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+1 #!/usr/bin/perl -w
+2 <span class="c">#</span>
+3 <span class="c"># $RCSfile: ModifyPDBFiles.pl,v $</span>
+4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
+5 <span class="c"># $Revision: 1.25 $</span>
+6 <span class="c">#</span>
+7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+8 <span class="c">#</span>
+9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+10 <span class="c">#</span>
+11 <span class="c"># This file is part of MayaChemTools.</span>
+12 <span class="c">#</span>
+13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+16 <span class="c"># later version.</span>
+17 <span class="c">#</span>
+18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+21 <span class="c"># details.</span>
+22 <span class="c">#</span>
+23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+27 <span class="c">#</span>
+28
+29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$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
+39 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span>
+40
+41 <span class="c"># Autoflush STDOUT</span>
+42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+43
+44 <span class="c"># Starting message...</span>
+45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
+46 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
+47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+48
+49 <span class="c"># Get the options and setup script...</span>
+50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+52   <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">&quot;$FindBin::Bin/$ScriptName&quot;</span><span class="s">)</span><span class="sc">;</span>
+53 <span class="s">}</span>
+54
+55 <span class="k">my</span><span class="s">(</span><span class="i">@PDBFilesList</span><span class="s">)</span><span class="sc">;</span>
+56 <span class="i">@PDBFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">&quot;pdb&quot;</span><span class="s">)</span><span class="sc">;</span>
+57
+58 <span class="c"># Process options...</span>
+59 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+60 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+62
+63 <span class="c"># Setup information about input files...</span>
+64 <span class="k">print</span> <span class="q">&quot;Checking input PDB file(s)...\n&quot;</span><span class="sc">;</span>
+65 <span class="k">my</span><span class="s">(</span><span class="i">%PDBFilesInfo</span><span class="s">)</span><span class="sc">;</span>
+66 <span class="i">RetrievePDBFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+67
+68 <span class="c"># Process input files..</span>
+69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+70 <span class="k">if</span> <span class="s">(</span><span class="i">@PDBFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+71   <span class="k">print</span> <span class="q">&quot;\nProcessing PDB files...\n&quot;</span><span class="sc">;</span>
+72 <span class="s">}</span>
+73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
+74   <span class="k">if</span> <span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+75     <span class="k">print</span> <span class="q">&quot;\nProcessing file $PDBFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+76     <span class="i">ModifyPDBFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+77   <span class="s">}</span>
+78 <span class="s">}</span>
+79 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+80
+81 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+82 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span>
+83 <span class="k">print</span> <span class="q">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+84
+85 <span class="c">###############################################################################</span>
+86
+87 <span class="c"># Modify appropriate information...</span>
+<a name="ModifyPDBFiles-"></a>  88 <span class="k">sub </span><span class="m">ModifyPDBFiles</span> <span class="s">{</span>
+89   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+90   <span class="k">my</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+91
+92   <span class="c"># Get PDB data...</span>
+93   <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+94   <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
+95
+96   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberAtoms$/i</span><span class="s">)</span> <span class="s">{</span>
+97     <span class="i">RenumberAtoms</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+98   <span class="s">}</span>
+99   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberResidues$/i</span><span class="s">)</span> <span class="s">{</span>
+100     <span class="i">RenumberResidues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+101   <span class="s">}</span>
+102   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberWaters$/i</span><span class="s">)</span> <span class="s">{</span>
+103     <span class="i">RenumberWaters</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+104   <span class="s">}</span>
+105   <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenameChainIDs$/i</span><span class="s">)</span> <span class="s">{</span>
+106     <span class="i">RenameChainsIDs</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+107   <span class="s">}</span>
+108 <span class="s">}</span>
+109
+110 <span class="c"># Renumber atom and hetro atom numbers...</span>
+<a name="RenumberAtoms-"></a> 111 <span class="k">sub </span><span class="m">RenumberAtoms</span> <span class="s">{</span>
+112   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+113   <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span>  <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="cm">,</span> <span class="i">$NewAtomNumber</span><span class="cm">,</span> <span class="i">$RecordType</span><span class="cm">,</span> <span class="i">%OldToNewAtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
+114
+115   <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
