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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/html/code/ExtractFromPDBFiles.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,1367 @@ +<html> +<head> +<title>MayaChemTools:Code:ExtractFromPDBFiles.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<pre> + 1 #!/usr/bin/perl -w + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: ExtractFromPDBFiles.pl,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span> + 5 <span class="c"># $Revision: 1.39 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> + 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> + 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">PDBFileUtil</span><span class="sc">;</span> + 38 <span class="k">use</span> <span class="w">AminoAcids</span><span class="sc">;</span> + 39 <span class="k">use</span> <span class="w">SequenceFileUtil</span><span class="sc">;</span> + 40 + 41 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span> + 42 + 43 <span class="c"># Autoflush STDOUT</span> + 44 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> + 45 + 46 <span class="c"># Starting message...</span> + 47 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> + 48 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> + 49 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 50 + 51 <span class="c"># Get the options and setup script...</span> + 52 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 53 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 54 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span> + 55 <span class="s">}</span> + 56 + 57 <span class="k">my</span><span class="s">(</span><span class="i">@PDBFilesList</span><span class="s">)</span><span class="sc">;</span> + 58 <span class="i">@PDBFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"pdb"</span><span class="s">)</span><span class="sc">;</span> + 59 + 60 <span class="c"># Process options...</span> + 61 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> + 62 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> + 63 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 64 + 65 <span class="c"># Setup information about input files...</span> + 66 <span class="k">print</span> <span class="q">"Checking input PDB file(s)...\n"</span><span class="sc">;</span> + 67 <span class="k">my</span><span class="s">(</span><span class="i">%PDBFilesInfo</span><span class="s">)</span><span class="sc">;</span> + 68 <span class="i">RetrievePDBFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 69 + 70 <span class="c"># Process input files..</span> + 71 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 72 <span class="k">if</span> <span class="s">(</span><span class="i">@PDBFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 73 <span class="k">print</span> <span class="q">"\nProcessing PDB files...\n"</span><span class="sc">;</span> + 74 <span class="s">}</span> + 75 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span> + 76 <span class="k">if</span> <span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> + 77 <span class="k">print</span> <span class="q">"\nProcessing file $PDBFilesList[$FileIndex]...\n"</span><span class="sc">;</span> + 78 <span class="i">ExtractFromPDBFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 79 <span class="s">}</span> + 80 <span class="s">}</span> + 81 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> + 82 + 83 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 84 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span> + 85 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 86 + 87 <span class="c">###############################################################################</span> + 88 + 89 <span class="c"># Extract appropriate information...</span> +<a name="ExtractFromPDBFiles-"></a> 90 <span class="k">sub </span><span class="m">ExtractFromPDBFiles</span> <span class="s">{</span> + 91 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 92 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 93 + 94 <span class="c"># Get PDB data...</span> + 95 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 96 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span> + 97 + 98 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/Chains/i</span><span class="s">)</span> <span class="s">{</span> + 99 <span class="i">ExtractChains</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 100 <span class="s">}</span> + 101 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/Sequences/i</span><span class="s">)</span> <span class="s">{</span> + 102 <span class="i">ExtractSequences</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 103 <span class="s">}</span> + 104 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(Atoms|CAlphas|AtomNums|AtomsRange|AtomNames)$/i</span><span class="s">)</span> <span class="s">{</span> + 105 <span class="i">ExtractByAtoms</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 106 <span class="s">}</span> + 107 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(ResidueNums|ResiduesRange|ResidueNames)$/i</span><span class="s">)</span> <span class="s">{</span> + 108 <span class="i">ExtractByResidues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 109 <span class="s">}</span> + 110 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/Distance/i</span><span class="s">)</span> <span class="s">{</span> + 111 <span class="i">ExtractByDistance</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 112 <span class="s">}</span> + 113 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/NonWater/i</span><span class="s">)</span> <span class="s">{</span> + 114 <span class="i">ExtractNonWaterRecords</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 115 <span class="s">}</span> + 116 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/NonHydrogens/i</span><span class="s">)</span> <span class="s">{</span> + 117 <span class="i">ExtractNonHydrogenRecords</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 118 <span class="s">}</span> + 119 <span class="s">}</span> + 120 + 121 <span class="c"># Extract chains and generate new PDB files...</span> + 122 <span class="c">#</span> +<a name="ExtractChains-"></a> 123 <span class="k">sub </span><span class="m">ExtractChains</span> <span class="s">{</span> + 124 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 125 <span class="k">my</span><span class="s">(</span><span class="i">$ChainIndex</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="cm">,</span> <span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$AtomChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%ChainAtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 126 + 127 <span class="c"># Get chains and residues data...</span> + 128 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="q">'AtomAndHetatm'</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> + 129 + 130 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span> + 131 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span> + 132 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> + 133 + 134 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> + 135 + 136 <span class="c"># Write out header and other older recors...</span> + 137 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 138 <span class="s">}</span> + 139 + 140 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span> + 141 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span> + 142 <span class="i">$ChainLabel</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span> + 143 + 144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span> + 145 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span> + 146 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> + 147 + 148 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> + 149 + 150 <span class="c"># Write out header and other older recors...</span> + 151 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 152 <span class="s">}</span> + 153 + 154 <span class="c"># Write out ATOM/HETATM line for chain and collect all ATOM/HETATM serial numbers</span> + 155 <span class="c"># for writing out appropriate CONECT records...</span> + 156 <span class="i">%ChainAtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 157 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Lines</span>}{<span class="i">$ChainID</span>}}<span class="s">)</span> <span class="s">{</span> + 158 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 159 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$AtomChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 160 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span> + 161 <span class="i">$ChainAtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span> + 162 <span class="s">}</span> + 163 <span class="c"># Write out TER record using information from last chain record...</span> + 164 <span class="i">$AtomNumber</span> += <span class="n">1</span><span class="sc">;</span> + 165 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$AtomChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 166 + 167 <span class="c"># Write out CONECT records...</span> + 168 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%ChainAtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 169 + 170 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 171 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 172 <span class="s">}</span> + 173 + 174 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span> + 175 <span class="c"># Write out END record...</span> + 176 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 177 + 178 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 179 <span class="s">}</span> + 180 <span class="s">}</span> + 181 + 182 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span> + 183 <span class="c"># Write out END record...</span> + 184 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 185 + 186 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 187 <span class="s">}</span> + 188 + 189 <span class="s">}</span> + 190 + 191 <span class="c"># Extract sequences for individual chains or combine all the chains...</span> +<a name="ExtractSequences-"></a> 192 <span class="k">sub </span><span class="m">ExtractSequences</span> <span class="s">{</span> + 193 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 194 <span class="k">my</span><span class="s">(</span><span class="i">$ChainIndex</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="cm">,</span> <span class="i">$SequenceFileName</span><span class="cm">,</span> <span class="i">$Residue</span><span class="cm">,</span> <span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="cm">,</span> <span class="i">$ChainSequence</span><span class="cm">,</span> <span class="i">$WrappedChainSequence</span><span class="cm">,</span> <span class="i">$ChainSequenceID</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$ChainResiduesRef</span><span class="cm">,</span> <span class="i">%ChainSequencesDataMap</span><span class="s">)</span><span class="sc">;</span> + 195 + 196 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} =~ <span class="q">/^SeqRes$/i</span><span class="s">)</span> <span class="s">{</span> + 197 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="q">'SeqRes'</span><span class="s">)</span><span class="sc">;</span> + 198 <span class="s">}</span> + 199 <span class="k">else</span> <span class="s">{</span> + 200 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 201 <span class="s">}</span> + 202 + 203 <span class="c"># Generate sequence data for all the chains...</span> + 204 <span class="i">%ChainSequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 205 <span class="i">@</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 206 <span class="i">%</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 207 <span class="i">%</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 208 + 209 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span> + 210 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span> + 211 <span class="i">$ChainLabel</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span> + 212 + 213 <span class="c"># Setup sequence ID...</span> + 214 <span class="i">$ChainSequenceID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span> + 215 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ChainSequenceID</span><span class="sc">;</span> + 216 <span class="i">$ChainSequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$ChainID</span>} = <span class="i">$ChainSequenceID</span><span class="sc">;</span> + 217 + 218 <span class="c"># Collect sequence data for the chain...</span> + 219 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} =~ <span class="q">/^SeqRes/i</span><span class="s">)</span> <span class="s">{</span> + 220 <span class="i">$ChainResiduesRef</span> = \<span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="sc">;</span> + 221 <span class="s">}</span> + 222 <span class="k">else</span> <span class="s">{</span> + 223 <span class="i">$ChainResiduesRef</span> = \<span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="sc">;</span> + 224 <span class="s">}</span> + 225 <span class="c"># Setup sequence data...</span> + 226 <span class="i">$ChainSequence</span> = <span class="q">''</span><span class="sc">;</span> + 227 <span class="j">RESIDUE:</span> <span class="k">for</span> <span class="i">$Residue</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainResiduesRef</span>}<span class="s">)</span> <span class="s">{</span> + 228 <span class="s">(</span><span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="s">)</span> = <span class="i">GetResidueCode</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="sc">;</span> + 229 <span class="k">if</span> <span class="s">(</span>!