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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/code/ModifyPDBFiles.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,654 @@ +<html> +<head> +<title>MayaChemTools:Code:ModifyPDBFiles.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<pre> + 1 #!/usr/bin/perl -w + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: ModifyPDBFiles.pl,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span> + 5 <span class="c"># $Revision: 1.25 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> + 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> + 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">PDBFileUtil</span><span class="sc">;</span> + 38 + 39 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span> + 40 + 41 <span class="c"># Autoflush STDOUT</span> + 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> + 43 + 44 <span class="c"># Starting message...</span> + 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> + 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> + 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 48 + 49 <span class="c"># Get the options and setup script...</span> + 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 52 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span> + 53 <span class="s">}</span> + 54 + 55 <span class="k">my</span><span class="s">(</span><span class="i">@PDBFilesList</span><span class="s">)</span><span class="sc">;</span> + 56 <span class="i">@PDBFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"pdb"</span><span class="s">)</span><span class="sc">;</span> + 57 + 58 <span class="c"># Process options...</span> + 59 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> + 60 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> + 61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 62 + 63 <span class="c"># Setup information about input files...</span> + 64 <span class="k">print</span> <span class="q">"Checking input PDB file(s)...\n"</span><span class="sc">;</span> + 65 <span class="k">my</span><span class="s">(</span><span class="i">%PDBFilesInfo</span><span class="s">)</span><span class="sc">;</span> + 66 <span class="i">RetrievePDBFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 67 + 68 <span class="c"># Process input files..</span> + 69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 70 <span class="k">if</span> <span class="s">(</span><span class="i">@PDBFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 71 <span class="k">print</span> <span class="q">"\nProcessing PDB files...\n"</span><span class="sc">;</span> + 72 <span class="s">}</span> + 73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span> + 74 <span class="k">if</span> <span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> + 75 <span class="k">print</span> <span class="q">"\nProcessing file $PDBFilesList[$FileIndex]...\n"</span><span class="sc">;</span> + 76 <span class="i">ModifyPDBFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 77 <span class="s">}</span> + 78 <span class="s">}</span> + 79 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> + 80 + 81 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 82 <span class="i">$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> + 83 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 84 + 85 <span class="c">###############################################################################</span> + 86 + 87 <span class="c"># Modify appropriate information...</span> +<a name="ModifyPDBFiles-"></a> 88 <span class="k">sub </span><span class="m">ModifyPDBFiles</span> <span class="s">{</span> + 89 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 90 <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> + 91 + 92 <span class="c"># Get PDB data...</span> + 93 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 94 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span> + 95 + 96 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberAtoms$/i</span><span class="s">)</span> <span class="s">{</span> + 97 <span class="i">RenumberAtoms</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 98 <span class="s">}</span> + 99 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberResidues$/i</span><span class="s">)</span> <span class="s">{</span> + 100 <span class="i">RenumberResidues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 101 <span class="s">}</span> + 102 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberWaters$/i</span><span class="s">)</span> <span class="s">{</span> + 103 <span class="i">RenumberWaters</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 104 <span class="s">}</span> + 105 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenameChainIDs$/i</span><span class="s">)</span> <span class="s">{</span> + 106 <span class="i">RenameChainsIDs</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 107 <span class="s">}</span> + 108 <span class="s">}</span> + 109 + 110 <span class="c"># Renumber atom and hetro atom numbers...</span> +<a name="RenumberAtoms-"></a> 111 <span class="k">sub </span><span class="m">RenumberAtoms</span> <span class="s">{</span> + 112 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 113 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$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">$Occupancy</span><span class="cm">,</span> <span class="i">$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">$AtomCharge</span><span class="cm">,</span> <span class="i">$NewAtomNumber</span><span class="cm">,</span> <span class="i">$RecordType</span><span class="cm">,</span> <span class="i">%OldToNewAtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 114 + 115 <span class="i">$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> + 116 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> + 117 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> + 118 + 119 <span class="c"># Write out header and other older recors...