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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:ModifyPDBFiles.pl</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 1 #!/usr/bin/perl -w | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: ModifyPDBFiles.pl,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span> | |
| 18 5 <span class="c"># $Revision: 1.25 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">PDBFileUtil</span><span class="sc">;</span> | |
| 51 38 | |
| 52 39 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span> | |
| 53 40 | |
| 54 41 <span class="c"># Autoflush STDOUT</span> | |
| 55 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> | |
| 56 43 | |
| 57 44 <span class="c"># Starting message...</span> | |
| 58 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> | |
| 59 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> | |
| 60 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> | |
| 61 48 | |
| 62 49 <span class="c"># Get the options and setup script...</span> | |
| 63 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 64 51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 65 52 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span> | |
| 66 53 <span class="s">}</span> | |
| 67 54 | |
| 68 55 <span class="k">my</span><span class="s">(</span><span class="i">@PDBFilesList</span><span class="s">)</span><span class="sc">;</span> | |
| 69 56 <span class="i">@PDBFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"pdb"</span><span class="s">)</span><span class="sc">;</span> | |
| 70 57 | |
| 71 58 <span class="c"># Process options...</span> | |
| 72 59 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> | |
| 73 60 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> | |
| 74 61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 75 62 | |
| 76 63 <span class="c"># Setup information about input files...</span> | |
| 77 64 <span class="k">print</span> <span class="q">"Checking input PDB file(s)...\n"</span><span class="sc">;</span> | |
| 78 65 <span class="k">my</span><span class="s">(</span><span class="i">%PDBFilesInfo</span><span class="s">)</span><span class="sc">;</span> | |
| 79 66 <span class="i">RetrievePDBFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 80 67 | |
| 81 68 <span class="c"># Process input files..</span> | |
| 82 69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 83 70 <span class="k">if</span> <span class="s">(</span><span class="i">@PDBFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 84 71 <span class="k">print</span> <span class="q">"\nProcessing PDB files...\n"</span><span class="sc">;</span> | |
| 85 72 <span class="s">}</span> | |
| 86 73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span> | |
| 87 74 <span class="k">if</span> <span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> | |
| 88 75 <span class="k">print</span> <span class="q">"\nProcessing file $PDBFilesList[$FileIndex]...\n"</span><span class="sc">;</span> | |
| 89 76 <span class="i">ModifyPDBFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 90 77 <span class="s">}</span> | |
| 91 78 <span class="s">}</span> | |
| 92 79 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> | |
| 93 80 | |
| 94 81 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> | |
| 95 82 <span class="i">$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> | |
| 96 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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> | |
| 97 84 | |
| 98 85 <span class="c">###############################################################################</span> | |
| 99 86 | |
| 100 87 <span class="c"># Modify appropriate information...</span> | |
| 101 <a name="ModifyPDBFiles-"></a> 88 <span class="k">sub </span><span class="m">ModifyPDBFiles</span> <span class="s">{</span> | |
| 102 89 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 103 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> | |
| 104 91 | |
| 105 92 <span class="c"># Get PDB data...</span> | |
| 106 93 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> | |
| 107 94 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span> | |
| 108 95 | |
| 109 96 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberAtoms$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 110 97 <span class="i">RenumberAtoms</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> | |
| 111 98 <span class="s">}</span> | |
| 112 99 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberResidues$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 113 100 <span class="i">RenumberResidues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> | |
| 114 101 <span class="s">}</span> | |
| 115 102 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberWaters$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 116 103 <span class="i">RenumberWaters</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> | |
| 117 104 <span class="s">}</span> | |
| 118 105 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenameChainIDs$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 119 106 <span class="i">RenameChainsIDs</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> | |
| 120 107 <span class="s">}</span> | |
| 121 108 <span class="s">}</span> | |
| 122 109 | |
| 123 110 <span class="c"># Renumber atom and hetro atom numbers...</span> | |
| 124 <a name="RenumberAtoms-"></a> 111 <span class="k">sub </span><span class="m">RenumberAtoms</span> <span class="s">{</span> | |
| 125 112 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 126 113 <span class="k">my</span><span class="s">(</span><span class="i">$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">$RecordType</span><span class="cm">,</span> <span class="i">%OldToNewAtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> | |
