span class="s">(</span><span class="i">CheckDistance</span><span class="s">(</span>\<span class="i">@Coords</span><span class="cm">,</span> <span class="i">$OriginCoordsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	674 661 <span class="c"># Distance criterion is met for at least one record in the residue...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	675 662 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	676 663 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	677 664 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	678 665 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	679 666 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	680 667 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	681 668
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	682 669 <span class="c"># Does record meets distance citerion specified by the user?</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	683 <a name="CheckDistance-"></a> 670 <span class="k">sub </span><span class="m">CheckDistance</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	684 671 <span class="k">my</span><span class="s">(</span><span class="i">$CoordsRef</span><span class="cm">,</span> <span class="i">$OriginCoordsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	685 672 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$DistanceSquare</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	686 673
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	687 674 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	688 675
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	689 676 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	690 677 <span class="c"># Go over coordinates of all the atoms in the residue...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	691 678 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueCoordsCount</span><span class="s">)</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$OriginCoordsRef</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	692 679 <span class="j">INDEX:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ResidueCoordsCount</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	693 680 <span class="i">$DistanceSquare</span> = <span class="s">(</span><span class="i">$CoordsRef</span>->[<span class="n">0</span>] - <span class="i">$OriginCoordsRef</span>->[<span class="i">$Index</span>]<span class="s">)</span><span class="n">2</span> + <span class="s">(</span><span class="i">$CoordsRef</span>->[<span class="n">1</span>] - <span class="i">$OriginCoordsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="s">)</span><span class="n">2</span> + <span class="s">(</span><span class="i">$CoordsRef</span>->[<span class="n">2</span>] - <span class="i">$OriginCoordsRef</span>->[<span class="i">$Index</span> + <span class="n">2</span>]<span class="s">)</span>**<span class="n">2</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	694 681 <span class="i">$Distance</span> = <span class="k">sqrt</span> <span class="i">$DistanceSquare</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	695 682 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance</span> <= <span class="i">$OptionsInfo</span>{<span class="w">MaxExtractionDistance</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	696 683 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	697 684 <span class="k">last</span> <span class="j">INDEX</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	698 685 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	699 686 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	700 687 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	701 688 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	702 689 <span class="i">$DistanceSquare</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	703 690 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	704 691 <span class="i">$DistanceSquare</span> += <span class="s">(</span><span class="i">$CoordsRef</span>->[<span class="i">$Index</span>] - <span class="i">$OriginCoordsRef</span>->[<span class="i">$Index</span>]<span class="s">)</span>**<span class="n">2</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	705 692 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	706 693 <span class="i">$Distance</span> = <span class="k">sqrt</span> <span class="i">$DistanceSquare</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	707 694 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$Distance</span> <= <span class="i">$OptionsInfo</span>{<span class="w">MaxExtractionDistance</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	708 695 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	709 696
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	710 697 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	711 698 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	712 699
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	713 700 <span class="c"># Write out modifed header and other older records...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	714 <a name="WriteHeaderAndOlderRecords-"></a> 701 <span class="k">sub </span><span class="m">WriteHeaderAndOlderRecords</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	715 702 <span class="k">my</span><span class="s">(</span><span class="i">$OutFileRef</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	716 703
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	717 704 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	718 705 <span class="c"># Write out modified HEADER record...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	719 706 <span class="k">my</span><span class="s">(</span><span class="i">$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">GetHeaderRecordInformation</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	720 707 <span class="i">$Classification</span> = <span class="q">'Data extracted using MayaChemTools'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	721 708 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">GenerateHeaderRecordLine</span><span class="s">(</span><span class="i">$IDCode</span><span class="cm">,</span> <span class="i">$Classification</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	722 709 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	723 710 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	724 711 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	725 712 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	726 713
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	727 714 <span class="c"># Write out any old records...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	728 715 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	729 716 <span class="k">my</span><span class="s">(</span><span class="i">$RecordLineIndex</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	730 717 <span class="c"># Skip HEADER record and write out older records all the way upto first MODEL/ATOM/HETATM records from input file...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	731 718 <span class="j">RECORDLINE:</span> <span class="k">for</span> <span class="i">$RecordLineIndex</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	732 719 <span class="i">$RecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="i">$RecordLineIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	733 720 <span class="k">if</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> \|\| <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> \|\| <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	734 721 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	735 722 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	736 723 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	737 724 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	738 725 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	739 726 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	740 727
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	741 728 <span class="c"># Get header record information assuming it's the first record...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	742 <a name="GetHeaderRecordInformation-"></a> 729 <span class="k">sub </span><span class="m">GetHeaderRecordInformation</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	743 730 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	744 731 <span class="k">my</span><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">$IDCode</span><span class="cm">,</span> <span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	745 732
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	746 733 <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">$IDCode</span><span class="s">)</span> = <span class="s">(</span><span class="q">''</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	747 734 <span class="i">$HeaderRecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	748 735 <span class="k">if</span> <span class="s">(</span><span class="i">IsHeaderRecordType</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	749 736 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	750 737 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	751 738 <span class="k">return</span> <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">$IDCode</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	752 739 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	753 740
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	754 741 <span class="c"># Get one letter residue code...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	755 <a name="GetResidueCode-"></a> 742 <span class="k">sub </span><span class="m">GetResidueCode</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	756 743 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	757 744 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	758 745