+116   <span class="k">print</span> <span class="q">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
+117   <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
+118
+119   <span class="c"># Write out header and other older recors...</span>
+120   <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+121
+122   <span class="c"># Write out all ATOM records along with TER and model records to indicate</span>
+123   <span class="c"># chains and multiple models..</span>
+124   <span class="i">%OldToNewAtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+125   <span class="i">$NewAtomNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>}<span class="sc">;</span>
+126   <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+127     <span class="k">if</span> <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+128       <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+129
+130       <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+131
+132       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$NewAtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+133
+134       <span class="i">$OldToNewAtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$NewAtomNumber</span><span class="sc">;</span>
+135       <span class="i">$NewAtomNumber</span>++<span class="sc">;</span>
+136     <span class="s">}</span>
+137     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+138       <span class="i">$NewAtomNumber</span>++<span class="sc">;</span>
+139       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$NewAtomNumber</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+140     <span class="s">}</span>
+141     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+142       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+143     <span class="s">}</span>
+144     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+145       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+146       <span class="c"># Restart numbering...</span>
+147       <span class="i">$NewAtomNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>}<span class="sc">;</span>
+148     <span class="s">}</span>
+149   <span class="s">}</span>
+150
+151   <span class="c"># Write out modified CONECT records...</span>
+152   <span class="k">my</span><span class="s">(</span><span class="i">$ModifiedConectAtomNum</span><span class="cm">,</span> <span class="i">$ConectAtomNum</span><span class="cm">,</span> <span class="i">@ConectAtomNums</span><span class="cm">,</span> <span class="i">@ModifiedConectAtomNums</span><span class="s">)</span><span class="sc">;</span>
+153   <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+154     <span class="k">if</span> <span class="s">(</span>!<span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+155       <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
+156     <span class="s">}</span>
+157     <span class="i">@ConectAtomNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+158     <span class="i">@ModifiedConectAtomNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+159     <span class="k">push</span> <span class="i">@ConectAtomNums</span><span class="cm">,</span> <span class="i">ParseConectRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+160     <span class="j">ATOMNUMBER:</span> <span class="k">for</span> <span class="i">$ConectAtomNum</span> <span class="s">(</span><span class="i">@ConectAtomNums</span><span class="s">)</span> <span class="s">{</span>
+161       <span class="i">$ModifiedConectAtomNum</span> = <span class="i">$ConectAtomNum</span><span class="sc">;</span>
+162       <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ConectAtomNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+163         <span class="i">$AtomNumber</span> = <span class="i">$ConectAtomNum</span><span class="sc">;</span>
+164         <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNumber</span><span class="s">)</span> <span class="s">{</span>
+165           <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OldToNewAtomNumbersMap</span>{<span class="i">$AtomNumber</span>}<span class="s">)</span> <span class="s">{</span>
+166             <span class="i">$ModifiedConectAtomNum</span> = <span class="i">$OldToNewAtomNumbersMap</span>{<span class="i">$AtomNumber</span>}<span class="sc">;</span>
+167           <span class="s">}</span>
+168         <span class="s">}</span>
+169       <span class="s">}</span>
+170       <span class="k">push</span> <span class="i">@ModifiedConectAtomNums</span><span class="cm">,</span> <span class="i">$ModifiedConectAtomNum</span><span class="sc">;</span>
+171     <span class="s">}</span>
+172     <span class="c"># Write out the record...</span>
+173     <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateConectRecordLine</span><span class="s">(</span><span class="i">@ModifiedConectAtomNums</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+174   <span class="s">}</span>
+175
+176   <span class="c"># Write out END record...</span>
+177   <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+178
+179   <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
+180 <span class="s">}</span>
+181
+182 <span class="c"># Renumber residues...</span>
+<a name="RenumberResidues-"></a> 183 <span class="k">sub </span><span class="m">RenumberResidues</span> <span class="s">{</span>
+184   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+185   <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span>  <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="cm">,</span> <span class="i">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$NewHetatmResidueNumber</span><span class="cm">,</span> <span class="i">$TERCount</span><span class="cm">,</span> <span class="i">$TotalTERCount</span><span class="cm">,</span> <span class="i">$PreviousResidueNumber</span><span class="cm">,</span> <span class="i">$PreviousHetatmResidueNumber</span><span class="cm">,</span> <span class="i">$RecordType</span><span class="s">)</span><span class="sc">;</span>
+186
+187   <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