| 127 114 | |
| 128 115 <span class="i">$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> | |
| 129 116 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> | |
| 130 117 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> | |
| 131 118 | |
| 132 119 <span class="c"># Write out header and other older recors...</span> | |
| 133 120 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> | |
| 134 121 | |
| 135 122 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span> | |
| 136 123 <span class="c"># chains and multiple models..</span> | |
| 137 124 <span class="i">%OldToNewAtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 138 125 <span class="i">$NewAtomNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>}<span class="sc">;</span> | |
| 139 126 <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> | |
| 140 127 <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> | |
| 141 128 <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> | |
| 142 129 | |
| 143 130 <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> | |
| 144 131 | |
| 145 132 <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> | |
| 146 133 | |
| 147 134 <span class="i">$OldToNewAtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$NewAtomNumber</span><span class="sc">;</span> | |
| 148 135 <span class="i">$NewAtomNumber</span>++<span class="sc">;</span> | |
| 149 136 <span class="s">}</span> | |
| 150 137 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 151 138 <span class="i">$NewAtomNumber</span>++<span class="sc">;</span> | |
| 152 139 <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">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> | |
| 153 140 <span class="s">}</span> | |
| 154 141 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 155 142 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 156 143 <span class="s">}</span> | |
| 157 144 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 158 145 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 159 146 <span class="c"># Restart numbering...</span> | |
| 160 147 <span class="i">$NewAtomNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>}<span class="sc">;</span> | |
| 161 148 <span class="s">}</span> | |
| 162 149 <span class="s">}</span> | |
| 163 150 | |
| 164 151 <span class="c"># Write out modified CONECT records...</span> | |
| 165 152 <span class="k">my</span><span class="s">(</span><span class="i">$ModifiedConectAtomNum</span><span class="cm">,</span> <span class="i">$ConectAtomNum</span><span class="cm">,</span> <span class="i">@ConectAtomNums</span><span class="cm">,</span> <span class="i">@ModifiedConectAtomNums</span><span class="s">)</span><span class="sc">;</span> | |
| 166 153 <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 167 154 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 168 155 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 169 156 <span class="s">}</span> | |
| 170 157 <span class="i">@ConectAtomNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 171 158 <span class="i">@ModifiedConectAtomNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 172 159 <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">$RecordLine</span><span class="s">)</span><span class="sc">;</span> | |
| 173 160 <span class="j">ATOMNUMBER:</span> <span class="k">for</span> <span class="i">$ConectAtomNum</span> <span class="s">(</span><span class="i">@ConectAtomNums</span><span class="s">)</span> <span class="s">{</span> | |
| 174 161 <span class="i">$ModifiedConectAtomNum</span> = <span class="i">$ConectAtomNum</span><span class="sc">;</span> | |
| 175 162 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ConectAtomNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 176 163 <span class="i">$AtomNumber</span> = <span class="i">$ConectAtomNum</span><span class="sc">;</span> | |
| 177 164 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 178 165 <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> | |
| 179 166 <span class="i">$ModifiedConectAtomNum</span> = <span class="i">$OldToNewAtomNumbersMap</span>{<span class="i">$AtomNumber</span>}<span class="sc">;</span> | |
| 180 167 <span class="s">}</span> | |
| 181 168 <span class="s">}</span> | |
| 182 169 <span class="s">}</span> | |
| 183 170 <span class="k">push</span> <span class="i">@ModifiedConectAtomNums</span><span class="cm">,</span> <span class="i">$ModifiedConectAtomNum</span><span class="sc">;</span> | |
| 184 171 <span class="s">}</span> | |
| 185 172 <span class="c"># Write out the record...</span> | |
| 186 173 <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> | |
| 187 174 <span class="s">}</span> | |
| 188 175 | |
| 189 176 <span class="c"># Write out END record...</span> | |
| 190 177 <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> | |
| 191 178 | |
| 192 179 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> | |
| 193 180 <span class="s">}</span> | |
| 194 181 | |
| 195 182 <span class="c"># Renumber residues...</span> | |
| 196 <a name="RenumberResidues-"></a> 183 <span class="k">sub </span><span class="m">RenumberResidues</span> <span class="s">{</span> | |
| 197 184 <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> | |
| 198 185 <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">$RecordType</span><span class="s">)</span><span class="sc">;</span> | |
| 199 186 | |
| 200 187 <span class="i">$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> | |
| 201 188 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> | |
| 202 189 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> | |
| 203 190 | |
| 204 191 <span class="c"># Write out header and other older recors...</span> | |
