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+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 $</span>
+6 <span class="c">#</span>
+7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+8 <span class="c">#</span>
+9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+10 <span class="c">#</span>
+11 <span class="c"># This file is part of MayaChemTools.</span>
+12 <span class="c">#</span>
+13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+16 <span class="c"># later version.</span>
+17 <span class="c">#</span>
+18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+21 <span class="c"># details.</span>
+22 <span class="c">#</span>
+23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+27 <span class="c">#</span>
+28
+29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</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">$0</span><span class="s">)</span><span class="sc">;</span>
+48 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</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> &lt; <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">&quot;$FindBin::Bin/$ScriptName&quot;</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">&quot;pdb&quot;</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">&quot;Processing options...\n&quot;</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">&quot;Checking input PDB file(s)...\n&quot;</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">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+72 <span class="k">if</span> <span class="s">(</span><span class="i">@PDBFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+73   <span class="k">print</span> <span class="q">&quot;\nProcessing PDB files...\n&quot;</span><span class="sc">;</span>
+74 <span class="s">}</span>
+75 <span class="k">for</span> <span class="i">$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">&quot;\nProcessing file $PDBFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+78     <span class="i">ExtractFromPDBFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+79   <span class="s">}</span>
+80 <span class="s">}</span>
+81 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</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">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+86
+87 <span class="c">###############################################################################</span>
+88
+89 <span class="c"># Extract appropriate information...</span>
+<a name="ExtractFromPDBFiles-"></a>  90 <span class="k">sub </span><span class="m">ExtractFromPDBFiles</span> <span class="s">{</span>
+91   <span class="k">my</span><span class="s">(</span><span class="i">$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">&#39;AtomAndHetatm&#39;</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">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
+133
+134     <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
+135
+136     <span class="c"># Write out header and other older recors...</span>
+137     <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$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">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
+147
+148       <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
+149
+150       <span class="c"># Write out header and other older recors...</span>
+151       <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$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>-&gt;{<span class="w">Lines</span>}{<span class="i">$ChainID</span>}}<span class="s">)</span> <span class="s">{</span>
+158       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</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">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+166
+167     <span class="c"># Write out CONECT records...</span>
+168     <span class="i">$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">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+171       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+172     <span class="s">}</span>
+173
+174     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span>
+175       <span class="c"># Write out END record...</span>
+176       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+177
+178       <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
+179     <span class="s">}</span>
+180   <span class="s">}</span>
+181
+182   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;\n&quot;</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">&#39;SeqRes&#39;</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">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">Residues</span>}{<span class="i">$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>-&gt;{<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">&#39;&#39;</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">&quot;Warning: Keeping nonstandard residue $Residue in $ChainLabel...\n&quot;</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">&quot;Warning: Ignoring nonstandard residue $Residue in $ChainLabel...\n&quot;</span><span class="sc">;</span>
+236           <span class="k">next</span> <span class="j">RESIDUE</span><span class="sc">;</span>
+237         <span class="s">}</span>
+238       <span class="s">}</span>
+239       <span class="i">$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">$Sequence</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+250     <span class="k">for</span> <span class="i">$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">$FileIndex</span>][<span class="n">0</span>] . <span class="q">&quot;_CombinedChains|PDB&quot;</span><span class="sc">;</span><span class="sc">;</span>
+256     <span class="i">$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">&quot;Generating sequence file $SequenceFileName...\n&quot;</span><span class="sc">;</span>
+260     <span class="i">%SequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+261     <span class="i">@</span>{<span class="i">$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">&quot;Generating sequence file $SequenceFileName...\n&quot;</span><span class="sc">;</span>