</span> + 120 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 121 + 122 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span> + 123 <span class="c"># chains and multiple models..</span> + 124 <span class="i">%OldToNewAtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 125 <span class="i">$NewAtomNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>}<span class="sc">;</span> + 126 <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> + 127 <span class="k">if</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> + 128 <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 129 + 130 <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">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 131 + 132 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$NewAtomNumber</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="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 133 + 134 <span class="i">$OldToNewAtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$NewAtomNumber</span><span class="sc">;</span> + 135 <span class="i">$NewAtomNumber</span>++<span class="sc">;</span> + 136 <span class="s">}</span> + 137 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 138 <span class="i">$NewAtomNumber</span>++<span class="sc">;</span> + 139 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$NewAtomNumber</span><span class="cm">,</span> <span class="i">$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">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 140 <span class="s">}</span> + 141 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 142 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 143 <span class="s">}</span> + 144 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 145 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 146 <span class="c"># Restart numbering...</span> + 147 <span class="i">$NewAtomNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>}<span class="sc">;</span> + 148 <span class="s">}</span> + 149 <span class="s">}</span> + 150 + 151 <span class="c"># Write out modified CONECT records...</span> + 152 <span class="k">my</span><span class="s">(</span><span class="i">$ModifiedConectAtomNum</span><span class="cm">,</span> <span class="i">$ConectAtomNum</span><span class="cm">,</span> <span class="i">@ConectAtomNums</span><span class="cm">,</span> <span class="i">@ModifiedConectAtomNums</span><span class="s">)</span><span class="sc">;</span> + 153 <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 154 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 155 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> + 156 <span class="s">}</span> + 157 <span class="i">@ConectAtomNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 158 <span class="i">@ModifiedConectAtomNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 159 <span class="k">push</span> <span class="i">@ConectAtomNums</span><span class="cm">,</span> <span class="i">ParseConectRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 160 <span class="j">ATOMNUMBER:</span> <span class="k">for</span> <span class="i">$ConectAtomNum</span> <span class="s">(</span><span class="i">@ConectAtomNums</span><span class="s">)</span> <span class="s">{</span> + 161 <span class="i">$ModifiedConectAtomNum</span> = <span class="i">$ConectAtomNum</span><span class="sc">;</span> + 162 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ConectAtomNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 163 <span class="i">$AtomNumber</span> = <span class="i">$ConectAtomNum</span><span class="sc">;</span> + 164 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNumber</span><span class="s">)</span> <span class="s">{</span> + 165 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OldToNewAtomNumbersMap</span>{<span class="i">$AtomNumber</span>}<span class="s">)</span> <span class="s">{</span> + 166 <span class="i">$ModifiedConectAtomNum</span> = <span class="i">$OldToNewAtomNumbersMap</span>{<span class="i">$AtomNumber</span>}<span class="sc">;</span> + 167 <span class="s">}</span> + 168 <span class="s">}</span> + 169 <span class="s">}</span> + 170 <span class="k">push</span> <span class="i">@ModifiedConectAtomNums</span><span class="cm">,</span> <span class="i">$ModifiedConectAtomNum</span><span class="sc">;</span> + 171 <span class="s">}</span> + 172 <span class="c"># Write out the record...</span> + 173 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateConectRecordLine</span><span class="s">(</span><span class="i">@ModifiedConectAtomNums</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 174 <span class="s">}</span> + 175 + 176 <span class="c"># Write out END record...</span> + 177 <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> + 178 + 179 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 180 <span class="s">}</span> + 181 + 182 <span class="c"># Renumber residues...</span> +<a name="RenumberResidues-"></a> 183 <span class="k">sub </span><span class="m">RenumberResidues</span> <span class="s">{</span> + 184 <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> + 185 <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">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$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">$Z</span><span class="cm">,</span> <span class="i">$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">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$NewHetatmResidueNumber</span><span class="cm">,</span> <span class="i">$TERCount</span><span class="cm">,</span> <span class="i">$TotalTERCount</span><span class="cm">,</span> <span class="i">$PreviousResidueNumber</span><span class="cm">,</span> <span class="i">$PreviousHetatmResidueNumber</span><span class="cm">,</span> <span class="i">$RecordType</span><span class="s">)</span><span class="sc">;</span> + 186 + 187 <span class="i">$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> + 188 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> + 189 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> + 190 + 191 <span class="c"># Write out header and other older recors...