| 205 192 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> | |
| 206 193 | |
| 207 194 <span class="c"># Do a quick count of all TER records...</span> | |
| 208 195 <span class="i">$TotalTERCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 209 196 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 210 197 <span class="k">if</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 211 198 <span class="i">$TotalTERCount</span>++<span class="sc">;</span> | |
| 212 199 <span class="s">}</span> | |
| 213 200 <span class="s">}</span> | |
| 214 201 | |
| 215 202 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span> | |
| 216 203 <span class="c"># chains and multiple models..</span> | |
| 217 204 <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>}<span class="sc">;</span> | |
| 218 205 <span class="i">$NewHetatmResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingHetatmResidueNumber</span>}<span class="sc">;</span> | |
| 219 206 | |
| 220 207 <span class="i">$TERCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 221 208 <span class="i">$PreviousResidueNumber</span> = <span class="n">0</span><span class="sc">;</span> | |
| 222 209 <span class="i">$PreviousHetatmResidueNumber</span> = <span class="n">0</span><span class="sc">;</span> | |
| 223 210 | |
| 224 211 <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> | |
| 225 212 <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> | |
| 226 213 <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> | |
| 227 214 <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> | |
| 228 215 | |
| 229 216 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousResidueNumber</span> && <span class="i">$PreviousResidueNumber</span> != <span class="i">$ResidueNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 230 217 <span class="i">$PreviousResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span> | |
| 231 218 <span class="i">$NewResidueNumber</span>++<span class="sc">;</span> | |
| 232 219 <span class="s">}</span> | |
| 233 220 <span class="k">else</span> <span class="s">{</span> | |
| 234 221 <span class="c"># First residue in a chain...</span> | |
| 235 222 <span class="i">$PreviousResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span> | |
| 236 223 <span class="s">}</span> | |
| 237 224 <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> | |
| 238 225 | |
| 239 226 <span class="s">}</span> | |
| 240 227 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 241 228 <span class="s">(</span><span class="i">$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">$RecordLine</span><span class="s">)</span><span class="sc">;</span> | |
| 242 229 | |
| 243 230 <span class="c"># User HETATM residue numbers...</span> | |
| 244 231 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousHetatmResidueNumber</span> && <span class="i">$PreviousHetatmResidueNumber</span> != <span class="i">$ResidueNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 245 232 <span class="i">$PreviousHetatmResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span> | |
| 246 233 <span class="i">$NewHetatmResidueNumber</span>++<span class="sc">;</span> | |
| 247 234 <span class="s">}</span> | |
| 248 235 <span class="k">else</span> <span class="s">{</span> | |
| 249 236 <span class="c"># First HETATM residue outside a chain...</span> | |
| 250 237 <span class="i">$PreviousHetatmResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span> | |
| 251 238 <span class="s">}</span> | |
| 252 239 | |
| 253 240 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateHetatmRecordLine</span><span class="s">(</span><span class="i">$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> | |
| 254 241 <span class="s">}</span> | |
| 255 242 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 256 243 <span class="i">$TERCount</span>++<span class="sc">;</span> | |
| 257 244 <span class="i">$AtomNumber</span>++<span class="sc">;</span> | |
| 258 245 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$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> | |
| 259 246 <span class="c"># For per chain numbering, start over again...</span> | |
| 260 247 <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> | |
| 261 248 <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> | |
| 262 249 <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>}<span class="sc">;</span> | |
| 263 250 <span class="s">}</span> | |
| 264 251 <span class="i">$PreviousResidueNumber</span> = <span class="n">0</span><span class="sc">;</span> | |
| 265 252 <span class="s">}</span> | |
| 266 253 <span class="s">}</span> | |
| 267 254 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 268 255 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 269 256 <span class="s">}</span> | |
| 270 257 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 271 258 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 272 259 <span class="s">}</span> | |
| 273 260 <span class="s">}</span> | |
| 274 261 | |
| 275 262 <span class="c"># Write out CONECT records...</span> | |
| 276 263 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 277 264 <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 278 265 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 279 266 <span class="s">}</span> | |
| 280 267 <span class="s">}</span> | |
| 281 268 | |
| 282 269 <span class="c"># Write out END record...</span> | |
| 283 270 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> | |
| 284 271 | |
| 285 272 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> | |
| 286 273 <span class="s">}</span> | |
| 287 274 | |
| 288 275 <span class="c"># Renumber water residues...</span> | |
| 289 <a name="RenumberWaters-"></a> 276 <span class="k">sub </span><span class="m">RenumberWaters</span> <span class="s">{</span> | |