+188   <span class="k">print</span> <span class="q">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
+189   <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
+190
+191   <span class="c"># Write out header and other older recors...</span>
+192   <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+193
+194   <span class="c"># Do a quick count of all TER records...</span>
+195   <span class="i">$TotalTERCount</span> = <span class="n">0</span><span class="sc">;</span>
+196   <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+197     <span class="k">if</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+198       <span class="i">$TotalTERCount</span>++<span class="sc">;</span>
+199     <span class="s">}</span>
+200   <span class="s">}</span>
+201
+202   <span class="c"># Write out all ATOM records along with TER and model records to indicate</span>
+203   <span class="c"># chains and multiple models..</span>
+204   <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>}<span class="sc">;</span>
+205   <span class="i">$NewHetatmResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingHetatmResidueNumber</span>}<span class="sc">;</span>
+206
+207   <span class="i">$TERCount</span> = <span class="n">0</span><span class="sc">;</span>
+208   <span class="i">$PreviousResidueNumber</span> = <span class="n">0</span><span class="sc">;</span>
+209   <span class="i">$PreviousHetatmResidueNumber</span> = <span class="n">0</span><span class="sc">;</span>
+210
+211   <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+212     <span class="k">if</span> <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="s">(</span><span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$TERCount</span> &lt; <span class="i">$TotalTERCount</span> || <span class="i">$OptionsInfo</span>{<span class="w">HetatmResidueNumberMode</span>} =~ <span class="q">/^Automatic$/i</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+213       <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+214       <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+215
+216       <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousResidueNumber</span> &amp;&amp; <span class="i">$PreviousResidueNumber</span> != <span class="i">$ResidueNumber</span><span class="s">)</span> <span class="s">{</span>
+217         <span class="i">$PreviousResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span>
+218         <span class="i">$NewResidueNumber</span>++<span class="sc">;</span>
+219       <span class="s">}</span>
+220       <span class="k">else</span> <span class="s">{</span>
+221         <span class="c"># First residue in a chain...</span>
+222         <span class="i">$PreviousResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span>
+223       <span class="s">}</span>
+224       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+225
+226     <span class="s">}</span>
+227     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+228       <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+229
+230       <span class="c"># User HETATM residue numbers...</span>
+231       <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousHetatmResidueNumber</span> &amp;&amp; <span class="i">$PreviousHetatmResidueNumber</span> != <span class="i">$ResidueNumber</span><span class="s">)</span> <span class="s">{</span>
+232         <span class="i">$PreviousHetatmResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span>
+233         <span class="i">$NewHetatmResidueNumber</span>++<span class="sc">;</span>
+234       <span class="s">}</span>
+235       <span class="k">else</span> <span class="s">{</span>
+236         <span class="c"># First HETATM residue outside a chain...</span>
+237         <span class="i">$PreviousHetatmResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span>
+238       <span class="s">}</span>
+239
+240       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateHetatmRecordLine</span><span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$NewHetatmResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+241     <span class="s">}</span>
+242     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+243       <span class="i">$TERCount</span>++<span class="sc">;</span>
+244       <span class="i">$AtomNumber</span>++<span class="sc">;</span>
+245       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+246       <span class="c"># For per chain numbering, start over again...</span>
+247       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ResidueNumberMode</span>} =~ <span class="q">/^PerChain$/i</span><span class="s">)</span> <span class="s">{</span>
+248         <span class="k">if</span> <span class="s">(</span><span class="i">$TERCount</span> &lt; <span class="i">$TotalTERCount</span> <span class="s">)</span> <span class="s">{</span>
+249           <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>}<span class="sc">;</span>
+250         <span class="s">}</span>
+251         <span class="i">$PreviousResidueNumber</span> = <span class="n">0</span><span class="sc">;</span>
+252       <span class="s">}</span>
+253     <span class="s">}</span>
+254     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+255       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+256     <span class="s">}</span>
+257     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+258       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+259     <span class="s">}</span>
+260   <span class="s">}</span>
+261
+262   <span class="c"># Write out CONECT records...</span>
+263   <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+264     <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+265       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+266     <span class="s">}</span>
+267   <span class="s">}</span>
+268
+269   <span class="c"># Write out END record...</span>
+270   <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+271
+272   <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
+273 <span class="s">}</span>
+274
+275 <span class="c"># Renumber water residues...</span>