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	759 746 <span class="i">$ResidueCode</span> = <span class="i">$OptionsInfo</span>{<span class="w">NonStandardSequenceCode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	760 747 <span class="i">$StandardResidue</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	761 748
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	762 749 <span class="k">if</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	763 750 <span class="c"># Assume it's an amino acid...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	764 751 <span class="k">if</span> <span class="s">(</span><span class="i">AminoAcids::IsAminoAcid</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	765 752 <span class="c"># Standard amino acid...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	766 753 <span class="i">$ResidueCode</span> = <span class="i">AminoAcids::GetAminoAcidOneLetterCode</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	767 754 <span class="i">$StandardResidue</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	768 755 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	769 756 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	770 757 <span class="k">elsif</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	771 758 <span class="c"># Assume it's a nucleic acid...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	772 759 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueName</span> =~ <span class="q">/^(A\|G\|T\|U\|C)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	773 760 <span class="i">$ResidueCode</span> = <span class="i">$ResidueName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	774 761 <span class="i">$StandardResidue</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	775 762 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	776 763 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	777 764
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	778 765 <span class="k">return</span> <span class="s">(</span><span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	779 766 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	780 767
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	781 768 <span class="c"># Process option values...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	782 <a name="ProcessOptions-"></a> 769 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	783 770 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	784 771 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	785 772
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	786 773 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedChains</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	787 774 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">chains</span>} =~ <span class="q">/^(First\|All)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	788 775 <span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} = <span class="i">$Options</span>{<span class="w">chains</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	789 776 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	790 777 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	791 778 <span class="i">@SpecifiedChains</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">chains</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	792 779 <span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} = <span class="q">'Specified'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	793 780 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	794 781 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedChains</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	795 782 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedChains</span>}}<span class="cm">,</span> <span class="i">@SpecifiedChains</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	796 783
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	797 784 <span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">combinechains</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	798 785
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	799 786 <span class="i">$OptionsInfo</span>{<span class="w">CombineChainSequences</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">combinechains</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	800 787
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	801 788 <span class="i">ProcessResiduesOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	802 789 <span class="i">ProcessAtomsOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	803 790 <span class="i">ProcessDistanceOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	804 791
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	805 792 <span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} = <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	806 793 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	807 794 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	808 795
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	809 796 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	810 797 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	811 798
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	812 799 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^NonWater$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	813 800 <span class="k">my</span><span class="s">(</span><span class="i">$WaterResidueName</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	814 801 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} =~ <span class="q">/Automatic/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	815 802 <span class="k">push</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="cm">,</span> <span class="s">(</span><span class="q">'HOH'</span><span class="cm">,</span> <span class="q">'WAT'</span><span class="cm">,</span> <span class="q">'H2O'</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	816 803 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	817 804 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	818 805 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	819 806 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	820 807 <span class="k">for</span> <span class="i">$WaterResidueName</span> <span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	821 808 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$WaterResidueName</span>} = <span class="i">$WaterResidueName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	822 809 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	823 810 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	824 811 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	825 812
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	826 813 <span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} = <span class="i">$Options</span>{<span class="w">recordmode</span>} ? <span class="i">$Options</span>{<span class="w">recordmode</span>} <span class="co">:</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^(Atoms\|CAlphas\|AtomNums\|AtomsRange\|AtomNames)$/i</span> ? <span class="q">"Atom"</span> <span class="co">:</span> <span class="q">"AtomAndHetatm"</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	827 814
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	828 815 <span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	829 816
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	830 817 <span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	831 818
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	832 819 <span class="i">$OptionsInfo</span>{<span class="w">KeepNonStandardSequences</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">nonstandardkeep</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	833 820 <span class="i">$OptionsInfo</span>{<span class="w">NonStandardSequenceCode</span>} = <span class="i">$Options</span>{<span class="w">nonstandardcode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	834 821 <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>} = <span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	835 822 <span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} = <span class="i">$Options</span>{<span class="w">sequencerecords</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	836 823 <span class="i">$OptionsInfo</span>{<span class="w">SequenceIDPrefixSource</span>} = <span class="i">$Options</span>{<span class="w">sequenceidprefix</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	837 824
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	838 825 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	839 826 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	840 827 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	841 828
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	842 829 <span class="c"># Process specified residue options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	843 <a name="ProcessResiduesOptions-"></a> 830 <span class="k">sub </span><span class="m">ProcessResiduesOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	844 831 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueNum</span><span class="cm">,</span> <span class="i">$StartResidueNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">@SpecifiedResidueNumsList</span><span class="cm">,</span> <span class="i">@SpecifiedResidueNamesList</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	845 832
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	846 833 <span class="i">@SpecifiedResidueNumsList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	847 834 <span class="s">(</span><span class="i">$StartResidueNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	848 835
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	849 836 <span class="i">@SpecifiedResidueNamesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	850 837