+283       <span class="i">%SequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+284       <span class="i">@</span>{<span class="i">$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">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
+304   <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
+305
+306   <span class="c"># Write out header and other older recors...</span>
+307   <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$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> &gt;= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartAtomNum</span>} &amp;&amp; <span class="i">$AtomNumber</span> &lt;= <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">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+341
+342         <span class="i">$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">&quot;\n&quot;</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">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+353       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</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">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+361   <span class="s">}</span>
+362
+363   <span class="c"># Write out END record...</span>
+364   <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+365
+366   <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
+367 <span class="s">}</span>
+368
+369 <span class="c"># Extract residues...</span>
+<a name="ExtractByResidues-"></a> 370 <span class="k">sub </span><span class="m">ExtractByResidues</span> <span class="s">{</span>
+371   <span class="k">my</span><span class="s">(</span><span class="i">$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">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
+376   <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
+377
+378   <span class="c"># Write out header and other older recors...</span>
+379   <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$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> &gt;= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartResidueNum</span>} &amp;&amp; <span class="i">$ResidueNumber</span> &lt;= <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">$ChainRecordCount</span>++<span class="sc">;</span>
+408         <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</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">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
+415         <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+416       <span class="s">}</span>
+417       <span class="i">$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">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+421     <span class="s">}</span>
+422   <span class="s">}</span>
+423
+424   <span class="c"># Write out appropriate CONECT records...</span>
+425   <span class="i">$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">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+427     <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</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">&quot;\n&quot;</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">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
+442   <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
+443
+444   <span class="c"># Write out header and other older recors...</span>
+445   <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$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">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+457         <span class="i">$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">&quot;\n&quot;</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">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+468       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</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">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+476   <span class="s">}</span>
+477   <span class="c"># Write out END record...</span>
+478   <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+479
+480   <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
+481 <span class="s">}</span>
+482
+483 <span class="c"># Extract non hydrogen records...</span>
+<a name="ExtractNonHydrogenRecords-"></a> 484 <span class="k">sub </span><span class="m">ExtractNonHydrogenRecords</span> <span class="s">{</span>
+485   <span class="k">my</span><span class="s">(</span><span class="i">$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">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
+490   <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
+491
+492   <span class="c"># Write out header and other older recors...</span>
+493   <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$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">$ChainRecordCount</span>++<span class="sc">;</span>
+504         <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</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">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
+511         <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+512       <span class="s">}</span>
+513       <span class="i">$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">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+517     <span class="s">}</span>
+518   <span class="s">}</span>
+519
+520   <span class="c"># Write out appropriate CONECT records...</span>
+521   <span class="i">$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">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+523     <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</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">&quot;\n&quot;</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">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
+538   <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
+539
+540   <span class="c"># Write out header and other older recors...</span>
+541   <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$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">&quot;${ResidueName}_${ResidueNumber}_${ChainID}&quot;</span><span class="sc">;</span>
