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author deepakjadmin
date Thu, 15 Dec 2016 14:18:03 -0500
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1 <html>
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2 <head>
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3 <title>MayaChemTools:Code:ExtractFromPDBFiles.pl</title>
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4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
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5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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6 </head>
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7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
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8 <br/>
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9 <center>
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10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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11 </center>
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12 <br/>
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13 <pre>
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14 1 #!/usr/bin/perl -w
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: ExtractFromPDBFiles.pl,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
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18 5 <span class="c"># $Revision: 1.39 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">PDBFileUtil</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">AminoAcids</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">SequenceFileUtil</span><span class="sc">;</span>
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53 40
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54 41 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span>
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55 42
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56 43 <span class="c"># Autoflush STDOUT</span>
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57 44 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
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58 45
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59 46 <span class="c"># Starting message...</span>
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60 47 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
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61 48 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
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62 49 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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63 50
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64 51 <span class="c"># Get the options and setup script...</span>
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65 52 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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66 53 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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67 54 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">&quot;$FindBin::Bin/$ScriptName&quot;</span><span class="s">)</span><span class="sc">;</span>
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68 55 <span class="s">}</span>
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69 56
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70 57 <span class="k">my</span><span class="s">(</span><span class="i">@PDBFilesList</span><span class="s">)</span><span class="sc">;</span>
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71 58 <span class="i">@PDBFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">&quot;pdb&quot;</span><span class="s">)</span><span class="sc">;</span>
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72 59
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73 60 <span class="c"># Process options...</span>
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74 61 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
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75 62 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
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76 63 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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77 64
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78 65 <span class="c"># Setup information about input files...</span>
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79 66 <span class="k">print</span> <span class="q">&quot;Checking input PDB file(s)...\n&quot;</span><span class="sc">;</span>
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80 67 <span class="k">my</span><span class="s">(</span><span class="i">%PDBFilesInfo</span><span class="s">)</span><span class="sc">;</span>
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81 68 <span class="i">RetrievePDBFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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82 69
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83 70 <span class="c"># Process input files..</span>
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84 71 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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85 72 <span class="k">if</span> <span class="s">(</span><span class="i">@PDBFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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86 73 <span class="k">print</span> <span class="q">&quot;\nProcessing PDB files...\n&quot;</span><span class="sc">;</span>
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87 74 <span class="s">}</span>
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88 75 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
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89 76 <span class="k">if</span> <span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
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90 77 <span class="k">print</span> <span class="q">&quot;\nProcessing file $PDBFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
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91 78 <span class="i">ExtractFromPDBFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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92 79 <span class="s">}</span>
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93 80 <span class="s">}</span>
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94 81 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
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95 82
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96 83 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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97 84 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span>
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98 85 <span class="k">print</span> <span class="q">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
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99 86
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100 87 <span class="c">###############################################################################</span>
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101 88
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102 89 <span class="c"># Extract appropriate information...</span>
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103 <a name="ExtractFromPDBFiles-"></a> 90 <span class="k">sub </span><span class="m">ExtractFromPDBFiles</span> <span class="s">{</span>
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104 91 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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105 92 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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106 93
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107 94 <span class="c"># Get PDB data...</span>
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108 95 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
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109 96 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
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110 97
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111 98 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/Chains/i</span><span class="s">)</span> <span class="s">{</span>
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112 99 <span class="i">ExtractChains</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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113 100 <span class="s">}</span>
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114 101 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/Sequences/i</span><span class="s">)</span> <span class="s">{</span>
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115 102 <span class="i">ExtractSequences</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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116 103 <span class="s">}</span>
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117 104 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(Atoms|CAlphas|AtomNums|AtomsRange|AtomNames)$/i</span><span class="s">)</span> <span class="s">{</span>
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118 105 <span class="i">ExtractByAtoms</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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119 106 <span class="s">}</span>
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120 107 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(ResidueNums|ResiduesRange|ResidueNames)$/i</span><span class="s">)</span> <span class="s">{</span>
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121 108 <span class="i">ExtractByResidues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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122 109 <span class="s">}</span>
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123 110 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/Distance/i</span><span class="s">)</span> <span class="s">{</span>