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	851 838 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(ResidueNums\|ResiduesRange\|ResidueNames)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	852 839 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">residues</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	853 840 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--Residues\" option in \"ResidueNums, ResiduesRange, or ResidueNames\" \"-m, --mode\". \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	854 841 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	855 842 <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>} = <span class="i">$Options</span>{<span class="w">residues</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	856 843 <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>} =~ <span class="q">s/ //g</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	857 844
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	858 845 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResidueNames$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	859 846 <span class="i">@SpecifiedResidueNamesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	860 847 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	861 848 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	862 849 <span class="i">@SpecifiedResidueNumsList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	863 850 <span class="k">for</span> <span class="i">$ResidueNum</span> <span class="s">(</span><span class="i">@SpecifiedResidueNumsList</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	864 851 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$ResidueNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	865 852 <span class="k">die</span> <span class="q">"Error: Invalid residue number value, $ResidueNum, for \"--Residues\" option during \"ResidueNumes\" or \"ResiduesRange\"value of \"-m --mode\" option: Residue number must be a positive integer.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	866 853 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	867 854 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	868 855 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResiduesRange$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	869 856 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedResidueNumsList</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	870 857 <span class="k">die</span> <span class="q">"Error: Invalid number of residue number values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedResidueNumsList</span><span class="s">)</span><span class="cm">,</span> <span class="q">", for \"--Residues\" option during \"ResiduesRange\" value of \"-m --mode\" option: The number of values must be 2 corresponding to start and end residue numbers.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	871 858 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	872 859 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedResidueNumsList</span>[<span class="n">0</span>] > <span class="i">$SpecifiedResidueNumsList</span>[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	873 860 <span class="k">die</span> <span class="q">"Error: Invalid residue number values, @SpecifiedResidueNumsList, for \"--Residues\" option during \"ResiduesRange\" value of \"-m --mode\" option: The start residue number must be less than end residue number.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	874 861 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	875 862 <span class="s">(</span><span class="i">$StartResidueNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="s">)</span> = <span class="i">@SpecifiedResidueNumsList</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	876 863 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	877 864 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	878 865 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	879 866
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	880 867 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	881 868 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedResidueNumsList</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	882 869
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	883 870 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartResidueNum</span>} = <span class="i">$StartResidueNum</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	884 871 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndResidueNum</span>} = <span class="i">$EndResNum</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	885 872
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	886 873 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	887 874 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedResidueNamesList</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	888 875
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	889 876 <span class="c"># Set up a specified residue numbers map...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	890 877 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	891 878 <span class="k">for</span> <span class="i">$ResidueNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsList</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	892 879 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsMap</span>}{<span class="i">$ResidueNum</span>} = <span class="i">$ResidueNum</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	893 880 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	894 881
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	895 882 <span class="c"># Set up a specified residue names map...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	896 883 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	897 884 <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesList</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	898 885 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesMap</span>}{<span class="k">lc</span> <span class="i">$ResidueName</span>} = <span class="k">lc</span> <span class="i">$ResidueName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	899 886 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	900 887
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	901 888 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	902 889
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	903 890 <span class="c"># Process specified atom options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	904 <a name="ProcessAtomsOptions-"></a> 891 <span class="k">sub </span><span class="m">ProcessAtomsOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	905 892 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$StartAtomNum</span><span class="cm">,</span> <span class="i">$EndAtomNum</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">@SpecifiedAtomNumsList</span><span class="cm">,</span> <span class="i">@SpecifiedAtomNamesList</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	906 893
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	907 894 <span class="i">@SpecifiedAtomNumsList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	908 895 <span class="s">(</span><span class="i">$StartAtomNum</span><span class="cm">,</span> <span class="i">$EndAtomNum</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	909 896
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	910 897 <span class="i">@SpecifiedAtomNamesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	911 898
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	912 899 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(AtomNums\|AtomsRange\|AtomNames)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	913 900 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">atoms</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	914 901 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--Atoms\" option in \"AtomNums, AtomsRange, or AtomNames\" \"-m, --mode\". \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	915 902 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	916 903 <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>} = <span class="i">$Options</span>{<span class="w">atoms</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	917 904 <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>} =~ <span class="q">s/ //g</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	918 905
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	919 906 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomNames$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	920 907 <span class="i">@SpecifiedAtomNamesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	921 908 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	922 909 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	923 910 <span class="i">@SpecifiedAtomNumsList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	924 911 <span class="k">for</span> <span class="i">$AtomNum</span> <span class="s">(</span><span class="i">@SpecifiedAtomNumsList</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	925 912 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$AtomNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	926 913 <span class="k">die</span> <span class="q">"Error: Invalid atom number value, $AtomNum, for \"--Atoms\" option during \"AtomNums\" or \"AtomsRange\"value of \"-m --mode\" option: Atom number must be a positive integer.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	927 914 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	928 915 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	929 916 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomsRange$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	930 917 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedAtomNumsList</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	931 918 <span class="k">die</span> <span class="q">"Error: Invalid number of atom number values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedAtomNumsList</span><span class="s">)</span><span class="cm">,</span> <span class="q">", for \"--Atoms\" option during \"AtomsRange\" value of \"-m --mode\" option: The number of values must be 2 corresponding to start and end atom numbers.