+567         <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$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&#39;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">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+592         <span class="i">$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">&quot;\n&quot;</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">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+603       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</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">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+611   <span class="s">}</span>
+612
+613   <span class="c"># Write out END record...</span>
+614   <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+615
+616   <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
+617 <span class="s">}</span>
+618
+619 <span class="c"># Does record type correspond to the specified record type?</span>
+<a name="CheckRecordType-"></a> 620 <span class="k">sub </span><span class="m">CheckRecordType</span> <span class="s">{</span>
+621   <span class="k">my</span><span class="s">(</span><span class="i">$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">$PDBRecordLinesRef</span>-&gt;[<span class="i">$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">$ResidueID</span> = <span class="q">&quot;${ResidueName}_${ResidueNumber}_${ChainID}&quot;</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$/i</span><span class="s">)</span> <span class="s">{</span>
+654       <span class="c"># It&#39;s a new residue line...</span>
+655       <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span>
+656     <span class="s">}</span>
+657
+658     <span class="c"># Check distance...</span>
+659     <span class="i">@Coords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">push</span> <span class="i">@Coords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$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> &lt; <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>-&gt;[<span class="n">0</span>] - <span class="i">$OriginCoordsRef</span>-&gt;[<span class="i">$Index</span>]<span class="s">)</span>**<span class="n">2</span> + <span class="s">(</span><span class="i">$CoordsRef</span>-&gt;[<span class="n">1</span>] - <span class="i">$OriginCoordsRef</span>-&gt;[<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>-&gt;[<span class="n">2</span>] - <span class="i">$OriginCoordsRef</span>-&gt;[<span class="i">$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">$Distance</span> &lt;= <span class="i">$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">$CoordsRef</span>-&gt;[<span class="i">$Index</span>] - <span class="i">$OriginCoordsRef</span>-&gt;[<span class="i">$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> &lt;= <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">&#39;Data extracted using MayaChemTools&#39;</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">$Classification</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+709   <span class="s">}</span>
+710   <span class="k">else</span> <span class="s">{</span>
+711     <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">$PDBRecordLinesRef</span>-&gt;[<span class="n">0</span>]<span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+712   <span class="s">}</span>
+713
+714   <span class="c"># Write out any old records...</span>
+715   <span class="k">if</span> <span class="s">(</span><span class="i">$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">$PDBRecordLinesRef</span>-&gt;[<span class="i">$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">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+724     <span class="s">}</span>
+725   <span class="s">}</span>
+726 <span class="s">}</span>
+727
+728 <span class="c"># Get header record information assuming it&#39;s the first record...</span>
+<a name="GetHeaderRecordInformation-"></a> 729 <span class="k">sub </span><span class="m">GetHeaderRecordInformation</span> <span class="s">{</span>
+730   <span class="k">my</span><span class="s">(</span><span class="i">$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">$IDCode</span><span class="s">)</span> = <span class="s">(</span><span class="q">&#39;&#39;</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
+734   <span class="i">$HeaderRecordLine</span> = <span class="i">$PDBRecordLinesRef</span>-&gt;[<span class="n">0</span>]<span class="sc">;</span>
+735   <span class="k">if</span> <span class="s">(</span><span class="i">IsHeaderRecordType</span><span class="s">(</span><span class="i">$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&#39;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">$ResidueName</span><span class="s">)</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+758     <span class="c"># Assume it&#39;s a nucleic acid...</span>
+759     <span class="k">if</span> <span class="s">(</span><span class="i">$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">&#39;Specified&#39;</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">&#39;HOH&#39;</span><span class="cm">,</span> <span class="q">&#39;WAT&#39;</span><span class="cm">,</span> <span class="q">&#39;H2O&#39;</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)$/i</span> ? <span class="q">&quot;Atom&quot;</span> <span class="co">:</span> <span class="q">&quot;AtomAndHetatm&quot;</span><span class="s">)</span><span class="sc">;</span>
+814
+815   <span class="i">$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">&quot;Error: You must specify a value for \&quot;--Residues\&quot; option in \&quot;ResidueNums, ResiduesRange, or ResidueNames\&quot; \&quot;-m, --mode\&quot;. \n&quot;</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">&quot;Error: Invalid residue number value, $ResidueNum, for \&quot;--Residues\&quot; option during \&quot;ResidueNumes\&quot; or \&quot;ResiduesRange\&quot;value of \&quot;-m --mode\&quot; option: Residue number must be a positive integer.\n&quot;</span><span class="sc">;</span>
+853         <span class="s">}</span>
+854       <span class="s">}</span>
+855       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResiduesRange$/i</span><span class="s">)</span> <span class="s">{</span>