| 290 277 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 291 278 <span class="k">my</span><span class="s">(</span><span class="i">$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">$RecordType</span><span class="s">)</span><span class="sc">;</span> | |
| 292 279 | |
| 293 280 <span class="i">$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> | |
| 294 281 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> | |
| 295 282 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> | |
| 296 283 | |
| 297 284 <span class="c"># Write out header and other older recors...</span> | |
| 298 285 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> | |
| 299 286 | |
| 300 287 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span> | |
| 301 288 <span class="c"># chains and multiple models..</span> | |
| 302 289 <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingWaterResidueNumber</span>}<span class="sc">;</span> | |
| 303 290 <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> | |
| 304 291 <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> | |
| 305 292 <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> | |
| 306 293 | |
| 307 294 <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> | |
| 308 295 | |
| 309 296 <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> | |
| 310 297 <span class="i">$ResidueNumber</span> = <span class="i">$NewResidueNumber</span><span class="sc">;</span> | |
| 311 298 <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> | |
| 312 299 <span class="i">$NewResidueNumber</span>++<span class="sc">;</span> | |
| 313 300 <span class="s">}</span> | |
| 314 301 <span class="k">else</span> <span class="s">{</span> | |
| 315 302 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 316 303 <span class="s">}</span> | |
| 317 304 <span class="s">}</span> | |
| 318 305 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 319 306 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 320 307 <span class="s">}</span> | |
| 321 308 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 322 309 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 323 310 <span class="s">}</span> | |
| 324 311 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 325 312 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 326 313 <span class="s">}</span> | |
| 327 314 <span class="s">}</span> | |
| 328 315 | |
| 329 316 <span class="c"># Write out CONECT records...</span> | |
| 330 317 <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> | |
| 331 318 <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 332 319 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 333 320 <span class="s">}</span> | |
| 334 321 <span class="s">}</span> | |
| 335 322 | |
| 336 323 <span class="c"># Write out END record...</span> | |
| 337 324 <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> | |
| 338 325 | |
| 339 326 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> | |
| 340 327 <span class="s">}</span> | |
| 341 328 | |
| 342 329 <span class="c"># Rename chain IDs...</span> | |
| 343 <a name="RenameChainsIDs-"></a> 330 <span class="k">sub </span><span class="m">RenameChainsIDs</span> <span class="s">{</span> | |
| 344 331 <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> | |
| 345 332 <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">$NewChainIDCounter</span><span class="cm">,</span> <span class="i">%OldToNewChainIDsMap</span><span class="s">)</span><span class="sc">;</span> | |
| 346 333 | |
| 347 334 <span class="i">$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> | |
| 348 335 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> | |
| 349 336 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> | |
| 350 337 | |
| 351 338 <span class="c"># Write out header and other older recors...</span> | |
| 352 339 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> | |
| 353 340 | |
| 354 341 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span> | |
| 355 342 <span class="c"># chains and multiple models..</span> | |
| 356 343 <span class="i">%OldToNewChainIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 357 344 <span class="i">$NewChainIDCounter</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingChainID</span>}<span class="sc">;</span> | |
| 358 345 <span class="i">$FirstChainID</span> = <span class="n">1</span><span class="sc">;</span> | |
| 359 346 <span class="i">$PreviousChainID</span> = <span class="q">''</span><span class="sc">;</span> | |
| 360 347 <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> | |
| 361 348 <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> | |
| 362 349 <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> | |
| 363 350 | |
| 364 351 <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> | |
| 365 352 | |
| 366 353 <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> | |
| 367 354 <span class="c"># Chain IDs are not assigned to water residues...</span> | |
| 368 355 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 369 356 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 370 357 <span class="s">}</span> | |
| 371 358 | |
| 372 359 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstChainID</span><span class="s">)</span> <span class="s">{</span> | |
| 373 360 <span class="i">$FirstChainID</span> = <span class="n">0</span><span class="sc">;</span> | |
| 374 361 <span class="i">$PreviousChainID</span> = <span class="i">$ChainID</span><span class="sc">;</span> | |
| 375 362 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 376 363 <span class="i">$NewChainID</span> = <span class="i">$NewChainIDCounter</span><span class="sc">;</span> | |