+<a name="RenumberWaters-"></a> 276 <span class="k">sub </span><span class="m">RenumberWaters</span> <span class="s">{</span>
+277   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+278   <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span>  <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="cm">,</span> <span class="i">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$RecordType</span><span class="s">)</span><span class="sc">;</span>
+279
+280   <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
+281   <span class="k">print</span> <span class="q">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
+282   <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
+283
+284   <span class="c"># Write out header and other older recors...</span>
+285   <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+286
+287   <span class="c"># Write out all ATOM records along with TER and model records to indicate</span>
+288   <span class="c"># chains and multiple models..</span>
+289   <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingWaterResidueNumber</span>}<span class="sc">;</span>
+290   <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+291     <span class="k">if</span> <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+292       <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+293
+294       <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+295
+296       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$ResidueName</span>}<span class="s">)</span> <span class="s">{</span>
+297         <span class="i">$ResidueNumber</span> = <span class="i">$NewResidueNumber</span><span class="sc">;</span>
+298         <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+299         <span class="i">$NewResidueNumber</span>++<span class="sc">;</span>
+300       <span class="s">}</span>
+301       <span class="k">else</span> <span class="s">{</span>
+302         <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+303       <span class="s">}</span>
+304     <span class="s">}</span>
+305     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+306       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+307     <span class="s">}</span>
+308     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+309       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+310     <span class="s">}</span>
+311     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+312       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+313     <span class="s">}</span>
+314   <span class="s">}</span>
+315
+316   <span class="c"># Write out CONECT records...</span>
+317   <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+318     <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+319       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+320     <span class="s">}</span>
+321   <span class="s">}</span>
+322
+323   <span class="c"># Write out END record...</span>
+324   <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+325
+326   <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
+327 <span class="s">}</span>
+328
+329 <span class="c"># Rename chain IDs...</span>
+<a name="RenameChainsIDs-"></a> 330 <span class="k">sub </span><span class="m">RenameChainsIDs</span> <span class="s">{</span>
+331   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+332   <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span>  <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="cm">,</span> <span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$PreviousChainID</span><span class="cm">,</span> <span class="i">$FirstChainID</span><span class="cm">,</span> <span class="i">$NewChainID</span><span class="cm">,</span> <span class="i">$NewChainIDCounter</span><span class="cm">,</span> <span class="i">%OldToNewChainIDsMap</span><span class="s">)</span><span class="sc">;</span>
+333
+334   <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
+335   <span class="k">print</span> <span class="q">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
+336   <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
+337
+338   <span class="c"># Write out header and other older recors...</span>
+339   <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+340
+341   <span class="c"># Write out all ATOM records along with TER and model records to indicate</span>
+342   <span class="c"># chains and multiple models..</span>
+343   <span class="i">%OldToNewChainIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+344   <span class="i">$NewChainIDCounter</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingChainID</span>}<span class="sc">;</span>
+345   <span class="i">$FirstChainID</span> = <span class="n">1</span><span class="sc">;</span>
+346   <span class="i">$PreviousChainID</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+347   <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+348     <span class="k">if</span> <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+349       <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+350
+351       <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+352
+353       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$ResidueName</span>}<span class="s">)</span> <span class="s">{</span>
+354         <span class="c"># Chain IDs are not assigned to water residues...</span>
+355         <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+356         <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
+357       <span class="s">}</span>
+358
+359       <span class="k">if</span> <span class="s">(</span><span class="i">$FirstChainID</span><span class="s">)</span> <span class="s">{</span>
+360         <span class="i">$FirstChainID</span> = <span class="n">0</span><span class="sc">;</span>
+361         <span class="i">$PreviousChainID</span> = <span class="i">$ChainID</span><span class="sc">;</span>
+362         <span class="k">if</span> <span class="s">(</span><span class="i">$ChainID</span> || <span class="s">(</span>!<span class="i">$ChainID</span> &amp;&amp; <span class="i">$OptionsInfo</span>{<span class="w">RenameEmptyChainIDs</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+363           <span class="i">$NewChainID</span> = <span class="i">$NewChainIDCounter</span><span class="sc">;</span>