</span> + 192 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 193 + 194 <span class="c"># Do a quick count of all TER records...</span> + 195 <span class="i">$TotalTERCount</span> = <span class="n">0</span><span class="sc">;</span> + 196 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 197 <span class="k">if</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 198 <span class="i">$TotalTERCount</span>++<span class="sc">;</span> + 199 <span class="s">}</span> + 200 <span class="s">}</span> + 201 + 202 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span> + 203 <span class="c"># chains and multiple models..</span> + 204 <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>}<span class="sc">;</span> + 205 <span class="i">$NewHetatmResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingHetatmResidueNumber</span>}<span class="sc">;</span> + 206 + 207 <span class="i">$TERCount</span> = <span class="n">0</span><span class="sc">;</span> + 208 <span class="i">$PreviousResidueNumber</span> = <span class="n">0</span><span class="sc">;</span> + 209 <span class="i">$PreviousHetatmResidueNumber</span> = <span class="n">0</span><span class="sc">;</span> + 210 + 211 <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> + 212 <span class="k">if</span> <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="s">(</span><span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> && <span class="s">(</span><span class="i">$TERCount</span> < <span class="i">$TotalTERCount</span> || <span class="i">$OptionsInfo</span>{<span class="w">HetatmResidueNumberMode</span>} =~ <span class="q">/^Automatic$/i</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 213 <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 214 <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">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 215 + 216 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousResidueNumber</span> && <span class="i">$PreviousResidueNumber</span> != <span class="i">$ResidueNumber</span><span class="s">)</span> <span class="s">{</span> + 217 <span class="i">$PreviousResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span> + 218 <span class="i">$NewResidueNumber</span>++<span class="sc">;</span> + 219 <span class="s">}</span> + 220 <span class="k">else</span> <span class="s">{</span> + 221 <span class="c"># First residue in a chain...</span> + 222 <span class="i">$PreviousResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span> + 223 <span class="s">}</span> + 224 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$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">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$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="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 225 + 226 <span class="s">}</span> + 227 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 228 <span class="s">(</span><span class="i">$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">ParseHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 229 + 230 <span class="c"># User HETATM residue numbers...</span> + 231 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousHetatmResidueNumber</span> && <span class="i">$PreviousHetatmResidueNumber</span> != <span class="i">$ResidueNumber</span><span class="s">)</span> <span class="s">{</span> + 232 <span class="i">$PreviousHetatmResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span> + 233 <span class="i">$NewHetatmResidueNumber</span>++<span class="sc">;</span> + 234 <span class="s">}</span> + 235 <span class="k">else</span> <span class="s">{</span> + 236 <span class="c"># First HETATM residue outside a chain...</span> + 237 <span class="i">$PreviousHetatmResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span> + 238 <span class="s">}</span> + 239 + 240 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateHetatmRecordLine</span><span class="s">(</span><span class="i">$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">$NewHetatmResidueNumber</span><span class="cm">,</span> <span class="i">$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="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 241 <span class="s">}</span> + 242 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 243 <span class="i">$TERCount</span>++<span class="sc">;</span> + 244 <span class="i">$AtomNumber</span>++<span class="sc">;</span> + 245 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 246 <span class="c"># For per chain numbering, start over again...</span> + 247 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ResidueNumberMode</span>} =~ <span class="q">/^PerChain$/i</span><span class="s">)</span> <span class="s">{</span> + 248 <span class="k">if</span> <span class="s">(</span><span class="i">$TERCount</span> < <span class="i">$TotalTERCount</span> <span class="s">)</span> <span class="s">{</span> + 249 <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>}<span class="sc">;</span> + 250 <span class="s">}</span> + 251 <span class="i">$PreviousResidueNumber</span> = <span class="n">0</span><span class="sc">;</span> + 252 <span class="s">}</span> + 253 <span class="s">}</span> + 254 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 255 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 256 <span class="s">}</span> + 257 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 258 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 259 <span class="s">}</span> + 260 <span class="s">}</span> + 261 + 262 <span class="c"># Write out CONECT records...