| 377 364 <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>} = <span class="i">$NewChainID</span><span class="sc">;</span> | |
| 378 365 <span class="s">}</span> | |
| 379 366 <span class="k">else</span> <span class="s">{</span> | |
| 380 367 <span class="i">$NewChainID</span> = <span class="q">''</span><span class="sc">;</span> | |
| 381 368 <span class="s">}</span> | |
| 382 369 <span class="s">}</span> | |
| 383 370 <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> | |
| 384 371 <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">$OptionsInfo</span>{<span class="w">RenameEmptyChainIDs</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 385 372 <span class="i">$PreviousChainID</span> = <span class="i">$ChainID</span><span class="sc">;</span> | |
| 386 373 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 387 374 <span class="i">$NewChainID</span> = <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>}<span class="sc">;</span> | |
| 388 375 <span class="s">}</span> | |
| 389 376 <span class="k">else</span> <span class="s">{</span> | |
| 390 377 <span class="i">$NewChainIDCounter</span>++<span class="sc">;</span> | |
| 391 378 <span class="i">$NewChainID</span> = <span class="i">$NewChainIDCounter</span><span class="sc">;</span> | |
| 392 379 <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>} = <span class="i">$NewChainID</span><span class="sc">;</span> | |
| 393 380 <span class="s">}</span> | |
| 394 381 <span class="s">}</span> | |
| 395 382 <span class="k">else</span> <span class="s">{</span> | |
| 396 383 <span class="i">$NewChainID</span> = <span class="q">''</span><span class="sc">;</span> | |
| 397 384 <span class="s">}</span> | |
| 398 385 <span class="s">}</span> | |
| 399 386 | |
| 400 387 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$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">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> | |
| 401 388 <span class="s">}</span> | |
| 402 389 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 403 390 <span class="i">$AtomNumber</span>++<span class="sc">;</span> | |
| 404 391 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$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> | |
| 405 392 <span class="s">}</span> | |
| 406 393 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 407 394 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 408 395 <span class="s">}</span> | |
| 409 396 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 410 397 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 411 398 <span class="s">}</span> | |
| 412 399 <span class="s">}</span> | |
| 413 400 | |
| 414 401 <span class="c"># Write out CONECT records...</span> | |
| 415 402 <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> | |
| 416 403 <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 417 404 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 418 405 <span class="s">}</span> | |
| 419 406 <span class="s">}</span> | |
| 420 407 | |
| 421 408 <span class="c"># Write out END record...</span> | |
| 422 409 <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> | |
| 423 410 | |
| 424 411 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> | |
| 425 412 <span class="s">}</span> | |
| 426 413 | |
| 427 414 | |
| 428 415 <span class="c"># Write out modifed header and other older records...</span> | |
| 429 <a name="WriteHeaderAndOlderRecords-"></a> 416 <span class="k">sub </span><span class="m">WriteHeaderAndOlderRecords</span> <span class="s">{</span> | |
| 430 417 <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> | |
| 431 418 | |
| 432 419 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>}<span class="s">)</span> <span class="s">{</span> | |
| 433 420 <span class="c"># Write out modified HEADER record...</span> | |
| 434 421 <span class="k">my</span><span class="s">(</span><span class="i">$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">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> | |
| 435 422 <span class="i">$Classification</span> = <span class="q">'Data modified using MayaChemTools'</span><span class="sc">;</span> | |
| 436 423 <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">$Classification</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> | |
| 437 424 <span class="s">}</span> | |
| 438 425 <span class="k">else</span> <span class="s">{</span> | |
| 439 426 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> | |
| 440 427 <span class="s">}</span> | |
| 441 428 | |
| 442 429 <span class="c"># Write out any old records...</span> | |
| 443 430 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>}<span class="s">)</span> <span class="s">{</span> | |
| 444 431 <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> | |
| 445 432 <span class="c"># Skip HEADER record and write out older records all the way upto first MODEL/ATOM/HETATM records from input file...</span> | |
| 446 433 <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">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 447 434 <span class="i">$RecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="i">$RecordLineIndex</span>]<span class="sc">;</span> | |
| 448 435 <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">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 449 436 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span> | |
| 450 437 <span class="s">}</span> | |
| 451 438 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> | |
| 452 439 <span class="s">}</span> | |
| 453 440 <span class="s">}</span> | |
| 454 441 <span class="s">}</span> | |
| 455 442 | |
| 456 443 <span class="c"># Get header record information assuming it's the first record...</span> | |
| 457 <a name="GetHeaderRecordInformation-"></a> 444 <span class="k">sub </span><span class="m">GetHeaderRecordInformation</span> <span class="s">{</span> | |