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124 111 <span class="i">ExtractByDistance</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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125 112 <span class="s">}</span>
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126 113 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/NonWater/i</span><span class="s">)</span> <span class="s">{</span>
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127 114 <span class="i">ExtractNonWaterRecords</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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128 115 <span class="s">}</span>
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129 116 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/NonHydrogens/i</span><span class="s">)</span> <span class="s">{</span>
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130 117 <span class="i">ExtractNonHydrogenRecords</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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131 118 <span class="s">}</span>
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132 119 <span class="s">}</span>
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133 120
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134 121 <span class="c"># Extract chains and generate new PDB files...</span>
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135 122 <span class="c">#</span>
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136 <a name="ExtractChains-"></a> 123 <span class="k">sub </span><span class="m">ExtractChains</span> <span class="s">{</span>
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137 124 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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138 125 <span class="k">my</span><span class="s">(</span><span class="i">$ChainIndex</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="cm">,</span> <span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$AtomChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%ChainAtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
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139 126
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140 127 <span class="c"># Get chains and residues data...</span>
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141 128 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="q">&#39;AtomAndHetatm&#39;</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
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142 129
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143 130 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span>
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144 131 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
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145 132 <span class="k">print</span> <span class="q">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
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146 133
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147 134 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
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148 135
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149 136 <span class="c"># Write out header and other older recors...</span>
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150 137 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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151 138 <span class="s">}</span>
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152 139
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153 140 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span>
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154 141 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
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155 142 <span class="i">$ChainLabel</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
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156 143
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157 144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span>
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158 145 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
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159 146 <span class="k">print</span> <span class="q">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
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160 147
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161 148 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
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162 149
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163 150 <span class="c"># Write out header and other older recors...</span>
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164 151 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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165 152 <span class="s">}</span>
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166 153
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167 154 <span class="c"># Write out ATOM/HETATM line for chain and collect all ATOM/HETATM serial numbers</span>
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168 155 <span class="c"># for writing out appropriate CONECT records...</span>
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169 156 <span class="i">%ChainAtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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170 157 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">Lines</span>}{<span class="i">$ChainID</span>}}<span class="s">)</span> <span class="s">{</span>
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171 158 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
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172 159 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$AtomChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
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173 160 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
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174 161 <span class="i">$ChainAtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
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175 162 <span class="s">}</span>
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176 163 <span class="c"># Write out TER record using information from last chain record...</span>
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177 164 <span class="i">$AtomNumber</span> += <span class="n">1</span><span class="sc">;</span>
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178 165 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$AtomChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
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179 166
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180 167 <span class="c"># Write out CONECT records...</span>
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181 168 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%ChainAtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
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182 169
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183 170 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
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184 171 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
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185 172 <span class="s">}</span>
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186 173
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187 174 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span>
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188 175 <span class="c"># Write out END record...</span>
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189 176 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
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190 177
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191 178 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
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192 179 <span class="s">}</span>
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193 180 <span class="s">}</span>
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194 181
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195 182 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>}<span class="s">)</span> <span class="s">{</span>
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196 183 <span class="c"># Write out END record...</span>
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197 184 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
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198 185
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199 186 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
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200 187 <span class="s">}</span>
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201 188
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202 189 <span class="s">}</span>
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203 190
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204 191 <span class="c"># Extract sequences for individual chains or combine all the chains...</span>
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205 <a name="ExtractSequences-"></a> 192 <span class="k">sub </span><span class="m">ExtractSequences</span> <span class="s">{</span>
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206 193 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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207 194 <span class="k">my</span><span class="s">(</span><span class="i">$ChainIndex</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="cm">,</span> <span class="i">$SequenceFileName</span><span class="cm">,</span> <span class="i">$Residue</span><span class="cm">,</span> <span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="cm">,</span> <span class="i">$ChainSequence</span><span class="cm">,</span> <span class="i">$WrappedChainSequence</span><span class="cm">,</span> <span class="i">$ChainSequenceID</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$ChainResiduesRef</span><span class="cm">,</span> <span class="i">%ChainSequencesDataMap</span><span class="s">)</span><span class="sc">;</span>