<span class="i">$StandardResidue</span><span class="s">)</span> <span class="s">{</span> + 230 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepNonStandardSequences</span>}<span class="s">)</span> <span class="s">{</span> + 231 <span class="i">$ResidueCode</span> = <span class="i">$OptionsInfo</span>{<span class="w">NonStandardSequenceCode</span>}<span class="sc">;</span> + 232 <span class="k">warn</span> <span class="q">"Warning: Keeping nonstandard residue $Residue in $ChainLabel...\n"</span><span class="sc">;</span> + 233 <span class="s">}</span> + 234 <span class="k">else</span> <span class="s">{</span> + 235 <span class="k">warn</span> <span class="q">"Warning: Ignoring nonstandard residue $Residue in $ChainLabel...\n"</span><span class="sc">;</span> + 236 <span class="k">next</span> <span class="j">RESIDUE</span><span class="sc">;</span> + 237 <span class="s">}</span> + 238 <span class="s">}</span> + 239 <span class="i">$ChainSequence</span> .= <span class="i">$ResidueCode</span><span class="sc">;</span> + 240 <span class="s">}</span> + 241 <span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ChainID</span>} = <span class="i">$ChainSequence</span><span class="sc">;</span> + 242 + 243 <span class="s">}</span> + 244 + 245 <span class="c"># Write out the sequence files...</span> + 246 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceID</span><span class="cm">,</span> <span class="i">$SequenceDescription</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">%SequencesDataMap</span> <span class="s">)</span><span class="sc">;</span> + 247 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChainSequences</span>}<span class="s">)</span> <span class="s">{</span> + 248 <span class="c"># Combine all the chain sequences...</span> + 249 <span class="i">$Sequence</span> = <span class="q">''</span><span class="sc">;</span> + 250 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span> + 251 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span> + 252 + 253 <span class="i">$Sequence</span> .= <span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ChainID</span>}<span class="sc">;</span> + 254 <span class="s">}</span> + 255 <span class="i">$SequenceID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>] . <span class="q">"_CombinedChains|PDB"</span><span class="sc">;</span><span class="sc">;</span> + 256 <span class="i">$SequenceDescription</span> = <span class="i">$SequenceID</span><span class="sc">;</span> + 257 <span class="i">$SequenceFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span> + 258 + 259 <span class="k">print</span> <span class="q">"Generating sequence file $SequenceFileName...\n"</span><span class="sc">;</span> + 260 <span class="i">%SequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 261 <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 262 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 263 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 264 + 265 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$SequenceID</span><span class="sc">;</span> + 266 <span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$SequenceID</span>} = <span class="i">$SequenceDescription</span><span class="sc">;</span> + 267 <span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$SequenceID</span>} = <span class="i">$Sequence</span><span class="sc">;</span> + 268 + 269 <span class="i">WritePearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFileName</span><span class="cm">,</span> \<span class="i">%SequencesDataMap</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>}<span class="s">)</span><span class="sc">;</span> + 270 <span class="s">}</span> + 271 <span class="k">else</span> <span class="s">{</span> + 272 <span class="c"># For each specifed chain, write out the sequences...</span> + 273 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span> + 274 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span> + 275 + 276 <span class="i">$SequenceFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span> + 277 + 278 <span class="i">$SequenceID</span> = <span class="i">$ChainSequencesDataMap</span>{<span class="w">IDs</span>}[<span class="i">$ChainIndex</span>]<span class="sc">;</span> + 279 <span class="i">$SequenceDescription</span> = <span class="i">$ChainSequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$ChainID</span>}<span class="sc">;</span> + 280 <span class="i">$Sequence</span> = <span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ChainID</span>}<span class="sc">;</span> + 281 + 282 <span class="k">print</span> <span class="q">"Generating sequence file $SequenceFileName...\n"</span><span class="sc">;</span> + 283 <span class="i">%SequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 284 <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 285 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 286 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 287 + 288 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$SequenceID</span><span class="sc">;</span> + 289 <span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$SequenceID</span>} = <span class="i">$SequenceDescription</span><span class="sc">;</span> + 290 <span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$SequenceID</span>} = <span class="i">$Sequence</span><span class="sc">;</span> + 291 + 292 <span class="i">WritePearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFileName</span><span class="cm">,</span> \<span class="i">%SequencesDataMap</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>}<span class="s">)</span><span class="sc">;</span> + 293 <span class="s">}</span> + 294 <span class="s">}</span> + 295 <span class="s">}</span> + 296 + 297 <span class="c"># Extract atoms...</span> +<a name="ExtractByAtoms-"></a> 298 <span class="k">sub </span><span class="m">ExtractByAtoms</span> <span class="s">{</span> + 299 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 300 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$IgnoreRecord</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 301 + 302 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span> + 303 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> + 304 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> + 305 + 306 <span class="c"># Write out header and other older recors...</span> + 307 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 308 + 309 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span> + 310 <span class="c"># chains and multiple models..</span> + 311 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 312 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span> + 313 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 314 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 315 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 316 + 317 <span class="c"># Check atoms...</span> + 318 <span class="i">$IgnoreRecord</span> = <span class="n">1</span><span class="sc">;</span> + 319 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Atoms$/i</span><span class="s">)</span> <span class="s">{</span> + 320 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span> + 321 <span class="s">}</span> + 322 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(CAlphas|AtomNames)$/i</span><span class="s">)</span> <span class="s">{</span> + 323 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesMap</span>}{<span class="k">lc</span> <span class="i">$AtomName</span>}<span class="s">)</span> <span class="s">{</span> + 324 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span> + 325 <span class="s">}</span> + 326 <span class="s">}</span> + 327 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomNums$/i</span><span class="s">)</span> <span class="s">{</span> + 328 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsMap</span>}{<span class="i">$AtomNumber</span>}<span class="s">)</span> <span class="s">{</span> + 329 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span> + 330 <span class="s">}</span> + 331 <span class="s">}</span> + 332 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomsRange$/i</span><span class="s">)</span> <span class="s">{</span> + 333 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNumber</span> >= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartAtomNum</span>} && <span class="i">$AtomNumber</span> <= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndAtomNum</span>}<span class="s">)</span> <span class="s">{</span> + 334 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span> + 335 <span class="s">}</span> + 336 <span class="s">}</span> + 337 + 338 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IgnoreRecord</span><span class="s">)</span> <span class="s">{</span> + 339 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span> + 340 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 341 + 342 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span> + 343 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span> + 344 <span class="s">}</span> + 345 <span class="s">}</span> + 346 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 347 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span> + 348 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 349 <span class="s">}</span> + 350 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span> + 351 <span class="s">}</span> + 352 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 353 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 354 <span class="s">}</span> + 355 <span class="s">}</span> + 356 + 357 <span class="c"># Write out appropriate CONECT records...</span> + 358 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 359 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 360 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 361 <span class="s">}</span> + 362 + 363 <span class="c"># Write out END record...</span> + 364 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 365 + 366 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 367 <span class="s">}</span> + 368 + 369 <span class="c"># Extract residues...</span> +<a name="ExtractByResidues-"></a> 370 <span class="k">sub </span><span class="m">ExtractByResidues</span> <span class="s">{</span> + 371 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 372 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$IgnoreRecord</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 373 + 374 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span> + 375 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> + 376 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> + 377 + 378 <span class="c"># Write out header and other older recors...</span> + 379 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 380 + 381 <span class="c"># Write out all ATOM records for specified residues with TER and model records to indicate</span> + 382 <span class="c"># chains and multiple models...</span> + 383 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 384 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span> + 385 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 386 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 387 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 388 + 389 <span class="c"># Check residues...</span> + 390 <span class="i">$IgnoreRecord</span> = <span class="n">1</span><span class="sc">;</span> + 391 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResidueNums$/i</span><span class="s">)</span> <span class="s">{</span> + 392 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsMap</span>}{<span class="i">$ResidueNumber</span>}<span class="s">)</span> <span class="s">{</span> + 393 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span> + 394 <span class="s">}</span> + 395 <span class="s">}</span> + 396 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResiduesRange$/i</span><span class="s">)</span> <span class="s">{</span> + 397 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueNumber</span> >= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartResidueNum</span>} && <span class="i">$ResidueNumber</span> <= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndResidueNum</span>}<span class="s">)</span> <span class="s">{</span> + 398 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span> + 399 <span class="s">}</span> + 400 <span class="s">}</span> + 401 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResidueNames$/i</span><span class="s">)</span> <span class="s">{</span> + 402 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesMap</span>}{<span class="k">lc</span> <span class="i">$ResidueName</span>}<span class="s">)</span> <span class="s">{</span> + 403 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span> + 404 <span class="s">}</span> + 405 <span class="s">}</span> + 406 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IgnoreRecord</span><span class="s">)</span> <span class="s">{</span> + 407 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span> + 408 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 409 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span> + 410 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span> + 411 <span class="s">}</span> + 412 <span class="s">}</span> + 413 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 414 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span> + 415 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 416 <span class="s">}</span> + 417 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span> + 418 <span class="s">}</span> + 419 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 420 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 421 <span class="s">}</span> + 422 <span class="s">}</span> + 423 + 424 <span class="c"># Write out appropriate CONECT records...