| 458 445 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 459 446 <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> | |
| 460 447 | |
| 461 448 <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">$IDCode</span><span class="s">)</span> = <span class="s">(</span><span class="q">''</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> | |
| 462 449 <span class="i">$HeaderRecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="sc">;</span> | |
| 463 450 <span class="k">if</span> <span class="s">(</span><span class="i">IsHeaderRecordType</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 464 451 <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> | |
| 465 452 <span class="s">}</span> | |
| 466 453 <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">$IDCode</span><span class="s">)</span><span class="sc">;</span> | |
| 467 454 <span class="s">}</span> | |
| 468 455 | |
| 469 456 | |
| 470 457 <span class="c"># Process option values...</span> | |
| 471 <a name="ProcessOptions-"></a> 458 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> | |
| 472 459 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 473 460 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> | |
| 474 461 | |
| 475 462 <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>} = <span class="i">$Options</span>{<span class="w">atomnumberstart</span>}<span class="sc">;</span> | |
| 476 463 <span class="i">$OptionsInfo</span>{<span class="w">StartingChainID</span>} = <span class="i">$Options</span>{<span class="w">chainidstart</span>}<span class="sc">;</span> | |
| 477 464 <span class="i">$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> | |
| 478 465 | |
| 479 466 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 480 467 <span class="i">$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> | |
| 481 468 | |
| 482 469 <span class="i">$OptionsInfo</span>{<span class="w">ResidueNumberMode</span>} = <span class="i">$Options</span>{<span class="w">residuenumbermode</span>}<span class="sc">;</span> | |
| 483 470 <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">residuenumberstart</span>}<span class="sc">;</span> | |
| 484 471 | |
| 485 472 <span class="i">$OptionsInfo</span>{<span class="w">HetatmResidueNumberMode</span>} = <span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>}<span class="sc">;</span> | |
| 486 473 <span class="i">$OptionsInfo</span>{<span class="w">StartingHetatmResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>}<span class="sc">;</span> | |
| 487 474 | |
| 488 475 <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> | |
| 489 476 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 490 477 | |
| 491 478 <span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} = <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span> | |
| 492 479 <span class="i">$OptionsInfo</span>{<span class="w">StartingWaterResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">waterresiduestart</span>}<span class="sc">;</span> | |
| 493 480 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 494 481 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 495 482 | |
| 496 483 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span><span class="sc">;</span> | |
| 497 484 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 498 485 <span class="k">my</span><span class="s">(</span><span class="i">$WaterResidueName</span><span class="s">)</span><span class="sc">;</span> | |
| 499 486 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} =~ <span class="q">/Automatic/i</span><span class="s">)</span> <span class="s">{</span> | |
| 500 487 <span class="k">push</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="cm">,</span> <span class="s">(</span><span class="q">'HOH'</span><span class="cm">,</span> <span class="q">'WAT'</span><span class="cm">,</span> <span class="q">'H2O'</span><span class="s">)</span><span class="sc">;</span> | |
| 501 488 <span class="s">}</span> | |
| 502 489 <span class="k">else</span> <span class="s">{</span> | |
| 503 490 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span> | |
| 504 491 <span class="s">}</span> | |
| 505 492 <span class="k">for</span> <span class="i">$WaterResidueName</span> <span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span> <span class="s">{</span> | |
| 506 493 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$WaterResidueName</span>} = <span class="i">$WaterResidueName</span><span class="sc">;</span> | |
| 507 494 <span class="s">}</span> | |
| 508 495 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="sc">;</span> | |
| 509 496 <span class="s">}</span> | |
| 510 497 | |
| 511 498 <span class="c"># Retrieve information about PDB files...</span> | |
| 512 <a name="RetrievePDBFilesInfo-"></a> 499 <span class="k">sub </span><span class="m">RetrievePDBFilesInfo</span> <span class="s">{</span> | |
| 513 500 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 514 501 | |
| 515 502 <span class="i">%PDBFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 516 503 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 517 504 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 518 505 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 519 506 | |
| 520 507 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span> | |
| 521 508 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> | |
| 522 509 | |
| 523 510 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> | |
| 524 511 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 525 512 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 526 513 | |
| 527 514 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 528 515 <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> | |