</span> + 263 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 264 <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 265 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 266 <span class="s">}</span> + 267 <span class="s">}</span> + 268 + 269 <span class="c"># Write out END record...</span> + 270 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 271 + 272 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 273 <span class="s">}</span> + 274 + 275 <span class="c"># Renumber water residues...</span> +<a name="RenumberWaters-"></a> 276 <span class="k">sub </span><span class="m">RenumberWaters</span> <span class="s">{</span> + 277 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 278 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$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">$Occupancy</span><span class="cm">,</span> <span class="i">$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">$AtomCharge</span><span class="cm">,</span> <span class="i">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$RecordType</span><span class="s">)</span><span class="sc">;</span> + 279 + 280 <span class="i">$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> + 281 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> + 282 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> + 283 + 284 <span class="c"># Write out header and other older recors...</span> + 285 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 286 + 287 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span> + 288 <span class="c"># chains and multiple models..</span> + 289 <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingWaterResidueNumber</span>}<span class="sc">;</span> + 290 <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> + 291 <span class="k">if</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> + 292 <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 293 + 294 <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">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 295 + 296 <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> + 297 <span class="i">$ResidueNumber</span> = <span class="i">$NewResidueNumber</span><span class="sc">;</span> + 298 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$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="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 299 <span class="i">$NewResidueNumber</span>++<span class="sc">;</span> + 300 <span class="s">}</span> + 301 <span class="k">else</span> <span class="s">{</span> + 302 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 303 <span class="s">}</span> + 304 <span class="s">}</span> + 305 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 306 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 307 <span class="s">}</span> + 308 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 309 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 310 <span class="s">}</span> + 311 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 312 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 313 <span class="s">}</span> + 314 <span class="s">}</span> + 315 + 316 <span class="c"># Write out CONECT records...</span> + 317 <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> + 318 <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 319 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 320 <span class="s">}</span> + 321 <span class="s">}</span> + 322 + 323 <span class="c"># Write out END record...</span> + 324 <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> + 325 + 326 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 327 <span class="s">}</span> + 328 + 329 <span class="c"># Rename chain IDs...</span> +<a name="RenameChainsIDs-"></a> 330 <span class="k">sub </span><span class="m">RenameChainsIDs</span> <span class="s">{</span> + 331 <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> + 332 <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">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$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">$Z</span><span class="cm">,</span> <span class="i">$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">$RecordType</span><span class="cm">,</span> <span class="i">$PreviousChainID</span><span class="cm">,</span> <span class="i">$FirstChainID</span><span class="cm">,</span> <span class="i">$NewChainID</span><span class="cm">,</span> <span class="i">$NewChainIDCounter</span><span class="cm">,</span> <span class="i">%OldToNewChainIDsMap</span><span class="s">)</span><span class="sc">;</span> + 333 + 334 <span class="i">$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> + 335 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> + 336 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> + 337 + 338 <span class="c"># Write out header and other older recors...</span> + 339 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 340 + 341 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span> + 342 <span class="c"># chains and multiple models..</span> + 343 <span class="i">%OldToNewChainIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 344 <span class="i">$NewChainIDCounter</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingChainID</span>}<span class="sc">;</span> + 345 <span class="i">$FirstChainID</span> = <span class="n">1</span><span class="sc">;</span> + 346 <span class="i">$PreviousChainID</span> = <span class="q">''</span><span class="sc">;</span> + 347 <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> + 348 <span class="k">if</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> + 349 <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 350 + 351 <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">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 352 + 353 <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> + 354 <span class="c"># Chain IDs are not assigned to water residues...