+364           <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>} = <span class="i">$NewChainID</span><span class="sc">;</span>
+365         <span class="s">}</span>
+366         <span class="k">else</span> <span class="s">{</span>
+367           <span class="i">$NewChainID</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+368         <span class="s">}</span>
+369       <span class="s">}</span>
+370       <span class="k">elsif</span> <span class="s">(</span><span class="i">$PreviousChainID</span> <span class="k">ne</span> <span class="i">$ChainID</span><span class="s">)</span> <span class="s">{</span>
+371         <span class="k">if</span> <span class="s">(</span><span class="i">$ChainID</span> || <span class="s">(</span>!<span class="i">$ChainID</span> &amp;&amp; <span class="i">$OptionsInfo</span>{<span class="w">RenameEmptyChainIDs</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+372           <span class="i">$PreviousChainID</span> = <span class="i">$ChainID</span><span class="sc">;</span>
+373           <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>}<span class="s">)</span> <span class="s">{</span>
+374             <span class="i">$NewChainID</span> = <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>}<span class="sc">;</span>
+375           <span class="s">}</span>
+376           <span class="k">else</span> <span class="s">{</span>
+377             <span class="i">$NewChainIDCounter</span>++<span class="sc">;</span>
+378             <span class="i">$NewChainID</span> = <span class="i">$NewChainIDCounter</span><span class="sc">;</span>
+379             <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>} = <span class="i">$NewChainID</span><span class="sc">;</span>
+380           <span class="s">}</span>
+381         <span class="s">}</span>
+382         <span class="k">else</span> <span class="s">{</span>
+383           <span class="i">$NewChainID</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+384         <span class="s">}</span>
+385       <span class="s">}</span>
+386
+387       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$NewChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+388     <span class="s">}</span>
+389     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+390       <span class="i">$AtomNumber</span>++<span class="sc">;</span>
+391       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$NewChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+392     <span class="s">}</span>
+393     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+394       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+395     <span class="s">}</span>
+396     <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+397       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+398     <span class="s">}</span>
+399   <span class="s">}</span>
+400
+401   <span class="c"># Write out CONECT records...</span>
+402   <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+403     <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+404       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+405     <span class="s">}</span>
+406   <span class="s">}</span>
+407
+408   <span class="c"># Write out END record...</span>
+409   <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+410
+411   <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
+412 <span class="s">}</span>
+413
+414
+415 <span class="c"># Write out modifed header and other older records...</span>
+<a name="WriteHeaderAndOlderRecords-"></a> 416 <span class="k">sub </span><span class="m">WriteHeaderAndOlderRecords</span> <span class="s">{</span>
+417   <span class="k">my</span><span class="s">(</span><span class="i">$OutFileRef</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+418
+419   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>}<span class="s">)</span> <span class="s">{</span>
+420     <span class="c"># Write out modified HEADER record...</span>
+421     <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="i">GetHeaderRecordInformation</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+422     <span class="i">$Classification</span> = <span class="q">&#39;Data modified using MayaChemTools&#39;</span><span class="sc">;</span>
+423     <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">GenerateHeaderRecordLine</span><span class="s">(</span><span class="i">$IDCode</span><span class="cm">,</span> <span class="i">$Classification</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+424   <span class="s">}</span>
+425   <span class="k">else</span> <span class="s">{</span>
+426     <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">$PDBRecordLinesRef</span>-&gt;[<span class="n">0</span>]<span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+427   <span class="s">}</span>
+428
+429   <span class="c"># Write out any old records...</span>
+430   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>}<span class="s">)</span> <span class="s">{</span>
+431     <span class="k">my</span><span class="s">(</span><span class="i">$RecordLineIndex</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
+432     <span class="c"># Skip HEADER record and write out older records all the way upto first MODEL/ATOM/HETATM records from input file...</span>
+433     <span class="j">RECORDLINE:</span> <span class="k">for</span> <span class="i">$RecordLineIndex</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
+434       <span class="i">$RecordLine</span> = <span class="i">$PDBRecordLinesRef</span>-&gt;[<span class="i">$RecordLineIndex</span>]<span class="sc">;</span>
+435       <span class="k">if</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+436         <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span>
+437       <span class="s">}</span>
+438       <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
+439     <span class="s">}</span>