| 529 516 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It doesn't exist\n"</span><span class="sc">;</span> | |
| 530 517 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 531 518 <span class="s">}</span> | |
| 532 519 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="q">"pdb"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 533 520 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It's not a PDB file\n"</span><span class="sc">;</span> | |
| 534 521 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 535 522 <span class="s">}</span> | |
| 536 523 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">PDBFILE</span><span class="cm">,</span> <span class="q">"$PDBFile"</span><span class="s">)</span> <span class="s">{</span> | |
| 537 524 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: Couldn't open it: $! \n"</span><span class="sc">;</span> | |
| 538 525 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 539 526 <span class="s">}</span> | |
| 540 527 <span class="k">close</span> <span class="w">PDBFILE</span><span class="sc">;</span> | |
| 541 528 | |
| 542 529 <span class="c"># Get PDB data...</span> | |
| 543 530 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span> | |
| 544 531 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> | |
| 545 532 <span class="k">if</span> <span class="s">(</span>!<span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 546 533 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: No chains found \n"</span><span class="sc">;</span> | |
| 547 534 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 548 535 <span class="s">}</span> | |
| 549 536 | |
| 550 537 <span class="c"># Setup output file names...</span> | |
| 551 538 <span class="i">@OutFileNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 552 539 <span class="i">$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> | |
| 553 540 <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> | |
| 554 541 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@PDBFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 555 542 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> | |
| 556 543 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> | |
| 557 544 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> | |
| 558 545 <span class="s">}</span> | |
| 559 546 <span class="k">else</span> <span class="s">{</span> | |
| 560 547 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> | |
| 561 548 <span class="s">}</span> | |
| 562 549 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> | |
| 563 550 <span class="s">}</span> | |
| 564 551 <span class="k">else</span> <span class="s">{</span> | |
| 565 552 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> | |
| 566 553 <span class="s">}</span> | |
| 567 554 <span class="i">$Mode</span> = <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="sc">;</span> | |
| 568 555 <span class="j">MODE:</span> <span class="s">{</span> | |
| 569 556 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 570 557 <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">$OutFileMode</span> = <span class="q">'RenumberResidues'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span> | |
| 571 558 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 572 559 <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">$OutFileMode</span> = <span class="q">'RenameChainIDs'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span> | |
| 573 560 <span class="i">$OutFileMode</span> = <span class="q">''</span><span class="sc">;</span> | |
| 574 561 <span class="s">}</span> | |
| 575 562 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}${OutFileMode}.pdb"</span><span class="sc">;</span> | |
| 576 563 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span> | |
| 577 564 | |
| 578 565 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> | |
| 579 566 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> | |
| 580 567 | |
| 581 568 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@OutFileNames</span><span class="sc">;</span> | |
| 582 569 <span class="s">}</span> | |
| 583 570 <span class="s">}</span> | |
| 584 571 | |
| 585 572 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> | |
| 586 <a name="SetupScriptUsage-"></a> 573 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> | |
| 587 574 | |
| 588 575 <span class="c"># Retrieve all the options...</span> | |
| 589 576 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 590 577 <span class="i">$Options</span>{<span class="w">atomnumberstart</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 591 578 <span class="i">$Options</span>{<span class="w">chainidstart</span>} = <span class="q">'A'</span><span class="sc">;</span> | |
| 592 579 <span class="i">$Options</span>{<span class="w">chainidrenameempty</span>} = <span class="q">'No'</span><span class="sc">;</span> | |
| 593 580 <span class="i">$Options</span>{<span class="w">keepoldrecords</span>} = <span class="q">'no'</span><span class="sc">;</span> | |
| 594 581 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'RenumberResidues'</span><span class="sc">;</span> | |
| 595 582 <span class="i">$Options</span>{<span class="w">modifyheader</span>} = <span class="q">'yes'</span><span class="sc">;</span> | |
| 596 583 <span class="i">$Options</span>{<span class="w">residuenumbermode</span>} = <span class="q">'PerChain'</span><span class="sc">;</span> | |
| 597 584 <span class="i">$Options</span>{<span class="w">residuenumberstart</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 598 585 <span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>} = <span class="q">'Automatic'</span><span class="sc">;</span> | |
| 599 586 <span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>} = <span class="n">6000</span><span class="sc">;</span> | |