</span> + 355 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 356 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> + 357 <span class="s">}</span> + 358 + 359 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstChainID</span><span class="s">)</span> <span class="s">{</span> + 360 <span class="i">$FirstChainID</span> = <span class="n">0</span><span class="sc">;</span> + 361 <span class="i">$PreviousChainID</span> = <span class="i">$ChainID</span><span class="sc">;</span> + 362 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainID</span> || <span class="s">(</span>!<span class="i">$ChainID</span> && <span class="i">$OptionsInfo</span>{<span class="w">RenameEmptyChainIDs</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 363 <span class="i">$NewChainID</span> = <span class="i">$NewChainIDCounter</span><span class="sc">;</span> + 364 <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>} = <span class="i">$NewChainID</span><span class="sc">;</span> + 365 <span class="s">}</span> + 366 <span class="k">else</span> <span class="s">{</span> + 367 <span class="i">$NewChainID</span> = <span class="q">''</span><span class="sc">;</span> + 368 <span class="s">}</span> + 369 <span class="s">}</span> + 370 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PreviousChainID</span> <span class="k">ne</span> <span class="i">$ChainID</span><span class="s">)</span> <span class="s">{</span> + 371 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainID</span> || <span class="s">(</span>!<span class="i">$ChainID</span> && <span class="i">$OptionsInfo</span>{<span class="w">RenameEmptyChainIDs</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 372 <span class="i">$PreviousChainID</span> = <span class="i">$ChainID</span><span class="sc">;</span> + 373 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>}<span class="s">)</span> <span class="s">{</span> + 374 <span class="i">$NewChainID</span> = <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>}<span class="sc">;</span> + 375 <span class="s">}</span> + 376 <span class="k">else</span> <span class="s">{</span> + 377 <span class="i">$NewChainIDCounter</span>++<span class="sc">;</span> + 378 <span class="i">$NewChainID</span> = <span class="i">$NewChainIDCounter</span><span class="sc">;</span> + 379 <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>} = <span class="i">$NewChainID</span><span class="sc">;</span> + 380 <span class="s">}</span> + 381 <span class="s">}</span> + 382 <span class="k">else</span> <span class="s">{</span> + 383 <span class="i">$NewChainID</span> = <span class="q">''</span><span class="sc">;</span> + 384 <span class="s">}</span> + 385 <span class="s">}</span> + 386 + 387 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</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">$NewChainID</span><span class="cm">,</span> <span class="i">$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">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 388 <span class="s">}</span> + 389 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 390 <span class="i">$AtomNumber</span>++<span class="sc">;</span> + 391 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$NewChainID</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> + 392 <span class="s">}</span> + 393 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 394 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 395 <span class="s">}</span> + 396 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 397 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 398 <span class="s">}</span> + 399 <span class="s">}</span> + 400 + 401 <span class="c"># Write out CONECT records...</span> + 402 <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> + 403 <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 404 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 405 <span class="s">}</span> + 406 <span class="s">}</span> + 407 + 408 <span class="c"># Write out END record...</span> + 409 <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> + 410 + 411 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 412 <span class="s">}</span> + 413 + 414 + 415 <span class="c"># Write out modifed header and other older records...</span> +<a name="WriteHeaderAndOlderRecords-"></a> 416 <span class="k">sub </span><span class="m">WriteHeaderAndOlderRecords</span> <span class="s">{</span> + 417 <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> + 418 + 419 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>}<span class="s">)</span> <span class="s">{</span> + 420 <span class="c"># Write out modified HEADER record...</span> + 421 <span class="k">my</span><span class="s">(</span><span class="i">$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">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 422 <span class="i">$Classification</span> = <span class="q">'Data modified using MayaChemTools'</span><span class="sc">;</span> + 423 <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">$Classification</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 424 <span class="s">}</span> + 425 <span class="k">else</span> <span class="s">{</span> + 426 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 427 <span class="s">}</span> + 428 + 429 <span class="c"># Write out any old records...</span> + 430 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>}<span class="s">)</span> <span class="s">{</span> + 431 <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> + 432 <span class="c"># Skip HEADER record and write out older records all the way upto first MODEL/ATOM/HETATM records from input file...