+440   <span class="s">}</span>
+441 <span class="s">}</span>
+442
+443 <span class="c"># Get header record information assuming it&#39;s the first record...</span>
+<a name="GetHeaderRecordInformation-"></a> 444 <span class="k">sub </span><span class="m">GetHeaderRecordInformation</span> <span class="s">{</span>
+445   <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+446   <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="cm">,</span> <span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="sc">;</span>
+447
+448   <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="s">(</span><span class="q">&#39;&#39;</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
+449   <span class="i">$HeaderRecordLine</span> = <span class="i">$PDBRecordLinesRef</span>-&gt;[<span class="n">0</span>]<span class="sc">;</span>
+450   <span class="k">if</span> <span class="s">(</span><span class="i">IsHeaderRecordType</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+451     <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="i">ParseHeaderRecordLine</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="sc">;</span>
+452   <span class="s">}</span>
+453   <span class="k">return</span> <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span><span class="sc">;</span>
+454 <span class="s">}</span>
+455
+456
+457 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 458 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+459   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+460   <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+461
+462   <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>} = <span class="i">$Options</span>{<span class="w">atomnumberstart</span>}<span class="sc">;</span>
+463   <span class="i">$OptionsInfo</span>{<span class="w">StartingChainID</span>} = <span class="i">$Options</span>{<span class="w">chainidstart</span>}<span class="sc">;</span>
+464   <span class="i">$OptionsInfo</span>{<span class="w">RenameEmptyChainIDs</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidrenameempty</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+465
+466   <span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+467   <span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+468
+469   <span class="i">$OptionsInfo</span>{<span class="w">ResidueNumberMode</span>} = <span class="i">$Options</span>{<span class="w">residuenumbermode</span>}<span class="sc">;</span>
+470   <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">residuenumberstart</span>}<span class="sc">;</span>
+471
+472   <span class="i">$OptionsInfo</span>{<span class="w">HetatmResidueNumberMode</span>} = <span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>}<span class="sc">;</span>
+473   <span class="i">$OptionsInfo</span>{<span class="w">StartingHetatmResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>}<span class="sc">;</span>
+474
+475   <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+476   <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+477
+478   <span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} = <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span>
+479   <span class="i">$OptionsInfo</span>{<span class="w">StartingWaterResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">waterresiduestart</span>}<span class="sc">;</span>
+480   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+481   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+482
+483   <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span><span class="sc">;</span>
+484   <span class="i">@SpecifiedWaterResiduesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+485   <span class="k">my</span><span class="s">(</span><span class="i">$WaterResidueName</span><span class="s">)</span><span class="sc">;</span>
+486   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} =~ <span class="q">/Automatic/i</span><span class="s">)</span> <span class="s">{</span>
+487     <span class="k">push</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="cm">,</span> <span class="s">(</span><span class="q">&#39;HOH&#39;</span><span class="cm">,</span> <span class="q">&#39;WAT&#39;</span><span class="cm">,</span> <span class="q">&#39;H2O&#39;</span><span class="s">)</span><span class="sc">;</span>
+488   <span class="s">}</span>
+489   <span class="k">else</span> <span class="s">{</span>
+490     <span class="i">@SpecifiedWaterResiduesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span>
+491   <span class="s">}</span>
+492   <span class="k">for</span> <span class="i">$WaterResidueName</span> <span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span> <span class="s">{</span>
+493     <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$WaterResidueName</span>} = <span class="i">$WaterResidueName</span><span class="sc">;</span>
+494   <span class="s">}</span>
+495   <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="sc">;</span>
+496 <span class="s">}</span>
+497
+498 <span class="c"># Retrieve information about PDB files...</span>
+<a name="RetrievePDBFilesInfo-"></a> 499 <span class="k">sub </span><span class="m">RetrievePDBFilesInfo</span> <span class="s">{</span>
+500   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$PDBFile</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span>  <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$OutFileMode</span><span class="cm">,</span> <span class="i">@OutFileNames</span><span class="s">)</span><span class="sc">;</span>
+501
+502   <span class="i">%PDBFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+503   <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+504   <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+505   <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+506
+507   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
+508     <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+509
+510     <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+511     <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+512     <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+513