| 600 587 <span class="i">$Options</span>{<span class="w">waterresiduenames</span>} = <span class="q">'Automatic'</span><span class="sc">;</span> | |
| 601 588 <span class="i">$Options</span>{<span class="w">waterresiduestart</span>} = <span class="n">8000</span><span class="sc">;</span> | |
| 602 589 | |
| 603 590 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"atomnumberstart|a=i"</span><span class="cm">,</span> <span class="q">"chainidstart|c=s"</span><span class="cm">,</span> <span class="q">"chainidrenameempty=s"</span><span class="cm">,</span> <span class="q">"keepoldrecords|k=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"modifyheader=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"residuenumbermode=s"</span><span class="cm">,</span> <span class="q">"residuenumberstart=i"</span><span class="cm">,</span> <span class="q">"residuenumberhetatmmode=s"</span><span class="cm">,</span> <span class="q">"residuenumberstarthetatm=i"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"sequencelength=i"</span><span class="cm">,</span> <span class="q">"waterresiduenames=s"</span><span class="cm">,</span> <span class="q">"waterresiduestart=i"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 604 591 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> | |
| 605 592 <span class="s">}</span> | |
| 606 593 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> | |
| 607 594 <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> | |
| 608 595 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> | |
| 609 596 <span class="s">}</span> | |
| 610 597 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span> | |
| 611 598 <span class="s">}</span> | |
| 612 599 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomnumberstart</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 613 600 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{atomnumberstart}, for option \"-a, --AtomNumberStart\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span> | |
| 614 601 <span class="s">}</span> | |
| 615 602 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$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> | |
| 616 603 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{chainidstart}, for option \"-c, --ChainIDStart\" is not valid. Allowed values: a single character from A to Z\n"</span><span class="sc">;</span> | |
| 617 604 <span class="s">}</span> | |
| 618 605 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidrenameempty</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 619 606 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{chainidrenameempty}, for option \"--chainidrenameempty\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> | |
| 620 607 <span class="s">}</span> | |
| 621 608 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 622 609 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keepoldrecords}, for option \"--KeepOldRecords\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> | |
| 623 610 <span class="s">}</span> | |
| 624 611 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(RenumberAtoms|RenumberResidues|RenumberWaters|RenameChainIDs)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 625 612 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: RenumberAtoms, RenumberResidues, RenumberWaters or RenameChainIDs\n"</span><span class="sc">;</span> | |
| 626 613 <span class="s">}</span> | |
| 627 614 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 628 615 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{modifyheader}, for option \"--ModifyHeader\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> | |
| 629 616 <span class="s">}</span> | |
| 630 617 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumbermode</span>} !~ <span class="q">/^(Sequential|PerChain)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 631 618 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumbermode}, for option \"--ResidueNumberMode\" is not valid. Allowed values: Sequential or PerChain\n"</span><span class="sc">;</span> | |
| 632 619 <span class="s">}</span> | |
| 633 620 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberstart</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 634 621 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumberstart}, for option \"--ResidueNumberStart\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span> | |
| 635 622 <span class="s">}</span> | |
| 636 623 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>} !~ <span class="q">/^(automatic|specify)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 637 624 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumberhetatmmode}, for option \"--residuenumbermode\" is not valid. Allowed values: automatic or specify\n"</span><span class="sc">;</span> | |
| 638 625 <span class="s">}</span> | |
| 639 626 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 640 627 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumberstarthetatm}, for option \"--residuenumberstartHetatm\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span> | |
| 641 628 <span class="s">}</span> | |
| 642 629 <span class="k">if</span> <span class="s">(</span>!<span class="w">IsPositiveInteger</span> <span class="i">$Options</span>{<span class="w">waterresiduestart</span>}<span class="s">)</span> <span class="s">{</span> | |
| 643 630 <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> | |
| 644 631 <span class="s">}</span> | |
| 645 632 <span class="s">}</span> | |
| 646 633 | |
| 647 <a name="EOF-"></a></pre> | |
| 648 <p> </p> | |
| 649 <br /> | |
| 650 <center> | |
| 651 <img src="../../../images/h2o2.png"> | |
| 652 </center> | |
| 653 </body> | |
| 654 </html> |