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208 195
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209 196 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} =~ <span class="q">/^SeqRes$/i</span><span class="s">)</span> <span class="s">{</span>
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210 197 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="q">&#39;SeqRes&#39;</span><span class="s">)</span><span class="sc">;</span>
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211 198 <span class="s">}</span>
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212 199 <span class="k">else</span> <span class="s">{</span>
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213 200 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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214 201 <span class="s">}</span>
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215 202
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216 203 <span class="c"># Generate sequence data for all the chains...</span>
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217 204 <span class="i">%ChainSequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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218 205 <span class="i">@</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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219 206 <span class="i">%</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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220 207 <span class="i">%</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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221 208
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222 209 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span>
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223 210 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
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224 211 <span class="i">$ChainLabel</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
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225 212
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226 213 <span class="c"># Setup sequence ID...</span>
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227 214 <span class="i">$ChainSequenceID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
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228 215 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ChainSequencesDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ChainSequenceID</span><span class="sc">;</span>
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229 216 <span class="i">$ChainSequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$ChainID</span>} = <span class="i">$ChainSequenceID</span><span class="sc">;</span>
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230 217
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231 218 <span class="c"># Collect sequence data for the chain...</span>
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232 219 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} =~ <span class="q">/^SeqRes/i</span><span class="s">)</span> <span class="s">{</span>
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233 220 <span class="i">$ChainResiduesRef</span> = \<span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="sc">;</span>
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234 221 <span class="s">}</span>
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235 222 <span class="k">else</span> <span class="s">{</span>
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236 223 <span class="i">$ChainResiduesRef</span> = \<span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}}<span class="sc">;</span>
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237 224 <span class="s">}</span>
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238 225 <span class="c"># Setup sequence data...</span>
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239 226 <span class="i">$ChainSequence</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
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240 227 <span class="j">RESIDUE:</span> <span class="k">for</span> <span class="i">$Residue</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ChainResiduesRef</span>}<span class="s">)</span> <span class="s">{</span>
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241 228 <span class="s">(</span><span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="s">)</span> = <span class="i">GetResidueCode</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="sc">;</span>
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242 229 <span class="k">if</span> <span class="s">(</span>!<span class="i">$StandardResidue</span><span class="s">)</span> <span class="s">{</span>
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243 230 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepNonStandardSequences</span>}<span class="s">)</span> <span class="s">{</span>
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244 231 <span class="i">$ResidueCode</span> = <span class="i">$OptionsInfo</span>{<span class="w">NonStandardSequenceCode</span>}<span class="sc">;</span>
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245 232 <span class="k">warn</span> <span class="q">&quot;Warning: Keeping nonstandard residue $Residue in $ChainLabel...\n&quot;</span><span class="sc">;</span>
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246 233 <span class="s">}</span>
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247 234 <span class="k">else</span> <span class="s">{</span>
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248 235 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring nonstandard residue $Residue in $ChainLabel...\n&quot;</span><span class="sc">;</span>
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249 236 <span class="k">next</span> <span class="j">RESIDUE</span><span class="sc">;</span>
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250 237 <span class="s">}</span>
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251 238 <span class="s">}</span>
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252 239 <span class="i">$ChainSequence</span> .= <span class="i">$ResidueCode</span><span class="sc">;</span>
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253 240 <span class="s">}</span>
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254 241 <span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ChainID</span>} = <span class="i">$ChainSequence</span><span class="sc">;</span>
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255 242
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256 243 <span class="s">}</span>
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257 244
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258 245 <span class="c"># Write out the sequence files...</span>
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259 246 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceID</span><span class="cm">,</span> <span class="i">$SequenceDescription</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">%SequencesDataMap</span> <span class="s">)</span><span class="sc">;</span>
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260 247 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChainSequences</span>}<span class="s">)</span> <span class="s">{</span>
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261 248 <span class="c"># Combine all the chain sequences...</span>
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262 249 <span class="i">$Sequence</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
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263 250 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span>
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264 251 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
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265 252
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266 253 <span class="i">$Sequence</span> .= <span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ChainID</span>}<span class="sc">;</span>
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267 254 <span class="s">}</span>
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268 255 <span class="i">$SequenceID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>] . <span class="q">&quot;_CombinedChains|PDB&quot;</span><span class="sc">;</span><span class="sc">;</span>
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269 256 <span class="i">$SequenceDescription</span> = <span class="i">$SequenceID</span><span class="sc">;</span>
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270 257 <span class="i">$SequenceFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
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271 258
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272 259 <span class="k">print</span> <span class="q">&quot;Generating sequence file $SequenceFileName...\n&quot;</span><span class="sc">;</span>
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273 260 <span class="i">%SequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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274 261 <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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275 262 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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276 263 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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277 264
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278 265 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$SequenceID</span><span class="sc">;</span>