+514     <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+515     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$PDBFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+516       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+517       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+518     <span class="s">}</span>
+519     <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="q">&quot;pdb&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+520       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: It&#39;s not a PDB file\n&quot;</span><span class="sc">;</span>
+521       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+522     <span class="s">}</span>
+523     <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">PDBFILE</span><span class="cm">,</span> <span class="q">&quot;$PDBFile&quot;</span><span class="s">)</span> <span class="s">{</span>
+524       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+525       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+526     <span class="s">}</span>
+527     <span class="k">close</span> <span class="w">PDBFILE</span><span class="sc">;</span>
+528
+529     <span class="c"># Get PDB data...</span>
+530     <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
+531     <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
+532     <span class="k">if</span> <span class="s">(</span>!<span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+533       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: No chains found \n&quot;</span><span class="sc">;</span>
+534       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+535     <span class="s">}</span>
+536
+537     <span class="c"># Setup output file names...</span>
+538     <span class="i">@OutFileNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+539     <span class="i">$FileDir</span> = <span class="q">&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>
+540     <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
+541     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@PDBFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+542       <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
+543       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+544         <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+545       <span class="s">}</span>
+546       <span class="k">else</span> <span class="s">{</span>
+547         <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
+548       <span class="s">}</span>
+549       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+550     <span class="s">}</span>
+551     <span class="k">else</span> <span class="s">{</span>
+552       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+553     <span class="s">}</span>
+554     <span class="i">$Mode</span> = <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="sc">;</span>
+555     <span class="j">MODE:</span> <span class="s">{</span>
+556         <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenumberAtoms$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">&#39;RenumberAtoms&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
+557         <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenumberResidues$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">&#39;RenumberResidues&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
+558         <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenumberWaters$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">&#39;RenumberWaters&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
+559         <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenameChainIDs$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">&#39;RenameChainIDs&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
+560         <span class="i">$OutFileMode</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+561     <span class="s">}</span>
+562     <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}${OutFileMode}.pdb&quot;</span><span class="sc">;</span>
+563     <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span>
+564
+565     <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+566     <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
+567
+568     <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@OutFileNames</span><span class="sc">;</span>
+569   <span class="s">}</span>
+570 <span class="s">}</span>
+571
+572 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 573 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+574
+575   <span class="c"># Retrieve all the options...</span>
+576   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+577   <span class="i">$Options</span>{<span class="w">atomnumberstart</span>} = <span class="n">1</span><span class="sc">;</span>
+578   <span class="i">$Options</span>{<span class="w">chainidstart</span>} = <span class="q">&#39;A&#39;</span><span class="sc">;</span>
+579   <span class="i">$Options</span>{<span class="w">chainidrenameempty</span>} = <span class="q">&#39;No&#39;</span><span class="sc">;</span>
+580   <span class="i">$Options</span>{<span class="w">keepoldrecords</span>} = <span class="q">&#39;no&#39;</span><span class="sc">;</span>
+581   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;RenumberResidues&#39;</span><span class="sc">;</span>
+582   <span class="i">$Options</span>{<span class="w">modifyheader</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
+583   <span class="i">$Options</span>{<span class="w">residuenumbermode</span>} = <span class="q">&#39;PerChain&#39;</span><span class="sc">;</span>
+584   <span class="i">$Options</span>{<span class="w">residuenumberstart</span>} = <span class="n">1</span><span class="sc">;</span>
+585   <span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>} = <span class="q">&#39;Automatic&#39;</span><span class="sc">;</span>
+586   <span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>} = <span class="n">6000</span><span class="sc">;</span>