</span> + 433 <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">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 434 <span class="i">$RecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="i">$RecordLineIndex</span>]<span class="sc">;</span> + 435 <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">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 436 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span> + 437 <span class="s">}</span> + 438 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 439 <span class="s">}</span> + 440 <span class="s">}</span> + 441 <span class="s">}</span> + 442 + 443 <span class="c"># Get header record information assuming it's the first record...</span> +<a name="GetHeaderRecordInformation-"></a> 444 <span class="k">sub </span><span class="m">GetHeaderRecordInformation</span> <span class="s">{</span> + 445 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 446 <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> + 447 + 448 <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">$IDCode</span><span class="s">)</span> = <span class="s">(</span><span class="q">''</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> + 449 <span class="i">$HeaderRecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="sc">;</span> + 450 <span class="k">if</span> <span class="s">(</span><span class="i">IsHeaderRecordType</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 451 <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> + 452 <span class="s">}</span> + 453 <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">$IDCode</span><span class="s">)</span><span class="sc">;</span> + 454 <span class="s">}</span> + 455 + 456 + 457 <span class="c"># Process option values...</span> +<a name="ProcessOptions-"></a> 458 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> + 459 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 460 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> + 461 + 462 <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>} = <span class="i">$Options</span>{<span class="w">atomnumberstart</span>}<span class="sc">;</span> + 463 <span class="i">$OptionsInfo</span>{<span class="w">StartingChainID</span>} = <span class="i">$Options</span>{<span class="w">chainidstart</span>}<span class="sc">;</span> + 464 <span class="i">$OptionsInfo</span>{<span class="w">RenameEmptyChainIDs</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidrenameempty</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 465 + 466 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 467 <span class="i">$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> + 468 + 469 <span class="i">$OptionsInfo</span>{<span class="w">ResidueNumberMode</span>} = <span class="i">$Options</span>{<span class="w">residuenumbermode</span>}<span class="sc">;</span> + 470 <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">residuenumberstart</span>}<span class="sc">;</span> + 471 + 472 <span class="i">$OptionsInfo</span>{<span class="w">HetatmResidueNumberMode</span>} = <span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>}<span class="sc">;</span> + 473 <span class="i">$OptionsInfo</span>{<span class="w">StartingHetatmResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>}<span class="sc">;</span> + 474 + 475 <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> + 476 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 477 + 478 <span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} = <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span> + 479 <span class="i">$OptionsInfo</span>{<span class="w">StartingWaterResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">waterresiduestart</span>}<span class="sc">;</span> + 480 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 481 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 482 + 483 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span><span class="sc">;</span> + 484 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 485 <span class="k">my</span><span class="s">(</span><span class="i">$WaterResidueName</span><span class="s">)</span><span class="sc">;</span> + 486 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} =~ <span class="q">/Automatic/i</span><span class="s">)</span> <span class="s">{</span> + 487 <span class="k">push</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="cm">,</span> <span class="s">(</span><span class="q">'HOH'</span><span class="cm">,</span> <span class="q">'WAT'</span><span class="cm">,</span> <span class="q">'H2O'</span><span class="s">)</span><span class="sc">;</span> + 488 <span class="s">}</span> + 489 <span class="k">else</span> <span class="s">{</span> + 490 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span> + 491 <span class="s">}</span> + 492 <span class="k">for</span> <span class="i">$WaterResidueName</span> <span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span> <span class="s">{</span> + 493 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$WaterResidueName</span>} = <span class="i">$WaterResidueName</span><span class="sc">;</span> + 494 <span class="s">}</span> + 495 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="sc">;</span> + 496 <span class="s">}</span> + 497 + 498 <span class="c"># Retrieve information about PDB files...