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279 266 <span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$SequenceID</span>} = <span class="i">$SequenceDescription</span><span class="sc">;</span>
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280 267 <span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$SequenceID</span>} = <span class="i">$Sequence</span><span class="sc">;</span>
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281 268
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282 269 <span class="i">WritePearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFileName</span><span class="cm">,</span> \<span class="i">%SequencesDataMap</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>}<span class="s">)</span><span class="sc">;</span>
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283 270 <span class="s">}</span>
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284 271 <span class="k">else</span> <span class="s">{</span>
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285 272 <span class="c"># For each specifed chain, write out the sequences...</span>
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286 273 <span class="k">for</span> <span class="i">$ChainIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span>
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287 274 <span class="i">$ChainID</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
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288 275
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289 276 <span class="i">$SequenceFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="i">$ChainIndex</span>]<span class="sc">;</span>
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290 277
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291 278 <span class="i">$SequenceID</span> = <span class="i">$ChainSequencesDataMap</span>{<span class="w">IDs</span>}[<span class="i">$ChainIndex</span>]<span class="sc">;</span>
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292 279 <span class="i">$SequenceDescription</span> = <span class="i">$ChainSequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$ChainID</span>}<span class="sc">;</span>
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293 280 <span class="i">$Sequence</span> = <span class="i">$ChainSequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ChainID</span>}<span class="sc">;</span>
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294 281
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295 282 <span class="k">print</span> <span class="q">&quot;Generating sequence file $SequenceFileName...\n&quot;</span><span class="sc">;</span>
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296 283 <span class="i">%SequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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297 284 <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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298 285 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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299 286 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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300 287
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301 288 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$SequenceID</span><span class="sc">;</span>
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302 289 <span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$SequenceID</span>} = <span class="i">$SequenceDescription</span><span class="sc">;</span>
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303 290 <span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$SequenceID</span>} = <span class="i">$Sequence</span><span class="sc">;</span>
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304 291
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305 292 <span class="i">WritePearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFileName</span><span class="cm">,</span> \<span class="i">%SequencesDataMap</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>}<span class="s">)</span><span class="sc">;</span>
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306 293 <span class="s">}</span>
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307 294 <span class="s">}</span>
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308 295 <span class="s">}</span>
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309 296
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310 297 <span class="c"># Extract atoms...</span>
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311 <a name="ExtractByAtoms-"></a> 298 <span class="k">sub </span><span class="m">ExtractByAtoms</span> <span class="s">{</span>
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312 299 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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313 300 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$IgnoreRecord</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
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314 301
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315 302 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
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316 303 <span class="k">print</span> <span class="q">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
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317 304 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
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318 305
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319 306 <span class="c"># Write out header and other older recors...</span>
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320 307 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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321 308
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322 309 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span>
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323 310 <span class="c"># chains and multiple models..</span>
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324 311 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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325 312 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
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326 313 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
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327 314 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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328 315 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
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329 316
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330 317 <span class="c"># Check atoms...</span>
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331 318 <span class="i">$IgnoreRecord</span> = <span class="n">1</span><span class="sc">;</span>
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332 319 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Atoms$/i</span><span class="s">)</span> <span class="s">{</span>
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333 320 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
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334 321 <span class="s">}</span>
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335 322 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(CAlphas|AtomNames)$/i</span><span class="s">)</span> <span class="s">{</span>
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336 323 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesMap</span>}{<span class="k">lc</span> <span class="i">$AtomName</span>}<span class="s">)</span> <span class="s">{</span>
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337 324 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
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338 325 <span class="s">}</span>
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339 326 <span class="s">}</span>
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340 327 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomNums$/i</span><span class="s">)</span> <span class="s">{</span>
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341 328 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsMap</span>}{<span class="i">$AtomNumber</span>}<span class="s">)</span> <span class="s">{</span>
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342 329 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
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343 330 <span class="s">}</span>
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344 331 <span class="s">}</span>
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345 332 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomsRange$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
346 333 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNumber</span> &gt;= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartAtomNum</span>} &amp;&amp; <span class="i">$AtomNumber</span> &lt;= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndAtomNum</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
347 334 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
348 335 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
349 336 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
350 337
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
351 338 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IgnoreRecord</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
352 339 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
353 340 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
354 341
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
355 342 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
356 343 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
357 344 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
358 345 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
359 346 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
360 347 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
361 348 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
