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<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>