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	932 919 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	933 920 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedAtomNumsList</span>[<span class="n">0</span>] > <span class="i">$SpecifiedAtomNumsList</span>[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	934 921 <span class="k">die</span> <span class="q">"Error: Invalid atom number values, @SpecifiedAtomNumsList, for \"--Atoms\" option during \"AtomsRange\" value of \"-m --mode\" option: The start atom number must be less than end atom number.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	935 922 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	936 923 <span class="s">(</span><span class="i">$StartAtomNum</span><span class="cm">,</span> <span class="i">$EndAtomNum</span><span class="s">)</span> = <span class="i">@SpecifiedAtomNumsList</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	937 924 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	938 925 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	939 926 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	940 927 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^CAlphas$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	941 928 <span class="i">@SpecifiedAtomNamesList</span> = <span class="s">(</span><span class="q">"CA"</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	942 929 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	943 930
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	944 931 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	945 932 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedAtomNumsList</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	946 933
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	947 934 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartAtomNum</span>} = <span class="i">$StartAtomNum</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	948 935 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndAtomNum</span>} = <span class="i">$EndAtomNum</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	949 936
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	950 937 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	951 938 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedAtomNamesList</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	952 939
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	953 940 <span class="c"># Set up a specified residue numbers map...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	954 941 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	955 942 <span class="k">for</span> <span class="i">$AtomNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsList</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	956 943 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsMap</span>}{<span class="i">$AtomNum</span>} = <span class="i">$AtomNum</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	957 944 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	958 945
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	959 946 <span class="c"># Set up a specified residue names map...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	960 947 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	961 948 <span class="k">for</span> <span class="i">$AtomName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesList</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	962 949 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesMap</span>}{<span class="k">lc</span> <span class="i">$AtomName</span>} = <span class="k">lc</span> <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	963 950 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	964 951
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	965 952 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	966 953
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	967 954 <span class="c"># Process specified distance options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	968 <a name="ProcessDistanceOptions-"></a> 955 <span class="k">sub </span><span class="m">ProcessDistanceOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	969 956 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	970 957
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	971 958 <span class="i">$OptionsInfo</span>{<span class="w">MaxExtractionDistance</span>} = <span class="i">$Options</span>{<span class="w">distance</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	972 959 <span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} = <span class="i">$Options</span>{<span class="w">distancemode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	973 960 <span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceOrigin</span>} = <span class="i">$Options</span>{<span class="w">distanceorigin</span>} ? <span class="i">$Options</span>{<span class="w">distanceorigin</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	974 961 <span class="i">$OptionsInfo</span>{<span class="w">DistanceSelectionMode</span>} = <span class="i">$Options</span>{<span class="w">distanceselectionmode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	975 962
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	976 963 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Distance$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	977 964 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">distanceorigin</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	978 965 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--distanceorigin\" option in \"Distance\" \"-m, --mode\". \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	979 966 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	980 967 <span class="i">@SpecifiedDistanceOrigin</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">distanceorigin</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	981 968 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Atom$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	982 969 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	983 970 <span class="k">die</span> <span class="q">"Error: Invalid number of values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">" for option \"distanceorigin\" option during \"Atom\" value of \"--distancemode\" : The number of values must be 2.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	984 971 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	985 972 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	986 973 <span class="k">die</span> <span class="q">"Error: Invalid atom number value, "</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">", for option \"distanceorigin\" option during \"Atom\" value of \"--distancemode\". Allowed values: > 0\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	987 974 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	988 975 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	989 976 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Hetatm$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	990 977 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	991 978 <span class="k">die</span> <span class="q">"Error: Invalid number of values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">" for option \"distanceorigin\" option during \"Hetatm\" value of \"--distancemode\" : The number of values must be 2.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	992 979 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	993 980 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	994 981 <span class="k">die</span> <span class="q">"Error: Invalid hetatm number value, "</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">", for option \"distanceorigin\" option during \"Hetatm\" value of \"--distancemode\". Allowed values: > 0\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	995 982 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	996 983 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	997 984 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	998 985 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> == <span class="n">2</span> \|\| <span class="i">@SpecifiedDistanceOrigin</span> == <span class="n">3</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	999 986 <span class="k">die</span> <span class="q">"Error: Invalid number of values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">" for option \"distanceorigin\" option during \"Residue\" value of \"--distancemode\" : The number of values must be either 2 or 3.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1000 987 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1001 988 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1002 989 <span class="k">die</span> <span class="q">"Error: Invalid residue number value, "</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">", for option \"distanceorigin\" option during \"Residue\" value of \"--distancemode\". Allowed values: > 0\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1003 990 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1004 991 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1005 992 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^XYZ$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1006 993 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> != <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1007 994 <span class="k">die</span> <span class="q">"Error: Invalid number of values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">" for option \"distanceorigin\" option during \"XYZ\" value of \"--distancemode\" : The number of values must be 3.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1008 995 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1009 996 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1010 997 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1011 998 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsNumerical</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1012 999 <span class="k">die</span> <span class="q">"Error: Invalid coordinate value, "</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">", for option \"distanceorigin\" option during \"XYZ\" value of \"--distancemode\". Allowed values: numerical\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1013 1000 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1014 1001 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1015 1002 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1016 1003 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1017 1004 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1018 1005 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDistanceOrigin</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1019 1006