</span> + 425 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 426 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 427 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 428 <span class="s">}</span> + 429 <span class="c"># Write out END record...</span> + 430 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 431 + 432 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 433 <span class="s">}</span> + 434 + 435 <span class="c"># Extract non water records...</span> +<a name="ExtractNonWaterRecords-"></a> 436 <span class="k">sub </span><span class="m">ExtractNonWaterRecords</span> <span class="s">{</span> + 437 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 438 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 439 + 440 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span> + 441 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> + 442 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> + 443 + 444 <span class="c"># Write out header and other older recors...</span> + 445 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 446 + 447 <span class="c"># Write out all ATOM/HETATM non water records along with TER and model records to indicate</span> + 448 <span class="c"># chains and multiple models..</span> + 449 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 450 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span> + 451 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 452 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 453 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 454 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$ResidueName</span>} <span class="s">)</span> <span class="s">{</span> + 455 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span> + 456 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 457 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span> + 458 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span> + 459 <span class="s">}</span> + 460 <span class="s">}</span> + 461 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 462 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span> + 463 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 464 <span class="s">}</span> + 465 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span> + 466 <span class="s">}</span> + 467 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 468 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 469 <span class="s">}</span> + 470 <span class="s">}</span> + 471 + 472 <span class="c"># Write out appropriate CONECT records...</span> + 473 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 474 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 475 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 476 <span class="s">}</span> + 477 <span class="c"># Write out END record...</span> + 478 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 479 + 480 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 481 <span class="s">}</span> + 482 + 483 <span class="c"># Extract non hydrogen records...</span> +<a name="ExtractNonHydrogenRecords-"></a> 484 <span class="k">sub </span><span class="m">ExtractNonHydrogenRecords</span> <span class="s">{</span> + 485 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 486 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 487 + 488 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span> + 489 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> + 490 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> + 491 + 492 <span class="c"># Write out header and other older recors...</span> + 493 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 494 + 495 <span class="c"># Write out all ATOM/HETATM non hydrogen records along with TER and model records to indicate</span> + 496 <span class="c"># chains and multiple models..</span> + 497 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 498 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span> + 499 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 500 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 501 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 502 <span class="k">if</span> <span class="s">(</span><span class="i">$ElementSymbol</span> !~ <span class="q">/^H$/i</span><span class="s">)</span> <span class="s">{</span> + 503 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span> + 504 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 505 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span> + 506 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span> + 507 <span class="s">}</span> + 508 <span class="s">}</span> + 509 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 510 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span> + 511 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 512 <span class="s">}</span> + 513 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span> + 514 <span class="s">}</span> + 515 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 516 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 517 <span class="s">}</span> + 518 <span class="s">}</span> + 519 + 520 <span class="c"># Write out appropriate CONECT records...</span> + 521 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 522 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 523 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 524 <span class="s">}</span> + 525 <span class="c"># Write out END record...</span> + 526 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 527 + 528 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 529 <span class="s">}</span> + 530 + 531 <span class="c"># Extract ATOM/HETATM records by distance...</span> +<a name="ExtractByDistance-"></a> 532 <span class="k">sub </span><span class="m">ExtractByDistance</span> <span class="s">{</span> + 533 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 534 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$RecordLineNum</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$IgnoreRecord</span><span class="cm">,</span> <span class="i">$ResidueID</span><span class="cm">,</span> <span class="i">@OriginCoords</span><span class="cm">,</span> <span class="i">@Coords</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="cm">,</span> <span class="i">%ResiduesDataMap</span><span class="s">)</span><span class="sc">;</span> + 535 + 536 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span> + 537 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span> + 538 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span> + 539 + 540 <span class="c"># Write out header and other older recors...</span> + 541 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 542 + 543 <span class="c"># Setup coordinates of origin to calculate distance...</span> + 544 <span class="i">@OriginCoords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 545 <span class="k">push</span> <span class="i">@OriginCoords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span> + 546 + 547 <span class="c"># Write out all ATOM records for which meet specified criteria along with TER and model records to indicate</span> + 548 <span class="c"># chains and multiple models...</span> + 549 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 550 + 551 <span class="i">%ResiduesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 552 <span class="i">%</span>{<span class="i">$ResiduesDataMap</span>{<span class="w">ID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 553 <span class="i">%</span>{<span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 554 + 555 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span> + 556 <span class="i">$RecordLineNum</span> = <span class="n">0</span><span class="sc">;</span> + 557 + 558 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 559 <span class="i">$RecordLineNum</span>++<span class="sc">;</span> + 560 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 561 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 562 <span class="i">@Coords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">push</span> <span class="i">@Coords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span> + 563 + 564 <span class="i">$IgnoreRecord</span> = <span class="n">1</span><span class="sc">;</span> + 565 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DistanceSelectionMode</span>} =~ <span class="q">/^ByResidue$/i</span><span class="s">)</span> <span class="s">{</span> + 566 <span class="i">$ResidueID</span> = <span class="q">"${ResidueName}_${ResidueNumber}_${ChainID}"</span><span class="sc">;</span> + 567 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ResiduesDataMap</span>{<span class="w">ID</span>}{<span class="i">$ResidueID</span>}<span class="s">)</span> <span class="s">{</span> + 568 <span class="c"># Residue data has been processed; check its selection status...</span> + 569 <span class="k">if</span> <span class="s">(</span><span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}{<span class="i">$ResidueID</span>}<span class="s">)</span> <span class="s">{</span> + 570 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span> + 571 <span class="s">}</span> + 572 <span class="s">}</span> + 573 <span class="k">else</span> <span class="s">{</span> + 574 <span class="c"># Residue hasn't been processed...</span> + 575 <span class="i">$ResiduesDataMap</span>{<span class="w">ID</span>}{<span class="i">$ResidueID</span>} = <span class="i">$ResidueID</span><span class="sc">;</span> + 576 <span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}{<span class="i">$ResidueID</span>} = <span class="n">0</span><span class="sc">;</span> + 577 <span class="k">if</span> <span class="s">(</span><span class="i">CheckResidueDistance</span><span class="s">(</span><span class="i">$ResidueID</span><span class="cm">,</span> <span class="i">$RecordLineNum</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">@OriginCoords</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 578 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span> + 579 <span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}{<span class="i">$ResidueID</span>} = <span class="n">1</span><span class="sc">;</span> + 580 <span class="s">}</span> + 581 <span class="s">}</span> + 582 <span class="s">}</span> + 583 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DistanceSelectionMode</span>} =~ <span class="q">/^ByAtom$/i</span><span class="s">)</span> <span class="s">{</span> + 584 <span class="k">if</span> <span class="s">(</span><span class="i">CheckDistance</span><span class="s">(</span>\<span class="i">@Coords</span><span class="cm">,</span> \<span class="i">@OriginCoords</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 585 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span> + 586 <span class="s">}</span> + 587 <span class="s">}</span> + 588 + 589 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IgnoreRecord</span><span class="s">)</span> <span class="s">{</span> + 590 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span> + 591 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 592 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span> + 593 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span> + 594 <span class="s">}</span> + 595 <span class="s">}</span> + 596 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 597 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span> + 598 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 599 <span class="s">}</span> + 600 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span> + 601 <span class="s">}</span> + 602 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 603 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 604 <span class="s">}</span> + 605 <span class="s">}</span> + 606 + 607 <span class="c"># Write out appropriate CONECT records...</span> + 608 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span> + 609 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 610 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 611 <span class="s">}</span> + 612 + 613 <span class="c"># Write out END record...</span> + 614 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 615 + 616 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 617 <span class="s">}</span> + 618 + 619 <span class="c"># Does record type correspond to the specified record type?</span> +<a name="CheckRecordType-"></a> 620 <span class="k">sub </span><span class="m">CheckRecordType</span> <span class="s">{</span> + 621 <span class="k">my</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 622 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> + 623 + 624 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> + 625 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} =~ <span class="q">/^Atom$/i</span><span class="s">)</span> <span class="s">{</span> + 626 <span class="i">$Status</span> = <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 627 <span class="s">}</span> + 628 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} =~ <span class="q">/^Hetatm$/i</span><span class="s">)</span> <span class="s">{</span> + 629 <span class="i">$Status</span> = <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 630 <span class="s">}</span> + 631 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} =~ <span class="q">/^AtomAndHetatm$/i</span><span class="s">)</span> <span class="s">{</span> + 632 <span class="i">$Status</span> = <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 633 <span class="s">}</span> + 634 + 635 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> + 636 <span class="s">}</span> + 637 + 638 <span class="c"># Does record meets distance citerion specified by the user?