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<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>