</span> +<a name="RetrievePDBFilesInfo-"></a> 499 <span class="k">sub </span><span class="m">RetrievePDBFilesInfo</span> <span class="s">{</span> + 500 <span class="k">my</span><span class="s">(</span><span class="i">$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">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$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">$Mode</span><span class="cm">,</span> <span class="i">$OutFileMode</span><span class="cm">,</span> <span class="i">@OutFileNames</span><span class="s">)</span><span class="sc">;</span> + 501 + 502 <span class="i">%PDBFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 503 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 504 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 505 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 506 + 507 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span> + 508 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> + 509 + 510 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 511 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 512 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 513 + 514 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> + 515 <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> + 516 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It doesn't exist\n"</span><span class="sc">;</span> + 517 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 518 <span class="s">}</span> + 519 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="q">"pdb"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 520 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It's not a PDB file\n"</span><span class="sc">;</span> + 521 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 522 <span class="s">}</span> + 523 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">PDBFILE</span><span class="cm">,</span> <span class="q">"$PDBFile"</span><span class="s">)</span> <span class="s">{</span> + 524 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: Couldn't open it: $! \n"</span><span class="sc">;</span> + 525 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 526 <span class="s">}</span> + 527 <span class="k">close</span> <span class="w">PDBFILE</span><span class="sc">;</span> + 528 + 529 <span class="c"># Get PDB data...</span> + 530 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span> + 531 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 532 <span class="k">if</span> <span class="s">(</span>!<span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span> + 533 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: No chains found \n"</span><span class="sc">;</span> + 534 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 535 <span class="s">}</span> + 536 + 537 <span class="c"># Setup output file names...</span> + 538 <span class="i">@OutFileNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 539 <span class="i">$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> + 540 <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> + 541 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@PDBFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 542 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> + 543 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> + 544 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> + 545 <span class="s">}</span> + 546 <span class="k">else</span> <span class="s">{</span> + 547 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> + 548 <span class="s">}</span> + 549 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> + 550 <span class="s">}</span> + 551 <span class="k">else</span> <span class="s">{</span> + 552 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> + 553 <span class="s">}</span> + 554 <span class="i">$Mode</span> = <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="sc">;</span> + 555 <span class="j">MODE:</span> <span class="s">{</span> + 556 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenumberAtoms$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">'RenumberAtoms'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span> + 557 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenumberResidues$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">'RenumberResidues'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span> + 558 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenumberWaters$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">'RenumberWaters'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span> + 559 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenameChainIDs$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">'RenameChainIDs'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span> + 560 <span class="i">$OutFileMode</span> = <span class="q">''</span><span class="sc">;</span> + 561 <span class="s">}</span> + 562 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}${OutFileMode}.pdb"</span><span class="sc">;</span> + 563 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span> + 564 + 565 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> + 566 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> + 567 + 568 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@OutFileNames</span><span class="sc">;</span> + 569 <span class="s">}</span> + 570 <span class="s">}</span> + 571 + 572 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> +<a name="SetupScriptUsage-"></a> 573 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> + 574 + 575 <span class="c"># Retrieve all the options...</span> + 576 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 577 <span class="i">$Options</span>{<span class="w">atomnumberstart</span>} = <span class="n">1</span><span class="sc">;</span> + 578 <span class="i">$Options</span>{<span class="w">chainidstart</span>} = <span class="q">'A'</span><span class="sc">;</span> + 579 <span class="i">$Options</span>{<span class="w">chainidrenameempty</span>} = <span class="q">'No'</span><span class="sc">;</span> + 580 <span class="i">$Options</span>{<span class="w">keepoldrecords</span>} = <span class="q">'no'</span><span class="sc">;</span> + 581 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'RenumberResidues'</span><span class="sc">;</span> + 582 <span class="i">$Options</span>{<span class="w">modifyheader</span>} = <span class="q">'yes'</span><span class="sc">;</span> + 583 <span class="i">$Options</span>{<span class="w">residuenumbermode</span>} = <span class="q">'PerChain'</span><span class="sc">;</span> + 584 <span class="i">$Options</span>{<span class="w">residuenumberstart</span>} = <span