</span> +<a name="CheckResidueDistance-"></a> 639 <span class="k">sub </span><span class="m">CheckResidueDistance</span> <span class="s">{</span> + 640 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedResidueID</span><span class="cm">,</span> <span class="i">$StartingLineNum</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="i">$OriginCoordsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 641 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$RecordLineIndex</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$ResidueID</span><span class="cm">,</span> <span class="i">@Coords</span><span class="s">)</span><span class="sc">;</span> + 642 + 643 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> + 644 + 645 <span class="j">RECORDLINE:</span> <span class="k">for</span> <span class="i">$RecordLineIndex</span> <span class="s">(</span><span class="s">(</span><span class="i">$StartingLineNum</span> - <span class="n">1</span><span class="s">)</span> .. <span class="i">$#</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 646 <span class="i">$RecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="i">$RecordLineIndex</span>]<span class="sc">;</span> + 647 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 648 <span class="k">next</span> <span class="j">RECORDLINE</span><span class="sc">;</span> + 649 <span class="s">}</span> + 650 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 651 <span class="i">$ResidueID</span> = <span class="q">"${ResidueName}_${ResidueNumber}_${ChainID}"</span><span class="sc">;</span> + 652 + 653 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueID</span> !~ <span class="q">/^$SpecifiedResidueID$/i</span><span class="s">)</span> <span class="s">{</span> + 654 <span class="c"># It's a new residue line...</span> + 655 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span> + 656 <span class="s">}</span> + 657 + 658 <span class="c"># Check distance...</span> + 659 <span class="i">@Coords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">push</span> <span class="i">@Coords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span> + 660 <span class="k">if</span> <span class="s">(</span><span class="i">CheckDistance</span><span class="s">(</span>\<span class="i">@Coords</span><span class="cm">,</span> <span class="i">$OriginCoordsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 661 <span class="c"># Distance criterion is met for at least one record in the residue...</span> + 662 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> + 663 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span> + 664 <span class="s">}</span> + 665 <span class="s">}</span> + 666 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> + 667 <span class="s">}</span> + 668 + 669 <span class="c"># Does record meets distance citerion specified by the user?</span> +<a name="CheckDistance-"></a> 670 <span class="k">sub </span><span class="m">CheckDistance</span> <span class="s">{</span> + 671 <span class="k">my</span><span class="s">(</span><span class="i">$CoordsRef</span><span class="cm">,</span> <span class="i">$OriginCoordsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 672 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$DistanceSquare</span><span class="s">)</span><span class="sc">;</span> + 673 + 674 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> + 675 + 676 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span> + 677 <span class="c"># Go over coordinates of all the atoms in the residue...</span> + 678 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueCoordsCount</span><span class="s">)</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$OriginCoordsRef</span>}<span class="sc">;</span> + 679 <span class="j">INDEX:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$ResidueCoordsCount</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">3</span><span class="s">)</span> <span class="s">{</span> + 680 <span class="i">$DistanceSquare</span> = <span class="s">(</span><span class="i">$CoordsRef</span>->[<span class="n">0</span>] - <span class="i">$OriginCoordsRef</span>->[<span class="i">$Index</span>]<span class="s">)</span>**<span class="n">2</span> + <span class="s">(</span><span class="i">$CoordsRef</span>->[<span class="n">1</span>] - <span class="i">$OriginCoordsRef</span>->[<span class="i">$Index</span> + <span class="n">1</span>]<span class="s">)</span>**<span class="n">2</span> + <span class="s">(</span><span class="i">$CoordsRef</span>->[<span class="n">2</span>] - <span class="i">$OriginCoordsRef</span>->[<span class="i">$Index</span> + <span class="n">2</span>]<span class="s">)</span>**<span class="n">2</span><span class="sc">;</span> + 681 <span class="i">$Distance</span> = <span class="k">sqrt</span> <span class="i">$DistanceSquare</span><span class="sc">;</span> + 682 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance</span> <= <span class="i">$OptionsInfo</span>{<span class="w">MaxExtractionDistance</span>}<span class="s">)</span> <span class="s">{</span> + 683 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> + 684 <span class="k">last</span> <span class="j">INDEX</span><span class="sc">;</span> + 685 <span class="s">}</span> + 686 <span class="s">}</span> + 687 <span class="s">}</span> + 688 <span class="k">else</span> <span class="s">{</span> + 689 <span class="i">$DistanceSquare</span> = <span class="n">0</span><span class="sc">;</span> + 690 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 691 <span class="i">$DistanceSquare</span> += <span class="s">(</span><span class="i">$CoordsRef</span>->[<span class="i">$Index</span>] - <span class="i">$OriginCoordsRef</span>->[<span class="i">$Index</span>]<span class="s">)</span>**<span class="n">2</span><span class="sc">;</span> + 692 <span class="s">}</span> + 693 <span class="i">$Distance</span> = <span class="k">sqrt</span> <span class="i">$DistanceSquare</span><span class="sc">;</span> + 694 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$Distance</span> <= <span class="i">$OptionsInfo</span>{<span class="w">MaxExtractionDistance</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 695 <span class="s">}</span> + 696 + 697 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> + 698 <span class="s">}</span> + 699 + 700 <span class="c"># Write out modifed header and other older records...</span> +<a name="WriteHeaderAndOlderRecords-"></a> 701 <span class="k">sub </span><span class="m">WriteHeaderAndOlderRecords</span> <span class="s">{</span> + 702 <span class="k">my</span><span class="s">(</span><span class="i">$OutFileRef</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 703 + 704 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>}<span class="s">)</span> <span class="s">{</span> + 705 <span class="c"># Write out modified HEADER record...</span> + 706 <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="i">GetHeaderRecordInformation</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> + 707 <span class="i">$Classification</span> = <span class="q">'Data extracted using MayaChemTools'</span><span class="sc">;</span> + 708 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">GenerateHeaderRecordLine</span><span class="s">(</span><span class="i">$IDCode</span><span class="cm">,</span> <span class="i">$Classification</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 709 <span class="s">}</span> + 710 <span class="k">else</span> <span class="s">{</span> + 711 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 712 <span class="s">}</span> + 713 + 714 <span class="c"># Write out any old records...</span> + 715 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>}<span class="s">)</span> <span class="s">{</span> + 716 <span class="k">my</span><span class="s">(</span><span class="i">$RecordLineIndex</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> + 717 <span class="c"># Skip HEADER record and write out older records all the way upto first MODEL/ATOM/HETATM records from input file...</span> + 718 <span class="j">RECORDLINE:</span> <span class="k">for</span> <span class="i">$RecordLineIndex</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> + 719 <span class="i">$RecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="i">$RecordLineIndex</span>]<span class="sc">;</span> + 720 <span class="k">if</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 721 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span> + 722 <span class="s">}</span> + 723 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span> + 724 <span class="s">}</span> + 725 <span class="s">}</span> + 726 <span class="s">}</span> + 727 + 728 <span class="c"># Get header record information assuming it's the first record...</span> +<a name="GetHeaderRecordInformation-"></a> 729 <span class="k">sub </span><span class="m">GetHeaderRecordInformation</span> <span class="s">{</span> + 730 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 731 <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="cm">,</span> <span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="sc">;</span> + 732 + 733 <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="s">(</span><span class="q">''</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> + 734 <span class="i">$HeaderRecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="sc">;</span> + 735 <span class="k">if</span> <span class="s">(</span><span class="i">IsHeaderRecordType</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 736 <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="i">ParseHeaderRecordLine</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="sc">;</span> + 737 <span class="s">}</span> + 738 <span class="k">return</span> <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span><span class="sc">;</span> + 739 <span class="s">}</span> + 740 + 741 <span class="c"># Get one letter residue code...</span> +<a name="GetResidueCode-"></a> 742 <span class="k">sub </span><span class="m">GetResidueCode</span> <span class="s">{</span> + 743 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 744 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="s">)</span><span class="sc">;</span> + 745 + 746 <span class="i">$ResidueCode</span> = <span class="i">$OptionsInfo</span>{<span class="w">NonStandardSequenceCode</span>}<span class="sc">;</span> + 747 <span class="i">$StandardResidue</span> = <span class="n">0</span><span class="sc">;</span> + 748 + 749 <span class="k">if</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span> + 750 <span class="c"># Assume it's an amino acid...</span> + 751 <span class="k">if</span> <span class="s">(</span><span class="i">AminoAcids::IsAminoAcid</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 752 <span class="c"># Standard amino acid...</span> + 753 <span class="i">$ResidueCode</span> = <span class="i">AminoAcids::GetAminoAcidOneLetterCode</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span><span class="sc">;</span> + 754 <span class="i">$StandardResidue</span> = <span class="n">1</span><span class="sc">;</span> + 755 <span class="s">}</span> + 756 <span class="s">}</span> + 757 <span class="k">elsif</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 758 <span class="c"># Assume it's a nucleic acid...</span> + 759 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueName</span> =~ <span class="q">/^(A|G|T|U|C)$/i</span><span class="s">)</span> <span class="s">{</span> + 760 <span class="i">$ResidueCode</span> = <span class="i">$ResidueName</span><span class="sc">;</span> + 761 <span class="i">$StandardResidue</span> = <span class="n">1</span><span class="sc">;</span> + 762 <span class="s">}</span> + 763 <span class="s">}</span> + 764 + 765 <span class="k">return</span> <span class="s">(</span><span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="s">)</span><span class="sc">;</span> + 766 <span class="s">}</span> + 767 + 768 <span class="c"># Process option values...