+856         <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedResidueNumsList</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+857           <span class="k">die</span> <span class="q">&quot;Error: Invalid number of residue number values, &quot;</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedResidueNumsList</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;, for \&quot;--Residues\&quot; option during \&quot;ResiduesRange\&quot; value of \&quot;-m --mode\&quot; option: The number of values must be 2 corresponding to start and end residue numbers.\n&quot;</span><span class="sc">;</span>
+858         <span class="s">}</span>
+859         <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedResidueNumsList</span>[<span class="n">0</span>] &gt; <span class="i">$SpecifiedResidueNumsList</span>[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span>
+860           <span class="k">die</span> <span class="q">&quot;Error: Invalid residue number values, @SpecifiedResidueNumsList, for \&quot;--Residues\&quot; option during \&quot;ResiduesRange\&quot; value of \&quot;-m --mode\&quot; option: The start residue number must be less than end residue number.\n&quot;</span><span class="sc">;</span>
+861         <span class="s">}</span>
+862         <span class="s">(</span><span class="i">$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">&quot;Error: You must specify a value for \&quot;--Atoms\&quot; option in \&quot;AtomNums, AtomsRange, or AtomNames\&quot; \&quot;-m, --mode\&quot;. \n&quot;</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">&quot;Error: Invalid atom number value, $AtomNum, for \&quot;--Atoms\&quot; option during \&quot;AtomNums\&quot; or \&quot;AtomsRange\&quot;value of \&quot;-m --mode\&quot; option: Atom number must be a positive integer.\n&quot;</span><span class="sc">;</span>
+914         <span class="s">}</span>
+915       <span class="s">}</span>
+916       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomsRange$/i</span><span class="s">)</span> <span class="s">{</span>
+917         <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedAtomNumsList</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+918           <span class="k">die</span> <span class="q">&quot;Error: Invalid number of atom number values, &quot;</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedAtomNumsList</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;, for \&quot;--Atoms\&quot; option during \&quot;AtomsRange\&quot; value of \&quot;-m --mode\&quot; option: The number of values must be 2 corresponding to start and end atom numbers.\n&quot;</span><span class="sc">;</span>
+919         <span class="s">}</span>
+920         <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedAtomNumsList</span>[<span class="n">0</span>] &gt; <span class="i">$SpecifiedAtomNumsList</span>[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span>
+921           <span class="k">die</span> <span class="q">&quot;Error: Invalid atom number values, @SpecifiedAtomNumsList, for \&quot;--Atoms\&quot; option during \&quot;AtomsRange\&quot; value of \&quot;-m --mode\&quot; option: The start atom number must be less than end atom number.\n&quot;</span><span class="sc">;</span>
+922         <span class="s">}</span>
+923         <span class="s">(</span><span class="i">$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$/i</span><span class="s">)</span> <span class="s">{</span>
+928     <span class="i">@SpecifiedAtomNamesList</span> = <span class="s">(</span><span class="q">&quot;CA&quot;</span><span class="s">)</span><span class="sc">;</span>
+929   <span class="s">}</span>
+930
+931   <span class="i">@</span>{<span class="i">$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">&#39;&#39;</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">$Options</span>{<span class="w">distanceorigin</span>}<span class="s">)</span> <span class="s">{</span>
+965       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--distanceorigin\&quot; option in \&quot;Distance\&quot; \&quot;-m, --mode\&quot;. \n&quot;</span><span class="sc">;</span>
+966     <span class="s">}</span>
+967     <span class="i">@SpecifiedDistanceOrigin</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$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">&quot;Error: Invalid number of values, &quot;</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">&quot; for option \&quot;distanceorigin\&quot; option during \&quot;Atom\&quot; value of \&quot;--distancemode\&quot; : The number of values must be 2.\n&quot;</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">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+973         <span class="k">die</span> <span class="q">&quot;Error: Invalid atom number value, &quot;</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">&quot;, for option \&quot;distanceorigin\&quot; option during \&quot;Atom\&quot; value of \&quot;--distancemode\&quot;. Allowed values: &gt; 0\n&quot;</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">&quot;Error: Invalid number of values, &quot;</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">&quot; for option \&quot;distanceorigin\&quot; option during \&quot;Hetatm\&quot; value of \&quot;--distancemode\&quot; : The number of values must be 2.\n&quot;</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">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+981         <span class="k">die</span> <span class="q">&quot;Error: Invalid hetatm number value, &quot;</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">&quot;, for option \&quot;distanceorigin\&quot; option during \&quot;Hetatm\&quot; value of \&quot;--distancemode\&quot;. Allowed values: &gt; 0\n&quot;</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">&quot;Error: Invalid number of values, &quot;</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">&quot; for option \&quot;distanceorigin\&quot; option during \&quot;Residue\&quot; value of \&quot;--distancemode\&quot; : The number of values must be either 2 or 3.