class="n">1</span><span class="sc">;</span> + 585 <span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>} = <span class="q">'Automatic'</span><span class="sc">;</span> + 586 <span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>} = <span class="n">6000</span><span class="sc">;</span> + 587 <span class="i">$Options</span>{<span class="w">waterresiduenames</span>} = <span class="q">'Automatic'</span><span class="sc">;</span> + 588 <span class="i">$Options</span>{<span class="w">waterresiduestart</span>} = <span class="n">8000</span><span class="sc">;</span> + 589 + 590 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"atomnumberstart|a=i"</span><span class="cm">,</span> <span class="q">"chainidstart|c=s"</span><span class="cm">,</span> <span class="q">"chainidrenameempty=s"</span><span class="cm">,</span> <span class="q">"keepoldrecords|k=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"modifyheader=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"residuenumbermode=s"</span><span class="cm">,</span> <span class="q">"residuenumberstart=i"</span><span class="cm">,</span> <span class="q">"residuenumberhetatmmode=s"</span><span class="cm">,</span> <span class="q">"residuenumberstarthetatm=i"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"sequencelength=i"</span><span class="cm">,</span> <span class="q">"waterresiduenames=s"</span><span class="cm">,</span> <span class="q">"waterresiduestart=i"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 591 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> + 592 <span class="s">}</span> + 593 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> + 594 <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> + 595 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> + 596 <span class="s">}</span> + 597 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span> + 598 <span class="s">}</span> + 599 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomnumberstart</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 600 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{atomnumberstart}, for option \"-a, --AtomNumberStart\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span> + 601 <span class="s">}</span> + 602 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidstart</span>}<span class="s">)</span> > <span class="n">1</span><span class="s">)</span> || <span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidstart</span>} !~ <span class="q">/[A-Z]/i</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 603 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{chainidstart}, for option \"-c, --ChainIDStart\" is not valid. Allowed values: a single character from A to Z\n"</span><span class="sc">;</span> + 604 <span class="s">}</span> + 605 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidrenameempty</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> + 606 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{chainidrenameempty}, for option \"--chainidrenameempty\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> + 607 <span class="s">}</span> + 608 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> + 609 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keepoldrecords}, for option \"--KeepOldRecords\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> + 610 <span class="s">}</span> + 611 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(RenumberAtoms|RenumberResidues|RenumberWaters|RenameChainIDs)$/i</span><span class="s">)</span> <span class="s">{</span> + 612 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: RenumberAtoms, RenumberResidues, RenumberWaters or RenameChainIDs\n"</span><span class="sc">;</span> + 613 <span class="s">}</span> + 614 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> + 615 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{modifyheader}, for option \"--ModifyHeader\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> + 616 <span class="s">}</span> + 617 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumbermode</span>} !~ <span class="q">/^(Sequential|PerChain)$/i</span><span class="s">)</span> <span class="s">{</span> + 618 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumbermode}, for option \"--ResidueNumberMode\" is not valid. Allowed values: Sequential or PerChain\n"</span><span class="sc">;</span> + 619 <span class="s">}</span> + 620 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberstart</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 621 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumberstart}, for option \"--ResidueNumberStart\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span> + 622 <span class="s">}</span> + 623 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>} !~ <span class="q">/^(automatic|specify)$/i</span><span class="s">)</span> <span class="s">{</span> + 624 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumberhetatmmode}, for option \"--residuenumbermode\" is not valid. Allowed values: automatic or specify\n"</span><span class="sc">;</span> + 625 <span class="s">}</span> + 626 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 627 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumberstarthetatm}, for option \"--residuenumberstartHetatm\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span> + 628 <span class="s">}</span> + 629 <span class="k">if</span> <span class="s">(</span>!<span class="w">IsPositiveInteger</span> <span class="i">$Options</span>{<span class="w">waterresiduestart</span>}<span class="s">)</span> <span class="s">{</span> + 630 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{waterresiduestart}, for option \"--waterresiduestart\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span> + 631 <span class="s">}</span> + 632 <span class="s">}</span> + 633 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>