</span> +<a name="ProcessOptions-"></a> 769 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> + 770 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 771 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> + 772 + 773 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedChains</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 774 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">chains</span>} =~ <span class="q">/^(First|All)$/i</span><span class="s">)</span> <span class="s">{</span> + 775 <span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} = <span class="i">$Options</span>{<span class="w">chains</span>}<span class="sc">;</span> + 776 <span class="s">}</span> + 777 <span class="k">else</span> <span class="s">{</span> + 778 <span class="i">@SpecifiedChains</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">chains</span>}<span class="sc">;</span> + 779 <span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} = <span class="q">'Specified'</span><span class="sc">;</span> + 780 <span class="s">}</span> + 781 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedChains</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 782 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedChains</span>}}<span class="cm">,</span> <span class="i">@SpecifiedChains</span><span class="sc">;</span> + 783 + 784 <span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">combinechains</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 785 + 786 <span class="i">$OptionsInfo</span>{<span class="w">CombineChainSequences</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">combinechains</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 787 + 788 <span class="i">ProcessResiduesOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 789 <span class="i">ProcessAtomsOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 790 <span class="i">ProcessDistanceOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 791 + 792 <span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} = <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span> + 793 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 794 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 795 + 796 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span><span class="sc">;</span> + 797 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 798 + 799 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^NonWater$/i</span><span class="s">)</span> <span class="s">{</span> + 800 <span class="k">my</span><span class="s">(</span><span class="i">$WaterResidueName</span><span class="s">)</span><span class="sc">;</span> + 801 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} =~ <span class="q">/Automatic/i</span><span class="s">)</span> <span class="s">{</span> + 802 <span class="k">push</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="cm">,</span> <span class="s">(</span><span class="q">'HOH'</span><span class="cm">,</span> <span class="q">'WAT'</span><span class="cm">,</span> <span class="q">'H2O'</span><span class="s">)</span><span class="sc">;</span> + 803 <span class="s">}</span> + 804 <span class="k">else</span> <span class="s">{</span> + 805 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span> + 806 <span class="s">}</span> + 807 <span class="k">for</span> <span class="i">$WaterResidueName</span> <span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span> <span class="s">{</span> + 808 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$WaterResidueName</span>} = <span class="i">$WaterResidueName</span><span class="sc">;</span> + 809 <span class="s">}</span> + 810 <span class="s">}</span> + 811 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="sc">;</span> + 812 + 813 <span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} = <span class="i">$Options</span>{<span class="w">recordmode</span>} ? <span class="i">$Options</span>{<span class="w">recordmode</span>} <span class="co">:</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^(Atoms|CAlphas|AtomNums|AtomsRange|AtomNames)$/i</span> ? <span class="q">"Atom"</span> <span class="co">:</span> <span class="q">"AtomAndHetatm"</span><span class="s">)</span><span class="sc">;</span> + 814 + 815 <span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 816 + 817 <span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 818 + 819 <span class="i">$OptionsInfo</span>{<span class="w">KeepNonStandardSequences</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">nonstandardkeep</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 820 <span class="i">$OptionsInfo</span>{<span class="w">NonStandardSequenceCode</span>} = <span class="i">$Options</span>{<span class="w">nonstandardcode</span>}<span class="sc">;</span> + 821 <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>} = <span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="sc">;</span> + 822 <span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} = <span class="i">$Options</span>{<span class="w">sequencerecords</span>}<span class="sc">;</span> + 823 <span class="i">$OptionsInfo</span>{<span class="w">SequenceIDPrefixSource</span>} = <span class="i">$Options</span>{<span class="w">sequenceidprefix</span>}<span class="sc">;</span> + 824 + 825 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 826 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 827 <span class="s">}</span> + 828 + 829 <span class="c"># Process specified residue options...</span> +<a name="ProcessResiduesOptions-"></a> 830 <span class="k">sub </span><span class="m">ProcessResiduesOptions</span> <span class="s">{</span> + 831 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueNum</span><span class="cm">,</span> <span class="i">$StartResidueNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">@SpecifiedResidueNumsList</span><span class="cm">,</span> <span class="i">@SpecifiedResidueNamesList</span><span class="s">)</span><span class="sc">;</span> + 832 + 833 <span class="i">@SpecifiedResidueNumsList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 834 <span class="s">(</span><span class="i">$StartResidueNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> + 835 + 836 <span class="i">@SpecifiedResidueNamesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 837 + 838 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(ResidueNums|ResiduesRange|ResidueNames)$/i</span><span class="s">)</span> <span class="s">{</span> + 839 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">residues</span>}<span class="s">)</span> <span class="s">{</span> + 840 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--Residues\" option in \"ResidueNums, ResiduesRange, or ResidueNames\" \"-m, --mode\". \n"</span><span class="sc">;</span> + 841 <span class="s">}</span> + 842 <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>} = <span class="i">$Options</span>{<span class="w">residues</span>}<span class="sc">;</span> + 843 <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>} =~ <span class="q">s/ //g</span><span class="sc">;</span> + 844 + 845 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResidueNames$/i</span><span class="s">)</span> <span class="s">{</span> + 846 <span class="i">@SpecifiedResidueNamesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>}<span class="sc">;</span> + 847 <span class="s">}</span> + 848 <span class="k">else</span> <span class="s">{</span> + 849 <span class="i">@SpecifiedResidueNumsList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>}<span class="sc">;</span> + 850 <span class="k">for</span> <span class="i">$ResidueNum</span> <span class="s">(</span><span class="i">@SpecifiedResidueNumsList</span><span class="s">)</span> <span class="s">{</span> + 851 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$ResidueNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 852 <span class="k">die</span> <span class="q">"Error: Invalid residue number value, $ResidueNum, for \"--Residues\" option during \"ResidueNumes\" or \"ResiduesRange\"value of \"-m --mode\" option: Residue number must be a positive integer.\n"</span><span class="sc">;</span> + 853 <span class="s">}</span> + 854 <span class="s">}</span> + 855 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResiduesRange$/i</span><span class="s">)</span> <span class="s">{</span> + 856 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedResidueNumsList</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 857 <span class="k">die</span> <span class="q">"Error: Invalid number of residue number values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedResidueNumsList</span><span class="s">)</span><span class="cm">,</span> <span class="q">", for \"--Residues\" option during \"ResiduesRange\" value of \"-m --mode\" option: The number of values must be 2 corresponding to start and end residue numbers.\n"</span><span class="sc">;</span> + 858 <span class="s">}</span> + 859 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedResidueNumsList</span>[<span class="n">0</span>] > <span class="i">$SpecifiedResidueNumsList</span>[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span> + 860 <span class="k">die</span> <span class="q">"Error: Invalid residue number values, @SpecifiedResidueNumsList, for \"--Residues\" option during \"ResiduesRange\" value of \"-m --mode\" option: The start residue number must be less than end residue number.\n"</span><span class="sc">;</span> + 861 <span class="s">}</span> + 862 <span class="s">(</span><span class="i">$StartResidueNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="s">)</span> = <span class="i">@SpecifiedResidueNumsList</span><span class="sc">;</span> + 863 <span class="s">}</span> + 864 <span class="s">}</span> + 865 <span class="s">}</span> + 866 + 867 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 868 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedResidueNumsList</span><span class="sc">;</span> + 869 + 870 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartResidueNum</span>} = <span class="i">$StartResidueNum</span><span class="sc">;</span> + 871 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndResidueNum</span>} = <span class="i">$EndResNum</span><span class="sc">;</span> + 872 + 873 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 874 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedResidueNamesList</span><span class="sc">;</span> + 875 + 876 <span class="c"># Set up a specified residue numbers map...</span> + 877 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 878 <span class="k">for</span> <span class="i">$ResidueNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsList</span>}}<span class="s">)</span> <span class="s">{</span> + 879 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsMap</span>}{<span class="i">$ResidueNum</span>} = <span class="i">$ResidueNum</span><span class="sc">;</span> + 880 <span class="s">}</span> + 881 + 882 <span class="c"># Set up a specified residue names map...</span> + 883 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 884 <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesList</span>}}<span class="s">)</span> <span class="s">{</span> + 885 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesMap</span>}{<span class="k">lc</span> <span class="i">$ResidueName</span>} = <span class="k">lc</span> <span class="i">$ResidueName</span><span class="sc">;</span> + 886 <span class="s">}</span> + 887 + 888 <span class="s">}</span> + 889 + 890 <span class="c"># Process specified atom options...</span> +<a name="ProcessAtomsOptions-"></a> 891 <span class="k">sub </span><span class="m">ProcessAtomsOptions</span> <span class="s">{</span> + 892 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$StartAtomNum</span><span class="cm">,</span> <span class="i">$EndAtomNum</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">@SpecifiedAtomNumsList</span><span class="cm">,</span> <span class="i">@SpecifiedAtomNamesList</span><span class="s">)</span><span class="sc">;</span> + 893 + 894 <span class="i">@SpecifiedAtomNumsList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 895 <span class="s">(</span><span class="i">$StartAtomNum</span><span class="cm">,</span> <span class="i">$EndAtomNum</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> + 896 + 897 <span class="i">@SpecifiedAtomNamesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 898 + 899 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(AtomNums|AtomsRange|AtomNames)$/i</span><span class="s">)</span> <span class="s">{</span> + 900 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">atoms</span>}<span class="s">)</span> <span class="s">{</span> + 901 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--Atoms\" option in \"AtomNums, AtomsRange, or AtomNames\" \"-m, --mode\". \n"</span><span class="sc">;</span> + 902 <span class="s">}</span> + 903 <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>} = <span class="i">$Options</span>{<span class="w">atoms</span>}<span class="sc">;</span> + 904 <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>} =~ <span class="q">s/ //g</span><span class="sc">;</span> + 905 + 906 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomNames$/i</span><span class="s">)</span> <span class="s">{</span> + 907 <span class="i">@SpecifiedAtomNamesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>}<span class="sc">;</span> + 908 <span class="s">}</span> + 909 <span class="k">else</span> <span class="s">{</span> + 910 <span class="i">@SpecifiedAtomNumsList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>}<span class="sc">;</span> + 911 <span class="k">for</span> <span class="i">$AtomNum</span> <span class="s">(</span><span class="i">@SpecifiedAtomNumsList</span><span class="s">)</span> <span class="s">{</span> + 912 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$AtomNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 913 <span class="k">die</span> <span class="q">"Error: Invalid atom number value, $AtomNum, for \"--Atoms\" option during \"AtomNums\" or \"AtomsRange\"value of \"-m --mode\" option: Atom number must be a positive integer.\n"</span><span class="sc">;</span> + 914 <span class="s">}</span> + 915 <span class="s">}</span> + 916 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomsRange$/i</span><span class="s">)</span> <span class="s">{</span> + 917 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedAtomNumsList</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 918 <span class="k">die</span> <span class="q">"Error: Invalid number of atom number values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedAtomNumsList</span><span class="s">)</span><span class="cm">,</span> <span class="q">", for \"--Atoms\" option during \"AtomsRange\" value of \"-m --mode\" option: The number of values must be 2 corresponding to start and end atom numbers.\n"</span><span class="sc">;</span> + 919 <span class="s">}</span> + 920 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedAtomNumsList</span>[<span class="n">0</span>] > <span class="i">$SpecifiedAtomNumsList</span>[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span> + 921 <span class="k">die</span> <span class="q">"Error: Invalid atom number values, @SpecifiedAtomNumsList, for \"--Atoms\" option during \"AtomsRange\" value of \"-m --mode\" option: The start atom number must be less than end atom number.