+587   <span class="i">$Options</span>{<span class="w">waterresiduenames</span>} = <span class="q">&#39;Automatic&#39;</span><span class="sc">;</span>
+588   <span class="i">$Options</span>{<span class="w">waterresiduestart</span>} = <span class="n">8000</span><span class="sc">;</span>
+589
+590   <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;atomnumberstart|a=i&quot;</span><span class="cm">,</span> <span class="q">&quot;chainidstart|c=s&quot;</span><span class="cm">,</span> <span class="q">&quot;chainidrenameempty=s&quot;</span><span class="cm">,</span> <span class="q">&quot;keepoldrecords|k=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;modifyheader=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;residuenumbermode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;residuenumberstart=i&quot;</span><span class="cm">,</span> <span class="q">&quot;residuenumberhetatmmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;residuenumberstarthetatm=i&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequencelength=i&quot;</span><span class="cm">,</span> <span class="q">&quot;waterresiduenames=s&quot;</span><span class="cm">,</span> <span class="q">&quot;waterresiduestart=i&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+591     <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+592   <span class="s">}</span>
+593   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+594     <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+595       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+596     <span class="s">}</span>
+597     <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
+598   <span class="s">}</span>
+599   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomnumberstart</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+600     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{atomnumberstart}, for option \&quot;-a, --AtomNumberStart\&quot; is not valid. Allowed values: &gt;0\n&quot;</span><span class="sc">;</span>
+601   <span class="s">}</span>
+602   <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidstart</span>}<span class="s">)</span> &gt; <span class="n">1</span><span class="s">)</span> || <span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidstart</span>} !~ <span class="q">/[A-Z]/i</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+603     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{chainidstart}, for option \&quot;-c, --ChainIDStart\&quot; is not valid. Allowed values: a single character from A to Z\n&quot;</span><span class="sc">;</span>
+604   <span class="s">}</span>
+605   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidrenameempty</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
+606     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{chainidrenameempty}, for option \&quot;--chainidrenameempty\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
+607   <span class="s">}</span>
+608   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
+609     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{keepoldrecords}, for option \&quot;--KeepOldRecords\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
+610   <span class="s">}</span>
+611   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(RenumberAtoms|RenumberResidues|RenumberWaters|RenameChainIDs)$/i</span><span class="s">)</span> <span class="s">{</span>
+612     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m, --mode\&quot; is not valid. Allowed values: RenumberAtoms, RenumberResidues, RenumberWaters or RenameChainIDs\n&quot;</span><span class="sc">;</span>
+613   <span class="s">}</span>
+614   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
+615     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{modifyheader}, for option \&quot;--ModifyHeader\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
+616   <span class="s">}</span>
+617   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumbermode</span>} !~ <span class="q">/^(Sequential|PerChain)$/i</span><span class="s">)</span> <span class="s">{</span>
+618     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{residuenumbermode}, for option \&quot;--ResidueNumberMode\&quot; is not valid. Allowed values: Sequential or PerChain\n&quot;</span><span class="sc">;</span>
+619   <span class="s">}</span>
+620   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberstart</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+621     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{residuenumberstart}, for option \&quot;--ResidueNumberStart\&quot; is not valid. Allowed values: &gt;0\n&quot;</span><span class="sc">;</span>
+622   <span class="s">}</span>
+623   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>} !~ <span class="q">/^(automatic|specify)$/i</span><span class="s">)</span> <span class="s">{</span>
+624     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{residuenumberhetatmmode}, for option \&quot;--residuenumbermode\&quot; is not valid. Allowed values: automatic or specify\n&quot;</span><span class="sc">;</span>
+625   <span class="s">}</span>
+626   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+627     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{residuenumberstarthetatm}, for option \&quot;--residuenumberstartHetatm\&quot; is not valid. Allowed values: &gt;0\n&quot;</span><span class="sc">;</span>
+628   <span class="s">}</span>
+629   <span class="k">if</span> <span class="s">(</span>!<span class="w">IsPositiveInteger</span> <span class="i">$Options</span>{<span class="w">waterresiduestart</span>}<span class="s">)</span> <span class="s">{</span>
+630     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{waterresiduestart}, for option \&quot;--waterresiduestart\&quot; is not valid. Allowed values: &gt;0\n&quot;</span><span class="sc">;</span>
+631   <span class="s">}</span>
+632 <span class="s">}</span>
+633
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
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Mercurial > repos > deepakjadmin > mayatool3_test1

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