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1020 1007 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1021 1008
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1022 1009 <span class="c"># Retrieve information about PDB files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1023 <a name="RetrievePDBFilesInfo-"></a>1010 <span class="k">sub </span><span class="m">RetrievePDBFilesInfo</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1024 1011 <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">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">@ChainLabels</span><span class="cm">,</span> <span class="i">@ChainSequenceIDs</span><span class="cm">,</span> <span class="i">@ChainSequenceIDsPrefix</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1025 1012
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1026 1013 <span class="i">%PDBFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1027 1014 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1028 1015 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1029 1016 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1030 1017 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1031 1018 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1032 1019 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1033 1020 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1034 1021 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1035 1022
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1036 1023 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1037 1024 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1038 1025
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1039 1026 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1040 1027 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1041 1028 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1042 1029 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1043 1030 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1044 1031 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1045 1032 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1046 1033 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1047 1034
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1048 1035 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1049 1036 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$PDBFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1050 1037 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It doesn't exist\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1051 1038 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1052 1039 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1053 1040 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="q">"pdb"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1054 1041 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It's not a PDB file\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1055 1042 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1056 1043 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1057 1044 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">PDBFILE</span><span class="cm">,</span> <span class="q">"$PDBFile"</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1058 1045 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: Couldn't open it: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1059 1046 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1060 1047 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1061 1048 <span class="k">close</span> <span class="w">PDBFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1062 1049
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1063 1050 <span class="c"># Get PDB data...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1064 1051 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1065 1052 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Sequences$/i</span> && <span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} =~ <span class="q">/^SeqRes$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1066 1053 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="q">'SeqRes'</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1067 1054 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1068 1055 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1069 1056 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1070 1057 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1071 1058 <span class="k">if</span> <span class="s">(</span>!<span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1072 1059 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: No chains found \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1073 1060 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1074 1061 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1075 1062
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1076 1063 <span class="c"># Make sure specified chains exist in PDB file...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1077 1064 <span class="i">@SpecifiedChains</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1078 1065 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} =~ <span class="q">/^Specified$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1079 1066 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedChains</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1080 1067 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1081 1068 <span class="k">push</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1082 1069 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1083 1070 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1084 1071 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: Specified chain, $ChainID, in \"-c, --chains\" option doesn't exist.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1085 1072 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1086 1073 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1087 1074 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1088 1075 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1089 1076 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} =~ <span class="q">/^First$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1090 1077 <span class="k">push</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}[<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1091 1078 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1092 1079 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1093 1080 <span class="k">push</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1094 1081 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1095 1082 <span class="c"># Setup chain labels to use for sequence IDs and generating output files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1096 1083 <span class="i">@ChainLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1097 1084 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@SpecifiedChains</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1098 1085 <span class="i">$ChainLabel</span> = <span class="i">$ChainID</span><span class="sc">;</span> <span class="i">$ChainLabel</span> =~ <span class="q">s/^None//ig</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1099 1086 <span class="i">$ChainLabel</span> = <span class="q">"Chain${ChainLabel}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1100 1087 <span class="k">push</span> <span class="i">@ChainLabels</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1101 1088 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1102 1089