\n"</span><span class="sc">;</span> + 922 <span class="s">}</span> + 923 <span class="s">(</span><span class="i">$StartAtomNum</span><span class="cm">,</span> <span class="i">$EndAtomNum</span><span class="s">)</span> = <span class="i">@SpecifiedAtomNumsList</span><span class="sc">;</span> + 924 <span class="s">}</span> + 925 <span class="s">}</span> + 926 <span class="s">}</span> + 927 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^CAlphas$/i</span><span class="s">)</span> <span class="s">{</span> + 928 <span class="i">@SpecifiedAtomNamesList</span> = <span class="s">(</span><span class="q">"CA"</span><span class="s">)</span><span class="sc">;</span> + 929 <span class="s">}</span> + 930 + 931 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 932 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedAtomNumsList</span><span class="sc">;</span> + 933 + 934 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartAtomNum</span>} = <span class="i">$StartAtomNum</span><span class="sc">;</span> + 935 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndAtomNum</span>} = <span class="i">$EndAtomNum</span><span class="sc">;</span> + 936 + 937 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 938 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedAtomNamesList</span><span class="sc">;</span> + 939 + 940 <span class="c"># Set up a specified residue numbers map...</span> + 941 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 942 <span class="k">for</span> <span class="i">$AtomNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsList</span>}}<span class="s">)</span> <span class="s">{</span> + 943 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsMap</span>}{<span class="i">$AtomNum</span>} = <span class="i">$AtomNum</span><span class="sc">;</span> + 944 <span class="s">}</span> + 945 + 946 <span class="c"># Set up a specified residue names map...</span> + 947 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 948 <span class="k">for</span> <span class="i">$AtomName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesList</span>}}<span class="s">)</span> <span class="s">{</span> + 949 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesMap</span>}{<span class="k">lc</span> <span class="i">$AtomName</span>} = <span class="k">lc</span> <span class="i">$AtomName</span><span class="sc">;</span> + 950 <span class="s">}</span> + 951 + 952 <span class="s">}</span> + 953 + 954 <span class="c"># Process specified distance options...</span> +<a name="ProcessDistanceOptions-"></a> 955 <span class="k">sub </span><span class="m">ProcessDistanceOptions</span> <span class="s">{</span> + 956 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 957 + 958 <span class="i">$OptionsInfo</span>{<span class="w">MaxExtractionDistance</span>} = <span class="i">$Options</span>{<span class="w">distance</span>}<span class="sc">;</span> + 959 <span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} = <span class="i">$Options</span>{<span class="w">distancemode</span>}<span class="sc">;</span> + 960 <span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceOrigin</span>} = <span class="i">$Options</span>{<span class="w">distanceorigin</span>} ? <span class="i">$Options</span>{<span class="w">distanceorigin</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> + 961 <span class="i">$OptionsInfo</span>{<span class="w">DistanceSelectionMode</span>} = <span class="i">$Options</span>{<span class="w">distanceselectionmode</span>}<span class="sc">;</span> + 962 + 963 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Distance$/i</span><span class="s">)</span> <span class="s">{</span> + 964 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">distanceorigin</span>}<span class="s">)</span> <span class="s">{</span> + 965 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--distanceorigin\" option in \"Distance\" \"-m, --mode\". \n"</span><span class="sc">;</span> + 966 <span class="s">}</span> + 967 <span class="i">@SpecifiedDistanceOrigin</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">distanceorigin</span>}<span class="sc">;</span> + 968 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Atom$/i</span><span class="s">)</span> <span class="s">{</span> + 969 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 970 <span class="k">die</span> <span class="q">"Error: Invalid number of values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">" for option \"distanceorigin\" option during \"Atom\" value of \"--distancemode\" : The number of values must be 2.\n"</span><span class="sc">;</span> + 971 <span class="s">}</span> + 972 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 973 <span class="k">die</span> <span class="q">"Error: Invalid atom number value, "</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">", for option \"distanceorigin\" option during \"Atom\" value of \"--distancemode\". Allowed values: > 0\n"</span><span class="sc">;</span> + 974 <span class="s">}</span> + 975 <span class="s">}</span> + 976 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Hetatm$/i</span><span class="s">)</span> <span class="s">{</span> + 977 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 978 <span class="k">die</span> <span class="q">"Error: Invalid number of values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">" for option \"distanceorigin\" option during \"Hetatm\" value of \"--distancemode\" : The number of values must be 2.\n"</span><span class="sc">;</span> + 979 <span class="s">}</span> + 980 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 981 <span class="k">die</span> <span class="q">"Error: Invalid hetatm number value, "</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">", for option \"distanceorigin\" option during \"Hetatm\" value of \"--distancemode\". Allowed values: > 0\n"</span><span class="sc">;</span> + 982 <span class="s">}</span> + 983 <span class="s">}</span> + 984 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span> + 985 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> == <span class="n">2</span> || <span class="i">@SpecifiedDistanceOrigin</span> == <span class="n">3</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 986 <span class="k">die</span> <span class="q">"Error: Invalid number of values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">" for option \"distanceorigin\" option during \"Residue\" value of \"--distancemode\" : The number of values must be either 2 or 3.\n"</span><span class="sc">;</span> + 987 <span class="s">}</span> + 988 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 989 <span class="k">die</span> <span class="q">"Error: Invalid residue number value, "</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">", for option \"distanceorigin\" option during \"Residue\" value of \"--distancemode\". Allowed values: > 0\n"</span><span class="sc">;</span> + 990 <span class="s">}</span> + 991 <span class="s">}</span> + 992 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^XYZ$/i</span><span class="s">)</span> <span class="s">{</span> + 993 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> != <span class="n">3</span><span class="s">)</span> <span class="s">{</span> + 994 <span class="k">die</span> <span class="q">"Error: Invalid number of values, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">" for option \"distanceorigin\" option during \"XYZ\" value of \"--distancemode\" : The number of values must be 3.\n"</span><span class="sc">;</span> + 995 <span class="s">}</span> + 996 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 997 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span> <span class="s">{</span> + 998 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsNumerical</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 999 <span class="k">die</span> <span class="q">"Error: Invalid coordinate value, "</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">", for option \"distanceorigin\" option during \"XYZ\" value of \"--distancemode\". Allowed values: numerical\n"</span><span class="sc">;</span> +1000 <span class="s">}</span> +1001 <span class="s">}</span> +1002 <span class="s">}</span> +1003 <span class="s">}</span> +1004 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1005 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDistanceOrigin</span><span class="sc">;</span> +1006 +1007 <span class="s">}</span> +1008 +1009 <span class="c"># Retrieve information about PDB files...</span> +<a name="RetrievePDBFilesInfo-"></a>1010 <span class="k">sub </span><span class="m">RetrievePDBFilesInfo</span> <span class="s">{</span> +1011 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$PDBFile</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">@ChainLabels</span><span class="cm">,</span> <span class="i">@ChainSequenceIDs</span><span class="cm">,</span> <span class="i">@ChainSequenceIDsPrefix</span><span class="s">)</span><span class="sc">;</span> +1012 +1013 <span class="i">%PDBFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1014 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1015 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1016 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1017 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1018 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1019 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1020 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1021 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1022 +1023 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span> +1024 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> +1025 +1026 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> +1027 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1028 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1029 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1030 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1031 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1032 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1033 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1034 +1035 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> +1036 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$PDBFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1037 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It doesn't exist\n"</span><span class="sc">;</span> +1038 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> +1039 <span class="s">}</span> +1040 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="q">"pdb"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1041 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It's not a PDB file\n"</span><span class="sc">;</span> +1042 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> +1043 <span class="s">}</span> +1044 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">PDBFILE</span><span class="cm">,</span> <span class="q">"$PDBFile"</span><span class="s">)</span> <span class="s">{</span> +1045 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: Couldn't open it: $! \n"</span><span class="sc">;</span> +1046 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> +1047 <span class="s">}</span> +1048 <span class="k">close</span> <span class="w">PDBFILE</span><span class="sc">;</span> +1049 +1050 <span class="c"># Get PDB data...</span> +1051 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span> +1052 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Sequences$/i</span> && <span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} =~ <span class="q">/^SeqRes$/i</span><span class="s">)</span> <span class="s">{</span> +1053 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="q">'SeqRes'</span><span class="s">)</span><span class="sc">;</span> +1054 <span class="s">}</span> +1055 <span class="k">else</span> <span class="s">{</span> +1056 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> +1057 <span class="s">}</span> +1058 <span class="k">if</span> <span class="s">(</span>!<span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span> +1059 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: No chains found \n"</span><span class="sc">;</span> +1060 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> +1061 <span class="s">}</span> +1062 +1063 <span class="c"># Make sure specified chains exist in PDB file...</span> +1064 <span class="i">@SpecifiedChains</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1065 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} =~ <span class="q">/^Specified$/i</span><span class="s">)</span> <span class="s">{</span> +1066 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedChains</span>}}<span class="s">)</span> <span class="s">{</span> +1067 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}<span class="s">)</span> <span class="s">{</span> +1068 <span class="k">push</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="sc">;</span> +1069 <span class="s">}</span> +1070 <span class="k">else</span> <span class="s">{</span> +1071 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: Specified chain, $ChainID, in \"-c, --chains\" option doesn't exist.