362 349 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
363 350 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
364 351 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
365 352 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
366 353 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
367 354 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
368 355 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
369 356
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
370 357 <span class="c"># Write out appropriate CONECT records...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
371 358 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
372 359 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
373 360 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
374 361 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
375 362
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
376 363 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
377 364 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
378 365
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
379 366 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
380 367 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
381 368
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
382 369 <span class="c"># Extract residues...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
383 <a name="ExtractByResidues-"></a> 370 <span class="k">sub </span><span class="m">ExtractByResidues</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
384 371 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
385 372 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$IgnoreRecord</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
386 373
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
387 374 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
388 375 <span class="k">print</span> <span class="q">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
389 376 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
390 377
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
391 378 <span class="c"># Write out header and other older recors...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
392 379 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
393 380
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
394 381 <span class="c"># Write out all ATOM records for specified residues with TER and model records to indicate</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
395 382 <span class="c"># chains and multiple models...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
396 383 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
397 384 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
398 385 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
399 386 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
400 387 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
401 388
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
402 389 <span class="c"># Check residues...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
403 390 <span class="i">$IgnoreRecord</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
404 391 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResidueNums$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
405 392 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsMap</span>}{<span class="i">$ResidueNumber</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
406 393 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
407 394 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
408 395 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
409 396 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResiduesRange$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
410 397 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueNumber</span> &gt;= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartResidueNum</span>} &amp;&amp; <span class="i">$ResidueNumber</span> &lt;= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndResidueNum</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
411 398 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
412 399 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
413 400 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
414 401 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResidueNames$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
415 402 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesMap</span>}{<span class="k">lc</span> <span class="i">$ResidueName</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
416 403 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
417 404 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
418 405 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
419 406 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IgnoreRecord</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
420 407 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
421 408 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
422 409 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
423 410 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
424 411 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
425 412 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
426 413 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
427 414 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
428 415 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
429 416 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
430 417 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
431 418 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
432 419 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
433 420 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
434 421 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
435 422 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
436 423
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
437 424 <span class="c"># Write out appropriate CONECT records...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
438 425 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
439 426 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
440 427 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
441 428 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
442 429 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
443 430 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
444 431
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
445 432 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
446 433 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
447 434
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
448 435 <span class="c"># Extract non water records...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
449 <a name="ExtractNonWaterRecords-"></a> 436 <span class="k">sub </span><span class="m">ExtractNonWaterRecords</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
450 437 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
451 438 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
452 439
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
453 440 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
454 441 <span class="k">print</span> <span class="q">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
455 442 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
456 443
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
457 444 <span class="c"># Write out header and other older recors...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
458 445 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
459 446
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
460 447 <span class="c"># Write out all ATOM/HETATM non water records along with TER and model records to indicate</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
461 448 <span class="c"># chains and multiple models..</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
462 449 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
463 450 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
464 451 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
465 452 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
466 453 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
467 454 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$ResidueName</span>} <span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
468 455 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
469 456 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
470 457 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
471 458 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
472 459 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
473 460 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
474 461 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
475 462 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
476 463 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
477 464 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
478 465 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
479 466 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
480 467 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
481 468 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
482 469 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
483 470 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
484 471
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
485 472 <span class="c"># Write out appropriate CONECT records...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
486 473 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
487 474 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
488 475 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
489 476 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
490 477 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
491 478 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
492 479
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
493 480 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
494 481 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