\n&quot;</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">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+989         <span class="k">die</span> <span class="q">&quot;Error: Invalid residue number value, &quot;</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">&quot;, for option \&quot;distanceorigin\&quot; option during \&quot;Residue\&quot; value of \&quot;--distancemode\&quot;. Allowed values: &gt; 0\n&quot;</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">&quot;Error: Invalid number of values, &quot;</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">&quot; for option \&quot;distanceorigin\&quot; option during \&quot;XYZ\&quot; value of \&quot;--distancemode\&quot; : The number of values must be 3.\n&quot;</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">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+999           <span class="k">die</span> <span class="q">&quot;Error: Invalid coordinate value, &quot;</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">&quot;, for option \&quot;distanceorigin\&quot; option during \&quot;XYZ\&quot; value of \&quot;--distancemode\&quot;. Allowed values: numerical\n&quot;</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">&#39;&#39;</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">&quot;Warning: Ignoring file $PDBFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+1038       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+1039     <span class="s">}</span>
+1040     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="q">&quot;pdb&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1041       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: It&#39;s not a PDB file\n&quot;</span><span class="sc">;</span>
+1042       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+1043     <span class="s">}</span>
+1044     <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">PDBFILE</span><span class="cm">,</span> <span class="q">&quot;$PDBFile&quot;</span><span class="s">)</span> <span class="s">{</span>
+1045       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+1046       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+1047     <span class="s">}</span>
+1048     <span class="k">close</span> <span class="w">PDBFILE</span><span class="sc">;</span>
+1049
+1050     <span class="c"># Get PDB data...</span>
+1051     <span class="i">$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$/i</span> &amp;&amp; <span class="i">$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">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="q">&#39;SeqRes&#39;</span><span class="s">)</span><span class="sc">;</span>
+1054     <span class="s">}</span>
+1055     <span class="k">else</span> <span class="s">{</span>
+1056       <span class="i">$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>-&gt;{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+1059       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: No chains found \n&quot;</span><span class="sc">;</span>
+1060       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+1061     <span class="s">}</span>
+1062
+1063     <span class="c"># Make sure specified chains exist in PDB file...</span>
+1064     <span class="i">@SpecifiedChains</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+1065     <span class="k">if</span> <span class="s">(</span><span class="i">$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>-&gt;{<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">&quot;Warning: Ignoring file $PDBFile: Specified chain, $ChainID, in \&quot;-c, --chains\&quot; option doesn&#39;t exist.\n&quot;</span><span class="sc">;</span>
+1072           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+1073         <span class="s">}</span>
+1074       <span class="s">}</span>
+1075     <span class="s">}</span>
+1076     <span class="k">elsif</span> <span class="s">(</span><span class="i">$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>-&gt;{<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">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}}<span class="sc">;</span>
+1081     <span class="s">}</span>
+1082     <span class="c"># Setup chain labels to use for sequence IDs and generating output files...</span>
+1083     <span class="i">@ChainLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+1084     <span class="k">for</span> <span class="i">$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">&quot;Chain${ChainLabel}&quot;</span><span class="sc">;</span>
+1087       <span class="k">push</span> <span class="i">@ChainLabels</span><span class="cm">,</span> <span class="i">$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$/i</span> &amp;&amp; <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$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> &amp;&amp; <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">$SpecifiedAtomNumber</span> &amp;&amp; <span class="i">$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">&quot;Warning: Ignoring file $PDBFile: &quot;</span><span class="cm">,</span> <span class="k">uc</span><span class="s">(</span><span class="i">$RecordType</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot; record corresponding to \&quot;--distanceorigin\&quot; option value, $OptionsInfo{ExtractionDistanceOrigin}, doesn&#39;t exist.\n&quot;</span><span class="sc">;</span>
+1113           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+1114         <span class="s">}</span>
+1115         <span class="k">push</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="s">(</span><span class="i">$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">&#39;&#39;</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">$SpecifiedChainID</span> &amp;&amp; <span class="s">(</span><span class="i">$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">$SpecifiedResidueNumber</span> &amp;&amp; <span class="i">$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">&quot;Warning: Ignoring file $PDBFile: ATOM/HETATM record corresponding to \&quot;--distanceorigin\&quot; option value, $OptionsInfo{ExtractionDistanceOrigin}, doesn&#39;t exist.\n&quot;</span><span class="sc">;</span>
+1146           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+1147         <span class="s">}</span>
+1148       <span class="s">}</span>