\n"</span><span class="sc">;</span> +1072 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> +1073 <span class="s">}</span> +1074 <span class="s">}</span> +1075 <span class="s">}</span> +1076 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} =~ <span class="q">/^First$/i</span><span class="s">)</span> <span class="s">{</span> +1077 <span class="k">push</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}[<span class="n">0</span>]<span class="sc">;</span> +1078 <span class="s">}</span> +1079 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> +1080 <span class="k">push</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="sc">;</span> +1081 <span class="s">}</span> +1082 <span class="c"># Setup chain labels to use for sequence IDs and generating output files...</span> +1083 <span class="i">@ChainLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1084 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@SpecifiedChains</span><span class="s">)</span> <span class="s">{</span> +1085 <span class="i">$ChainLabel</span> = <span class="i">$ChainID</span><span class="sc">;</span> <span class="i">$ChainLabel</span> =~ <span class="q">s/^None//ig</span><span class="sc">;</span> +1086 <span class="i">$ChainLabel</span> = <span class="q">"Chain${ChainLabel}"</span><span class="sc">;</span> +1087 <span class="k">push</span> <span class="i">@ChainLabels</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="sc">;</span> +1088 <span class="s">}</span> +1089 +1090 <span class="c"># Make sure specified distance origin is valid...</span> +1091 <span class="i">@DistanceOrigin</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1092 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Distance$/i</span><span class="s">)</span> <span class="s">{</span> +1093 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^(Atom|Hetatm)$/i</span><span class="s">)</span> <span class="s">{</span> +1094 <span class="k">my</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$SpecifiedAtomName</span><span class="cm">,</span> <span class="i">$SpecifiedAtomNumber</span><span class="cm">,</span> <span class="i">$RecordFound</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> +1095 <span class="i">$RecordType</span> = <span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>}<span class="sc">;</span> +1096 <span class="s">(</span><span class="i">$SpecifiedAtomNumber</span><span class="cm">,</span> <span class="i">$SpecifiedAtomName</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span> +1097 <span class="i">$RecordFound</span> = <span class="n">0</span><span class="sc">;</span> +1098 <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> +1099 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1100 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> +1101 <span class="s">}</span> +1102 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> +1103 <span class="i">$AtomName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$AtomName</span><span class="s">)</span><span class="sc">;</span> +1104 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$RecordType</span> =~ <span class="q">/^Atom$/i</span> && <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> || <span class="s">(</span><span class="i">$RecordType</span> =~ <span class="q">/^Hetatm$/i</span> && <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1105 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNumber</span> == <span class="i">$SpecifiedAtomNumber</span> && <span class="i">$AtomName</span> <span class="k">eq</span> <span class="i">$SpecifiedAtomName</span><span class="s">)</span> <span class="s">{</span> +1106 <span class="i">$RecordFound</span> = <span class="n">1</span><span class="sc">;</span> +1107 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> +1108 <span class="s">}</span> +1109 <span class="s">}</span> +1110 <span class="s">}</span> +1111 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RecordFound</span><span class="s">)</span> <span class="s">{</span> +1112 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: "</span><span class="cm">,</span> <span class="k">uc</span><span class="s">(</span><span class="i">$RecordType</span><span class="s">)</span><span class="cm">,</span> <span class="q">" record corresponding to \"--distanceorigin\" option value, $OptionsInfo{ExtractionDistanceOrigin}, doesn't exist.\n"</span><span class="sc">;</span> +1113 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> +1114 <span class="s">}</span> +1115 <span class="k">push</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span> +1116 <span class="s">}</span> +1117 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span> +1118 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedResidueNumber</span><span class="cm">,</span> <span class="i">$SpecifiedResidueName</span><span class="cm">,</span> <span class="i">$SpecifiedChainID</span><span class="cm">,</span> <span class="i">$RecordFound</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> +1119 <span class="i">$SpecifiedChainID</span> = <span class="q">''</span><span class="sc">;</span> +1120 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}} == <span class="n">3</span><span class="s">)</span> <span class="s">{</span> +1121 <span class="s">(</span><span class="i">$SpecifiedResidueNumber</span><span class="cm">,</span> <span class="i">$SpecifiedResidueName</span><span class="cm">,</span> <span class="i">$SpecifiedChainID</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span> +1122 <span class="s">}</span> +1123 <span class="k">else</span> <span class="s">{</span> +1124 <span class="s">(</span><span class="i">$SpecifiedResidueNumber</span><span class="cm">,</span> <span class="i">$SpecifiedResidueName</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span> +1125 <span class="s">}</span> +1126 <span class="i">$RecordFound</span> = <span class="n">0</span><span class="sc">;</span> +1127 <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span> +1128 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1129 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> +1130 <span class="s">}</span> +1131 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span> +1132 <span class="i">$ResidueName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span><span class="sc">;</span> +1133 <span class="i">$ChainID</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="sc">;</span> +1134 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedChainID</span> && <span class="s">(</span><span class="i">$SpecifiedChainID</span> <span class="k">ne</span> <span class="i">$ChainID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1135 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> +1136 <span class="s">}</span> +1137 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueNumber</span> == <span class="i">$SpecifiedResidueNumber</span> && <span class="i">$ResidueName</span> <span class="k">eq</span> <span class="i">$SpecifiedResidueName</span><span class="s">)</span> <span class="s">{</span> +1138 <span class="c"># Store coordinates for all the atoms...</span> +1139 <span class="i">$RecordFound</span> = <span class="n">1</span><span class="sc">;</span> +1140 <span class="k">push</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span> +1141 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> +1142 <span class="s">}</span> +1143 <span class="s">}</span> +1144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RecordFound</span><span class="s">)</span> <span class="s">{</span> +1145 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: ATOM/HETATM record corresponding to \"--distanceorigin\" option value, $OptionsInfo{ExtractionDistanceOrigin}, doesn't exist.\n"</span><span class="sc">;</span> +1146 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> +1147 <span class="s">}</span> +1148 <span class="s">}</span> +1149 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^XYZ$/i</span><span class="s">)</span> <span class="s">{</span> +1150 <span class="k">push</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span> +1151 <span class="s">}</span> +1152 <span class="s">}</span> +1153 <span class="c"># Setup output file names...</span> +1154 <span class="i">@OutFileNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1155 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> +1156 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span> +1157 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@PDBFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1158 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> +1159 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> +1160 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> +1161 <span class="s">}</span> +1162 <span class="k">else</span> <span class="s">{</span> +1163 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> +1164 <span class="s">}</span> +1165 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> +1166 <span class="s">}</span> +1167 <span class="k">else</span> <span class="s">{</span> +1168 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> +1169 <span class="s">}</span> +1170 <span class="i">$Mode</span> = <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="sc">;</span> +1171 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(Atoms|CAlphas|AtomNums|AtomsRange|AtomNames|ResidueNums|ResiduesRange|ResidueNames|Distance|NonWater|NonHydrogens)$/i</span><span class="s">)</span> <span class="s">{</span> +1172 <span class="i">$OutFileName</span> = <span class="q">''</span><span class="sc">;</span> +1173 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^CAlphas$/i</span><span class="s">)</span> <span class="s">{</span> +1174 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}CAlphas.pdb"</span><span class="sc">;</span> +1175 <span class="s">}</span> +1176 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Atoms$/i</span><span class="s">)</span> <span class="s">{</span> +1177 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}Atoms.pdb"</span><span class="sc">;</span> +1178 <span class="s">}</span> +1179 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomNums$/i</span><span class="s">)</span> <span class="s">{</span> +1180 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}AtomNums.pdb"</span><span class="sc">;</span> +1181 <span class="s">}</span> +1182 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomsRange$/i</span><span class="s">)</span> <span class="s">{</span> +1183 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}AtomsRange.pdb"</span><span class="sc">;</span> +1184 <span class="s">}</span> +1185 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomNames$/i</span><span class="s">)</span> <span class="s">{</span> +1186 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}AtomNames.pdb"</span><span class="sc">;</span> +1187 <span class="s">}</span> +1188 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ResidueNums$/i</span><span class="s">)</span> <span class="s">{</span> +1189 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}ResidueNums.pdb"</span><span class="sc">;</span> +1190 <span class="s">}</span> +1191 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ResiduesRange$/i</span><span class="s">)</span> <span class="s">{</span> +1192 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}ResiduesRange.pdb"</span><span class="sc">;</span> +1193 <span class="s">}</span> +1194 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ResidueNames$/i</span><span class="s">)</span> <span class="s">{</span> +1195 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}ResidueNames.pdb"</span><span class="sc">;</span> +1196 <span class="s">}</span> +1197 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^NonWater$/i</span><span class="s">)</span> <span class="s">{</span> +1198 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}NonWater.pdb"</span><span class="sc">;</span> +1199 <span class="s">}</span> +1200 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^NonHydrogens$/i</span><span class="s">)</span> <span class="s">{</span> +1201 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}NonHydrogens.pdb"</span><span class="sc">;</span> +1202 <span class="s">}</span> +1203 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Distance$/i</span><span class="s">)</span> <span class="s">{</span> +1204 <span class="k">my</span><span class="s">(</span><span class="i">$DistanceMode</span><span class="s">)</span> = <span class="q">''</span><span class="sc">;</span> +1205 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Atom$/i</span><span class="s">)</span> <span class="s">{</span> +1206 <span class="i">$DistanceMode</span> = <span class="q">'Atom'</span><span class="sc">;</span> +1207 <span class="s">}</span> +1208 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Hetatm$/i</span><span class="s">)</span> <span class="s">{</span> +1209 <span class="i">$DistanceMode</span> = <span class="q">'Hetatm'</span><span class="sc">;</span> +1210 <span class="s">}</span> +1211 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span> +1212 <span class="i">$DistanceMode</span> = <span class="q">'Residue'</span><span class="sc">;</span> +1213 <span class="s">}</span> +1214 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^XYZ$/i</span><span class="s">)</span> <span class="s">{</span> +1215 <span class="i">$DistanceMode</span> = <span class="q">'XYZ'</span><span class="sc">;</span> +1216 <span class="s">}</span> +1217 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}DistanceBy${DistanceMode}.pdb"</span><span class="sc">;</span> +1218 <span class="s">}</span> +1219 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span> +1220 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} && <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1221 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n"</span><span class="sc">;</span> +1222 