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1103 1090 <span class="c"># Make sure specified distance origin is valid...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1104 1091 <span class="i">@DistanceOrigin</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1105 1092 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Distance$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1106 1093 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^(Atom\|Hetatm)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1107 1094 <span class="k">my</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$SpecifiedAtomName</span><span class="cm">,</span> <span class="i">$SpecifiedAtomNumber</span><span class="cm">,</span> <span class="i">$RecordFound</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1108 1095 <span class="i">$RecordType</span> = <span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1109 1096 <span class="s">(</span><span class="i">$SpecifiedAtomNumber</span><span class="cm">,</span> <span class="i">$SpecifiedAtomName</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1110 1097 <span class="i">$RecordFound</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1111 1098 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1112 1099 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> \|\| <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1113 1100 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1114 1101 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1115 1102 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1116 1103 <span class="i">$AtomName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$AtomName</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1117 1104 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$RecordType</span> =~ <span class="q">/^Atom$/i</span> && <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> \|\| <span class="s">(</span><span class="i">$RecordType</span> =~ <span class="q">/^Hetatm$/i</span> && <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1118 1105 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNumber</span> == <span class="i">$SpecifiedAtomNumber</span> && <span class="i">$AtomName</span> <span class="k">eq</span> <span class="i">$SpecifiedAtomName</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1119 1106 <span class="i">$RecordFound</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1120 1107 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1121 1108 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1122 1109 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1123 1110 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1124 1111 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RecordFound</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1125 1112 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: "</span><span class="cm">,</span> <span class="k">uc</span><span class="s">(</span><span class="i">$RecordType</span><span class="s">)</span><span class="cm">,</span> <span class="q">" record corresponding to \"--distanceorigin\" option value, $OptionsInfo{ExtractionDistanceOrigin}, doesn't exist.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1126 1113 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1127 1114 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1128 1115 <span class="k">push</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1129 1116 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1130 1117 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1131 1118 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedResidueNumber</span><span class="cm">,</span> <span class="i">$SpecifiedResidueName</span><span class="cm">,</span> <span class="i">$SpecifiedChainID</span><span class="cm">,</span> <span class="i">$RecordFound</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1132 1119 <span class="i">$SpecifiedChainID</span> = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1133 1120 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}} == <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1134 1121 <span class="s">(</span><span class="i">$SpecifiedResidueNumber</span><span class="cm">,</span> <span class="i">$SpecifiedResidueName</span><span class="cm">,</span> <span class="i">$SpecifiedChainID</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1135 1122 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1136 1123 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1137 1124 <span class="s">(</span><span class="i">$SpecifiedResidueNumber</span><span class="cm">,</span> <span class="i">$SpecifiedResidueName</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1138 1125 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1139 1126 <span class="i">$RecordFound</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1140 1127 <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1141 1128 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> \|\| <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1142 1129 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1143 1130 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1144 1131 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1145 1132 <span class="i">$ResidueName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1146 1133 <span class="i">$ChainID</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1147 1134 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedChainID</span> && <span class="s">(</span><span class="i">$SpecifiedChainID</span> <span class="k">ne</span> <span class="i">$ChainID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1148 1135 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1149 1136 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1150 1137 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueNumber</span> == <span class="i">$SpecifiedResidueNumber</span> && <span class="i">$ResidueName</span> <span class="k">eq</span> <span class="i">$SpecifiedResidueName</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1151 1138 <span class="c"># Store coordinates for all the atoms...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1152 1139 <span class="i">$RecordFound</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1153 1140 <span class="k">push</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1154 1141 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1155 1142 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1156 1143 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1157 1144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RecordFound</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1158 1145 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: ATOM/HETATM record corresponding to \"--distanceorigin\" option value, $OptionsInfo{ExtractionDistanceOrigin}, doesn't exist.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1159 1146 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1160 1147 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1161 1148 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1162 1149 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^XYZ$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1163 1150 <span class="k">push</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1164 1151 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1165 1152 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1166 1153 <span class="c"># Setup output file names...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1167 1154 <span class="i">@OutFileNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1168 1155 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1169 1156 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1170 1157 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@PDBFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1171 1158 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1172 1159 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1173 1160 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1174 1161 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1175 1162 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1176 1163 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1177 1164 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1178 1165 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1179 1166 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1180 1167 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1181 1168 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1182 1169 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1183 1170 <span class="i">$Mode</span> = <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1184 1171 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(Atoms\|CAlphas\|AtomNums\|AtomsRange\|AtomNames\|ResidueNums\|ResiduesRange\|ResidueNames\|Distance\|NonWater\|NonHydrogens)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1185 1172 <span class="i">$OutFileName</span> = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1186 1173 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^CAlphas$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1187 1174 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}CAlphas.pdb"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1188 1175 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1189 1176 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Atoms$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1190 1177 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}Atoms.pdb"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1191 1178 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1192 1179 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomNums$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1193 1180 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}AtomNums.pdb"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1194 1181 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1195 1182 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomsRange$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1196 1183 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}AtomsRange.pdb"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1197 1184 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1198 1185 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomNames$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1199 1186 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}AtomNames.pdb"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1200 1187 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1201 1188 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ResidueNums$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1202 1189 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}ResidueNums.pdb"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1203 1190 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1204 1191 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ResiduesRange$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1205 1192 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}ResiduesRange.pdb"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1206 1193 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1207 1194 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ResidueNames$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1208 1195 