+1149       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">$FileDir</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+1156     <span class="s">(</span><span class="i">$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>} &amp;&amp; <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">$RootFileName</span> &amp;&amp; <span class="i">$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">$OutFileName</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+1173       <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;${OutFileRoot}CAlphas.pdb&quot;</span><span class="sc">;</span>
+1175       <span class="s">}</span>
+1176       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&quot;${OutFileRoot}Atoms.pdb&quot;</span><span class="sc">;</span>
+1178       <span class="s">}</span>
+1179       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&quot;${OutFileRoot}AtomNums.pdb&quot;</span><span class="sc">;</span>
+1181       <span class="s">}</span>
+1182       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&quot;${OutFileRoot}AtomsRange.pdb&quot;</span><span class="sc">;</span>
+1184       <span class="s">}</span>
+1185       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&quot;${OutFileRoot}AtomNames.pdb&quot;</span><span class="sc">;</span>
+1187       <span class="s">}</span>
+1188       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&quot;${OutFileRoot}ResidueNums.pdb&quot;</span><span class="sc">;</span>
+1190       <span class="s">}</span>
+1191       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&quot;${OutFileRoot}ResiduesRange.pdb&quot;</span><span class="sc">;</span>
+1193       <span class="s">}</span>
+1194       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&quot;${OutFileRoot}ResidueNames.pdb&quot;</span><span class="sc">;</span>
+1196       <span class="s">}</span>
+1197       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&quot;${OutFileRoot}NonWater.pdb&quot;</span><span class="sc">;</span>
+1199       <span class="s">}</span>
+1200       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&quot;${OutFileRoot}NonHydrogens.pdb&quot;</span><span class="sc">;</span>
+1202       <span class="s">}</span>
+1203       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&#39;&#39;</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">$DistanceMode</span> = <span class="q">&#39;Atom&#39;</span><span class="sc">;</span>
+1207         <span class="s">}</span>
+1208         <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&#39;Hetatm&#39;</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">$DistanceMode</span> = <span class="q">&#39;Residue&#39;</span><span class="sc">;</span>
+1213         <span class="s">}</span>
+1214         <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">&#39;XYZ&#39;</span><span class="sc">;</span>
+1216         <span class="s">}</span>
+1217         <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}DistanceBy${DistanceMode}.pdb&quot;</span><span class="sc">;</span>
+1218       <span class="s">}</span>
+1219       <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span>
+1220       <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} &amp;&amp; <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1221         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n&quot;</span><span class="sc">;</span>
+1222         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+1223       <span class="s">}</span>
+1224     <span class="s">}</span>
+1225     <span class="k">elsif</span> <span class="s">(</span><span class="i">$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$/i</span><span class="s">)</span> ? <span class="q">&quot;${OutFileRoot}ExtractedChains.pdb&quot;</span> <span class="co">:</span> <span class="q">&quot;${OutFileRoot}SequencesChainsCombined.fasta&quot;</span><span class="sc">;</span>
+1228         <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span>
+1229         <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} &amp;&amp; <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1230           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n&quot;</span><span class="sc">;</span>
+1231           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+1232         <span class="s">}</span>
+1233       <span class="s">}</span>
+1234       <span class="k">else</span> <span class="s">{</span>
+1235         <span class="k">for</span> <span class="i">$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$/i</span><span class="s">)</span> ? <span class="q">&quot;${OutFileRoot}${ChainLabel}.pdb&quot;</span> <span class="co">:</span> <span class="q">&quot;${OutFileRoot}Sequences${ChainLabel}.fasta&quot;</span><span class="sc">;</span>
+1237           <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span>
+1238           <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} &amp;&amp; <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1239             <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n&quot;</span><span class="sc">;</span>
+1240             <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+1241           <span class="s">}</span>
+1242         <span class="s">}</span>
+1243       <span class="s">}</span>
+1244     <span class="s">}</span>
+1245     <span class="i">@ChainSequenceIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+1246     <span class="i">@ChainSequenceIDsPrefix</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+1247     <span class="k">if</span> <span class="s">(</span><span class="i">$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">$IDCode</span> <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
+1256       <span class="s">}</span>
+1257       <span class="k">else</span> <span class="s">{</span>
+1258         <span class="i">$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">$IDPrefix</span><span class="sc">;</span>
+1263         <span class="k">push</span> <span class="i">@ChainSequenceIDs</span><span class="cm">,</span> <span class="q">&quot;${IDPrefix}_${ChainLabel}|PDB&quot;</span><span class="sc">;</span>
+1264       <span class="s">}</span>
+1265     <span class="s">}</span>
+1266
+1267     <span class="i">$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">$Options</span>{<span class="w">chains</span>} = <span class="q">&#39;First&#39;</span><span class="sc">;</span>