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> +1223 <span class="s">}</span> +1224 <span class="s">}</span> +1225 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(Chains|Sequences)$/i</span><span class="s">)</span> <span class="s">{</span> +1226 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChainSequences</span>}<span class="s">)</span> <span class="s">{</span> +1227 <span class="i">$OutFileName</span> = <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Chains$/i</span><span class="s">)</span> ? <span class="q">"${OutFileRoot}ExtractedChains.pdb"</span> <span class="co">:</span> <span class="q">"${OutFileRoot}SequencesChainsCombined.fasta"</span><span class="sc">;</span> +1228 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span> +1229 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} && <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1230 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n"</span><span class="sc">;</span> +1231 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> +1232 <span class="s">}</span> +1233 <span class="s">}</span> +1234 <span class="k">else</span> <span class="s">{</span> +1235 <span class="k">for</span> <span class="i">$ChainLabel</span> <span class="s">(</span><span class="i">@ChainLabels</span><span class="s">)</span> <span class="s">{</span> +1236 <span class="i">$OutFileName</span> = <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Chains$/i</span><span class="s">)</span> ? <span class="q">"${OutFileRoot}${ChainLabel}.pdb"</span> <span class="co">:</span> <span class="q">"${OutFileRoot}Sequences${ChainLabel}.fasta"</span><span class="sc">;</span> +1237 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span> +1238 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} && <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1239 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n"</span><span class="sc">;</span> +1240 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> +1241 <span class="s">}</span> +1242 <span class="s">}</span> +1243 <span class="s">}</span> +1244 <span class="s">}</span> +1245 <span class="i">@ChainSequenceIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1246 <span class="i">@ChainSequenceIDsPrefix</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1247 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Sequences$/i</span><span class="s">)</span> <span class="s">{</span> +1248 <span class="k">my</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="cm">,</span> <span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="cm">,</span> <span class="i">$IDPrefix</span><span class="s">)</span><span class="sc">;</span> +1249 <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="i">GetHeaderRecordInformation</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span> +1250 +1251 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceIDPrefixSource</span>} =~ <span class="q">/^FileName$/i</span><span class="s">)</span> <span class="s">{</span> +1252 <span class="i">$IDPrefix</span> = <span class="i">$FileName</span><span class="sc">;</span> +1253 <span class="s">}</span> +1254 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceIDPrefixSource</span>} =~ <span class="q">/^HeaderRecord$/i</span><span class="s">)</span> <span class="s">{</span> +1255 <span class="i">$IDPrefix</span> = <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$IDCode</span><span class="s">)</span> ? <span class="i">$IDCode</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> +1256 <span class="s">}</span> +1257 <span class="k">else</span> <span class="s">{</span> +1258 <span class="i">$IDPrefix</span> = <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$IDCode</span><span class="s">)</span> ? <span class="i">$IDCode</span> <span class="co">:</span> <span class="i">$FileName</span><span class="sc">;</span> +1259 <span class="s">}</span> +1260 +1261 <span class="k">for</span> <span class="i">$ChainLabel</span> <span class="s">(</span><span class="i">@ChainLabels</span><span class="s">)</span> <span class="s">{</span> +1262 <span class="k">push</span> <span class="i">@ChainSequenceIDsPrefix</span><span class="cm">,</span> <span class="i">$IDPrefix</span><span class="sc">;</span> +1263 <span class="k">push</span> <span class="i">@ChainSequenceIDs</span><span class="cm">,</span> <span class="q">"${IDPrefix}_${ChainLabel}|PDB"</span><span class="sc">;</span> +1264 <span class="s">}</span> +1265 <span class="s">}</span> +1266 +1267 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> +1268 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> +1269 +1270 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@OutFileNames</span><span class="sc">;</span> +1271 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@ChainLabels</span><span class="sc">;</span> +1272 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@ChainSequenceIDsPrefix</span><span class="sc">;</span> +1273 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@ChainSequenceIDs</span><span class="sc">;</span> +1274 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@SpecifiedChains</span><span class="sc">;</span> +1275 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@DistanceOrigin</span><span class="sc">;</span> +1276 <span class="s">}</span> +1277 <span class="s">}</span> +1278 +1279 +1280 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> +<a name="SetupScriptUsage-"></a>1281 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> +1282 +1283 <span class="c"># Retrieve all the options...</span> +1284 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1285 <span class="i">$Options</span>{<span class="w">chains</span>} = <span class="q">'First'</span><span class="sc">;</span> +1286 <span class="i">$Options</span>{<span class="w">combinechains</span>} = <span class="q">'no'</span><span class="sc">;</span> +1287 <span class="i">$Options</span>{<span class="w">distance</span>} = <span class="n">10.0</span><span class="sc">;</span> +1288 <span class="i">$Options</span>{<span class="w">distancemode</span>} = <span class="q">'XYZ'</span><span class="sc">;</span> +1289 <span class="i">$Options</span>{<span class="w">distanceselectionmode</span>} = <span class="q">'ByAtom'</span><span class="sc">;</span> +1290 <span class="i">$Options</span>{<span class="w">keepoldrecords</span>} = <span class="q">'no'</span><span class="sc">;</span> +1291 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'NonWater'</span><span class="sc">;</span> +1292 <span class="i">$Options</span>{<span class="w">modifyheader</span>} = <span class="q">'yes'</span><span class="sc">;</span> +1293 <span class="i">$Options</span>{<span class="w">nonstandardkeep</span>} = <span class="q">'yes'</span><span class="sc">;</span> +1294 <span class="i">$Options</span>{<span class="w">nonstandardcode</span>} = <span class="q">'X'</span><span class="sc">;</span> +1295 <span class="i">$Options</span>{<span class="w">sequencelength</span>} = <span class="n">80</span><span class="sc">;</span> +1296 <span class="i">$Options</span>{<span class="w">sequenceidprefix</span>} = <span class="q">'Automatic'</span><span class="sc">;</span> +1297 <span class="i">$Options</span>{<span class="w">sequencerecords</span>} = <span class="q">'Atom'</span><span class="sc">;</span> +1298 <span class="i">$Options</span>{<span class="w">waterresiduenames</span>} = <span class="q">'Automatic'</span><span class="sc">;</span> +1299 +1300 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"atoms|a=s"</span><span class="cm">,</span> <span class="q">"chains|c=s"</span><span class="cm">,</span> <span class="q">"combinechains=s"</span><span class="cm">,</span> <span class="q">"distance|d=f"</span><span class="cm">,</span> <span class="q">"distancemode=s"</span><span class="cm">,</span> <span class="q">"distanceorigin=s"</span><span class="cm">,</span> <span class="q">"distanceselectionmode=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"keepoldrecords|k=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"modifyheader=s"</span><span class="cm">,</span> <span class="q">"nonstandardkeep=s"</span><span class="cm">,</span> <span class="q">"nonstandardcode=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"recordmode=s"</span><span class="cm">,</span> <span class="q">"residues=s"</span><span class="cm">,</span> <span class="q">"sequencelength=i"</span><span class="cm">,</span> <span class="q">"sequenceidprefix=s"</span><span class="cm">,</span> <span class="q">"sequencerecords=s"</span><span class="cm">,</span> <span class="q">"waterresiduenames=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1301 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> +1302 <span class="s">}</span> +1303 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> +1304 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> +1305 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> +1306 <span class="s">}</span> +1307 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span> +1308 <span class="s">}</span> +1309 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">combinechains</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> +1310 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{combinechains}, for option \"--CombineChains\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> +1311 <span class="s">}</span> +1312 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">distancemode</span>} !~ <span class="q">/^(Atom|Hetatm|Residue|XYZ)$/i</span><span class="s">)</span> <span class="s">{</span> +1313 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{distancemode}, for option \"--DistanceMode\" is not valid. Allowed values: Atom, Hetatm, Residue, or XYZ\n"</span><span class="sc">;</span> +1314 <span class="s">}</span> +1315 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">distanceselectionmode</span>} !~ <span class="q">/^(ByAtom|ByResidue)$/i</span><span class="s">)</span> <span class="s">{</span> +1316 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{distanceselectionmode}, for option \"--DistanceSelectionMode\" is not valid. Allowed values: ByAtom or ByResidue\n"</span><span class="sc">;</span> +1317 <span class="s">}</span> +1318 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> +1319 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keepoldrecords}, for option \"--KeepOldRecords\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> +1320 <span class="s">}</span> +1321 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(Chains|Sequences|Atoms|CAlphas|AtomNums|AtomsRange|AtomNames|ResidueNums|ResidueNames|ResiduesRange|Distance|NonWater|NonHydrogens)$/i</span><span class="s">)</span> <span class="s">{</span> +1322 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"m, --mode\" is not valid. Allowed values: Chains, Sequences, Atoms, CAlphas, AtomNums, AtomsRange, AtomNames, ResidueNums, ResiduesRange, ResidueNames, Distance, NonWater, NonHydrogens\n"</span><span class="sc">;</span> +1323 <span class="s">}</span> +1324 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> +1325 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{modifyheader}, for option \"--ModifyHeader\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> +1326 <span class="s">}</span> +1327 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">nonstandardkeep</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> +1328 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{nonstandardkeep}, for option \"--NonStandardKeep\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> +1329 <span class="s">}</span> +1330 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">nonstandardcode</span>} !~ <span class="q">/^(\?|\-|X)$/i</span><span class="s">)</span> <span class="s">{</span> +1331 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{nonstandardcode}, for option \"--NonStandardCode\" is not valid. Allowed values: ?, -, or X\n"</span><span class="sc">;</span> +1332 <span class="s">}</span> +1333 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">recordmode</span>} && <span class="i">$Options</span>{<span class="w">recordmode</span>} !~ <span class="q">/^(Atom|Hetatm|AtomAndHetatm)$/i</span><span class="s">)</span> <span class="s">{</span> +1334 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{recordmode}, for option \"--RecordMode\" is not valid. Allowed values: Atom, Hetatm, AtomAndHetatm\n"</span><span class="sc">;</span> +1335 <span class="s">}</span> +1336 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1337 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{sequencelength}, for option \"--SequenceLength\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span> +1338 <span class="s">}</span> +1339 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequencerecords</span>} !~ <span class="q">/^(Atom|SeqRes)$/i</span><span class="s">)</span> <span class="s">{</span> +1340 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{sequencerecords}, for option \"--SequenceRecords\" is not valid. Allowed values: Atom or SeqRes\n"</span><span class="sc">;</span> +1341 <span class="s">}</span> +1342 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequenceidprefix</span>} !~ <span class="q">/^(FileName|HeaderRecord|Automatic)$/i</span><span class="s">)</span> <span class="s">{</span> +1343 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{sequenceidprefix}, for option \"--SequenceIDPrefix\" is not valid. Allowed values: FileName, HeaderRecord, or AutomaticAtom\n"</span><span class="sc">;</span> +1344 <span class="s">}</span> +1345 <span class="s">}</span> +1346 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>