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}ResidueNames.pdb"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1209 1196 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1210 1197 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^NonWater$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1211 1198 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}NonWater.pdb"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1212 1199 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1213 1200 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^NonHydrogens$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1214 1201 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}NonHydrogens.pdb"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1215 1202 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1216 1203 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Distance$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1217 1204 <span class="k">my</span><span class="s">(</span><span class="i">$DistanceMode</span><span class="s">)</span> = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1218 1205 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Atom$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1219 1206 <span class="i">$DistanceMode</span> = <span class="q">'Atom'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1220 1207 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1221 1208 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Hetatm$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1222 1209 <span class="i">$DistanceMode</span> = <span class="q">'Hetatm'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1223 1210 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1224 1211 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1225 1212 <span class="i">$DistanceMode</span> = <span class="q">'Residue'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1226 1213 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1227 1214 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^XYZ$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1228 1215 <span class="i">$DistanceMode</span> = <span class="q">'XYZ'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1229 1216 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1230 1217 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}DistanceBy${DistanceMode}.pdb"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1231 1218 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1232 1219 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1233 1220 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} && <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1234 1221 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1235 1222 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1236 1223 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1237 1224 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1238 1225 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(Chains\|Sequences)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1239 1226 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChainSequences</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1240 1227 <span class="i">$OutFileName</span> = <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Chains$/i</span><span class="s">)</span> ? <span class="q">"${OutFileRoot}ExtractedChains.pdb"</span> <span class="co">:</span> <span class="q">"${OutFileRoot}SequencesChainsCombined.fasta"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1241 1228 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1242 1229 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} && <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1243 1230 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1244 1231 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1245 1232 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1246 1233 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1247 1234 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1248 1235 <span class="k">for</span> <span class="i">$ChainLabel</span> <span class="s">(</span><span class="i">@ChainLabels</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1249 1236 <span class="i">$OutFileName</span> = <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Chains$/i</span><span class="s">)</span> ? <span class="q">"${OutFileRoot}${ChainLabel}.pdb"</span> <span class="co">:</span> <span class="q">"${OutFileRoot}Sequences${ChainLabel}.fasta"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1250 1237 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1251 1238 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} && <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1252 1239 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1253 1240 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1254 1241 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1255 1242 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1256 1243 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1257 1244 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1258 1245 <span class="i">@ChainSequenceIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1259 1246 <span class="i">@ChainSequenceIDsPrefix</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1260 1247 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Sequences$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1261 1248 <span class="k">my</span><span class="s">(</span><span class="i">$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">$IDCode</span><span class="cm">,</span> <span class="i">$IDPrefix</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1262 1249 <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">$IDCode</span><span class="s">)</span> = <span class="i">GetHeaderRecordInformation</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1263 1250
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1264 1251 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceIDPrefixSource</span>} =~ <span class="q">/^FileName$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1265 1252 <span class="i">$IDPrefix</span> = <span class="i">$FileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1266 1253 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1267 1254 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceIDPrefixSource</span>} =~ <span class="q">/^HeaderRecord$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1268 1255 <span class="i">$IDPrefix</span> = <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$IDCode</span><span class="s">)</span> ? <span class="i">$IDCode</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1269 1256 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1270 1257 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1271 1258 <span class="i">$IDPrefix</span> = <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$IDCode</span><span class="s">)</span> ? <span class="i">$IDCode</span> <span class="co">:</span> <span class="i">$FileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1272 1259 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1273 1260
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1274 1261 <span class="k">for</span> <span class="i">$ChainLabel</span> <span class="s">(</span><span class="i">@ChainLabels</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1275 1262 <span class="k">push</span> <span class="i">@ChainSequenceIDsPrefix</span><span class="cm">,</span> <span class="i">$IDPrefix</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1276 1263 <span class="k">push</span> <span class="i">@ChainSequenceIDs</span><span class="cm">,</span> <span class="q">"${IDPrefix}_${ChainLabel}\|PDB"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1277 1264 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1278 1265 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1279 1266
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1280 1267 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1281 1268 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1282 1269
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1283 1270 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@OutFileNames</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1284 1271 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@ChainLabels</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1285 1272 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@ChainSequenceIDsPrefix</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1286 1273 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@ChainSequenceIDs</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1287 1274 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@SpecifiedChains</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1288 1275 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@DistanceOrigin</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1289 1276 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1290 1277 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1291 1278
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1292 1279
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1293 1280 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1294 <a name="SetupScriptUsage-"></a>1281 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1295 1282