+1286   <span class="i">$Options</span>{<span class="w">combinechains</span>} = <span class="q">&#39;no&#39;</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">&#39;XYZ&#39;</span><span class="sc">;</span>
+1289   <span class="i">$Options</span>{<span class="w">distanceselectionmode</span>} = <span class="q">&#39;ByAtom&#39;</span><span class="sc">;</span>
+1290   <span class="i">$Options</span>{<span class="w">keepoldrecords</span>} = <span class="q">&#39;no&#39;</span><span class="sc">;</span>
+1291   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;NonWater&#39;</span><span class="sc">;</span>
+1292   <span class="i">$Options</span>{<span class="w">modifyheader</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+1293   <span class="i">$Options</span>{<span class="w">nonstandardkeep</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+1294   <span class="i">$Options</span>{<span class="w">nonstandardcode</span>} = <span class="q">&#39;X&#39;</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">&#39;Automatic&#39;</span><span class="sc">;</span>
+1297   <span class="i">$Options</span>{<span class="w">sequencerecords</span>} = <span class="q">&#39;Atom&#39;</span><span class="sc">;</span>
+1298   <span class="i">$Options</span>{<span class="w">waterresiduenames</span>} = <span class="q">&#39;Automatic&#39;</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">&quot;atoms|a=s&quot;</span><span class="cm">,</span> <span class="q">&quot;chains|c=s&quot;</span><span class="cm">,</span> <span class="q">&quot;combinechains=s&quot;</span><span class="cm">,</span> <span class="q">&quot;distance|d=f&quot;</span><span class="cm">,</span> <span class="q">&quot;distancemode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;distanceorigin=s&quot;</span><span class="cm">,</span> <span class="q">&quot;distanceselectionmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;keepoldrecords|k=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;modifyheader=s&quot;</span><span class="cm">,</span> <span class="q">&quot;nonstandardkeep=s&quot;</span><span class="cm">,</span> <span class="q">&quot;nonstandardcode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;recordmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;residues=s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequencelength=i&quot;</span><span class="cm">,</span> <span class="q">&quot;sequenceidprefix=s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequencerecords=s&quot;</span><span class="cm">,</span> <span class="q">&quot;waterresiduenames=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+1301     <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+1302   <span class="s">}</span>
+1303   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+1306     <span class="s">}</span>
+1307     <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
+1308   <span class="s">}</span>
+1309   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{combinechains}, for option \&quot;--CombineChains\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
+1311   <span class="s">}</span>
+1312   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{distancemode}, for option \&quot;--DistanceMode\&quot; is not valid. Allowed values: Atom, Hetatm, Residue, or XYZ\n&quot;</span><span class="sc">;</span>
+1314   <span class="s">}</span>
+1315   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{distanceselectionmode}, for option \&quot;--DistanceSelectionMode\&quot; is not valid. Allowed values: ByAtom or ByResidue\n&quot;</span><span class="sc">;</span>
+1317   <span class="s">}</span>
+1318   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{keepoldrecords}, for option \&quot;--KeepOldRecords\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
+1320   <span class="s">}</span>
+1321   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{mode}, for option \&quot;m, --mode\&quot; is not valid. Allowed values: Chains, Sequences, Atoms, CAlphas, AtomNums, AtomsRange, AtomNames, ResidueNums, ResiduesRange, ResidueNames, Distance, NonWater, NonHydrogens\n&quot;</span><span class="sc">;</span>
+1323   <span class="s">}</span>
+1324   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{modifyheader}, for option \&quot;--ModifyHeader\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
+1326   <span class="s">}</span>
+1327   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{nonstandardkeep}, for option \&quot;--NonStandardKeep\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
+1329   <span class="s">}</span>
+1330   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{nonstandardcode}, for option \&quot;--NonStandardCode\&quot; is not valid. Allowed values: ?, -, or X\n&quot;</span><span class="sc">;</span>
+1332   <span class="s">}</span>
+1333   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">recordmode</span>} &amp;&amp; <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">&quot;Error: The value specified, $Options{recordmode}, for option \&quot;--RecordMode\&quot; is not valid. Allowed values: Atom, Hetatm, AtomAndHetatm\n&quot;</span><span class="sc">;</span>
+1335   <span class="s">}</span>
+1336   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{sequencelength}, for option \&quot;--SequenceLength\&quot; is not valid. Allowed values: &gt;0\n&quot;</span><span class="sc">;</span>
+1338   <span class="s">}</span>
+1339   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{sequencerecords}, for option \&quot;--SequenceRecords\&quot; is not valid. Allowed values: Atom or SeqRes\n&quot;</span><span class="sc">;</span>
+1341   <span class="s">}</span>
+1342   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{sequenceidprefix}, for option \&quot;--SequenceIDPrefix\&quot; is not valid. Allowed values: FileName, HeaderRecord, or AutomaticAtom\n&quot;</span><span class="sc">;</span>
+1344   <span class="s">}</span>
+1345 <span class="s">}</span>
+1346
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>

Mercurial > repos > deepakjadmin > mayatool3_test3

comparison mayachemtools/docs/scripts/html/code/ExtractFromPDBFiles.html @ 0:73ae111cf86f draft