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1296 1283 <span class="c"># Retrieve all the options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1297 1284 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1298 1285 <span class="i">$Options</span>{<span class="w">chains</span>} = <span class="q">'First'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1299 1286 <span class="i">$Options</span>{<span class="w">combinechains</span>} = <span class="q">'no'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1300 1287 <span class="i">$Options</span>{<span class="w">distance</span>} = <span class="n">10.0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1301 1288 <span class="i">$Options</span>{<span class="w">distancemode</span>} = <span class="q">'XYZ'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1302 1289 <span class="i">$Options</span>{<span class="w">distanceselectionmode</span>} = <span class="q">'ByAtom'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1303 1290 <span class="i">$Options</span>{<span class="w">keepoldrecords</span>} = <span class="q">'no'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1304 1291 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'NonWater'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1305 1292 <span class="i">$Options</span>{<span class="w">modifyheader</span>} = <span class="q">'yes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1306 1293 <span class="i">$Options</span>{<span class="w">nonstandardkeep</span>} = <span class="q">'yes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1307 1294 <span class="i">$Options</span>{<span class="w">nonstandardcode</span>} = <span class="q">'X'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1308 1295 <span class="i">$Options</span>{<span class="w">sequencelength</span>} = <span class="n">80</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1309 1296 <span class="i">$Options</span>{<span class="w">sequenceidprefix</span>} = <span class="q">'Automatic'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1310 1297 <span class="i">$Options</span>{<span class="w">sequencerecords</span>} = <span class="q">'Atom'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1311 1298 <span class="i">$Options</span>{<span class="w">waterresiduenames</span>} = <span class="q">'Automatic'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1312 1299
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1313 1300 <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">"atoms\|a=s"</span><span class="cm">,</span> <span class="q">"chains\|c=s"</span><span class="cm">,</span> <span class="q">"combinechains=s"</span><span class="cm">,</span> <span class="q">"distance\|d=f"</span><span class="cm">,</span> <span class="q">"distancemode=s"</span><span class="cm">,</span> <span class="q">"distanceorigin=s"</span><span class="cm">,</span> <span class="q">"distanceselectionmode=s"</span><span class="cm">,</span> <span class="q">"help\|h"</span><span class="cm">,</span> <span class="q">"keepoldrecords\|k=s"</span><span class="cm">,</span> <span class="q">"mode\|m=s"</span><span class="cm">,</span> <span class="q">"modifyheader=s"</span><span class="cm">,</span> <span class="q">"nonstandardkeep=s"</span><span class="cm">,</span> <span class="q">"nonstandardcode=s"</span><span class="cm">,</span> <span class="q">"overwrite\|o"</span><span class="cm">,</span> <span class="q">"root\|r=s"</span><span class="cm">,</span> <span class="q">"recordmode=s"</span><span class="cm">,</span> <span class="q">"residues=s"</span><span class="cm">,</span> <span class="q">"sequencelength=i"</span><span class="cm">,</span> <span class="q">"sequenceidprefix=s"</span><span class="cm">,</span> <span class="q">"sequencerecords=s"</span><span class="cm">,</span> <span class="q">"waterresiduenames=s"</span><span class="cm">,</span> <span class="q">"workingdir\|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1314 1301 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1315 1302 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1316 1303 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1317 1304 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1318 1305 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1319 1306 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1320 1307 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1321 1308 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1322 1309 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">combinechains</span>} !~ <span class="q">/^(yes\|no)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1323 1310 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{combinechains}, for option \"--CombineChains\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1324 1311 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1325 1312 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">distancemode</span>} !~ <span class="q">/^(Atom\|Hetatm\|Residue\|XYZ)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1326 1313 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{distancemode}, for option \"--DistanceMode\" is not valid. Allowed values: Atom, Hetatm, Residue, or XYZ\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1327 1314 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1328 1315 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">distanceselectionmode</span>} !~ <span class="q">/^(ByAtom\|ByResidue)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1329 1316 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{distanceselectionmode}, for option \"--DistanceSelectionMode\" is not valid. Allowed values: ByAtom or ByResidue\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1330 1317 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1331 1318 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} !~ <span class="q">/^(yes\|no)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1332 1319 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keepoldrecords}, for option \"--KeepOldRecords\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1333 1320 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1334 1321 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(Chains\|Sequences\|Atoms\|CAlphas\|AtomNums\|AtomsRange\|AtomNames\|ResidueNums\|ResidueNames\|ResiduesRange\|Distance\|NonWater\|NonHydrogens)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1335 1322 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"m, --mode\" is not valid. Allowed values: Chains, Sequences, Atoms, CAlphas, AtomNums, AtomsRange, AtomNames, ResidueNums, ResiduesRange, ResidueNames, Distance, NonWater, NonHydrogens\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1336 1323 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1337 1324 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} !~ <span class="q">/^(yes\|no)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1338 1325 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{modifyheader}, for option \"--ModifyHeader\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1339 1326 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1340 1327 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">nonstandardkeep</span>} !~ <span class="q">/^(yes\|no)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1341 1328 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{nonstandardkeep}, for option \"--NonStandardKeep\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1342 1329 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1343 1330 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">nonstandardcode</span>} !~ <span class="q">/^(\?\|\-\|X)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1344 1331 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{nonstandardcode}, for option \"--NonStandardCode\" is not valid. Allowed values: ?, -, or X\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1345 1332 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1346 1333 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">recordmode</span>} && <span class="i">$Options</span>{<span class="w">recordmode</span>} !~ <span class="q">/^(Atom\|Hetatm\|AtomAndHetatm)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1347 1334 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{recordmode}, for option \"--RecordMode\" is not valid. Allowed values: Atom, Hetatm, AtomAndHetatm\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1348 1335 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1349 1336 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1350 1337 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{sequencelength}, for option \"--SequenceLength\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1351 1338 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1352 1339 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequencerecords</span>} !~ <span class="q">/^(Atom\|SeqRes)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1353 1340 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{sequencerecords}, for option \"--SequenceRecords\" is not valid. Allowed values: Atom or SeqRes\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1354 1341 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1355 1342 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequenceidprefix</span>} !~ <span class="q">/^(FileName\|HeaderRecord\|Automatic)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1356 1343 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{sequenceidprefix}, for option \"--SequenceIDPrefix\" is not valid. Allowed values: FileName, HeaderRecord, or AutomaticAtom\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1357 1344 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1358 1345 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1359 1346
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1360 <a name="EOF-"></a></pre>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1361 <p> </p>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1362 <br />
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1363 <center>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1364 <img src="../../../images/h2o2.png">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1365 </center>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1366 </body>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1367 </html>

Mercurial > repos > deepakjadmin > mayatool3_test3

annotate mayachemtools/docs/scripts/html/code/ExtractFromPDBFiles.html @ 2:dfff2614510e draft