495 482
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
496 483 <span class="c"># Extract non hydrogen records...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
497 <a name="ExtractNonHydrogenRecords-"></a> 484 <span class="k">sub </span><span class="m">ExtractNonHydrogenRecords</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
498 485 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
499 486 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
500 487
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
501 488 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
502 489 <span class="k">print</span> <span class="q">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
503 490 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
504 491
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
505 492 <span class="c"># Write out header and other older recors...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
506 493 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
507 494
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
508 495 <span class="c"># Write out all ATOM/HETATM non hydrogen records along with TER and model records to indicate</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
509 496 <span class="c"># chains and multiple models..</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
510 497 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
511 498 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
512 499 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
513 500 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
514 501 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
515 502 <span class="k">if</span> <span class="s">(</span><span class="i">$ElementSymbol</span> !~ <span class="q">/^H$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
516 503 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
517 504 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
518 505 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
519 506 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
520 507 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
521 508 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
522 509 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
523 510 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
524 511 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
525 512 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
526 513 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
527 514 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
528 515 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
529 516 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
530 517 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
531 518 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
532 519
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
533 520 <span class="c"># Write out appropriate CONECT records...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
534 521 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
535 522 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
536 523 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
537 524 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
538 525 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
539 526 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
540 527
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
541 528 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
542 529 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
543 530
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
544 531 <span class="c"># Extract ATOM/HETATM records by distance...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
545 <a name="ExtractByDistance-"></a> 532 <span class="k">sub </span><span class="m">ExtractByDistance</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
546 533 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
547 534 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$RecordLineNum</span><span class="cm">,</span> <span class="i">$ChainRecordCount</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$IgnoreRecord</span><span class="cm">,</span> <span class="i">$ResidueID</span><span class="cm">,</span> <span class="i">@OriginCoords</span><span class="cm">,</span> <span class="i">@Coords</span><span class="cm">,</span> <span class="i">%AtomNumbersMap</span><span class="cm">,</span> <span class="i">%ResiduesDataMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
548 535
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
549 536 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
550 537 <span class="k">print</span> <span class="q">&quot;Generating PDBFileName file $PDBFileName...\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
551 538 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$PDBFileName&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $PDBFileName: $! \n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
552 539
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
553 540 <span class="c"># Write out header and other older recors...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
554 541 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
555 542
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
556 543 <span class="c"># Setup coordinates of origin to calculate distance...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
557 544 <span class="i">@OriginCoords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
558 545 <span class="k">push</span> <span class="i">@OriginCoords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
559 546
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
560 547 <span class="c"># Write out all ATOM records for which meet specified criteria along with TER and model records to indicate</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
561 548 <span class="c"># chains and multiple models...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
562 549 <span class="i">%AtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
563 550
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
564 551 <span class="i">%ResiduesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
565 552 <span class="i">%</span>{<span class="i">$ResiduesDataMap</span>{<span class="w">ID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
566 553 <span class="i">%</span>{<span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
567 554
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
568 555 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
569 556 <span class="i">$RecordLineNum</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
570 557
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
571 558 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
572 559 <span class="i">$RecordLineNum</span>++<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
573 560 <span class="k">if</span> <span class="s">(</span><span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
574 561 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
575 562 <span class="i">@Coords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">push</span> <span class="i">@Coords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
576 563
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
577 564 <span class="i">$IgnoreRecord</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
578 565 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DistanceSelectionMode</span>} =~ <span class="q">/^ByResidue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
579 566 <span class="i">$ResidueID</span> = <span class="q">&quot;${ResidueName}_${ResidueNumber}_${ChainID}&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
580 567 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ResiduesDataMap</span>{<span class="w">ID</span>}{<span class="i">$ResidueID</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
581 568 <span class="c"># Residue data has been processed; check its selection status...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
582 569 <span class="k">if</span> <span class="s">(</span><span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}{<span class="i">$ResidueID</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
583 570 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
584 571 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
585 572 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
586 573 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
587 574 <span class="c"># Residue hasn&#39;t been processed...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
588 575 <span class="i">$ResiduesDataMap</span>{<span class="w">ID</span>}{<span class="i">$ResidueID</span>} = <span class="i">$ResidueID</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
589 576 <span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}{<span class="i">$ResidueID</span>} = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
590 577 <span class="k">if</span> <span class="s">(</span><span class="i">CheckResidueDistance</span><span class="s">(</span><span class="i">$ResidueID</span><span class="cm">,</span> <span class="i">$RecordLineNum</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">@OriginCoords</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
591 578 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
592 579 <span class="i">$ResiduesDataMap</span>{<span class="w">Status</span>}{<span class="i">$ResidueID</span>} = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
593 580 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
594 581 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
595 582 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
596 583 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DistanceSelectionMode</span>} =~ <span class="q">/^ByAtom$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
597 584 <span class="k">if</span> <span class="s">(</span><span class="i">CheckDistance</span><span class="s">(</span>\<span class="i">@Coords</span><span class="cm">,</span> \<span class="i">@OriginCoords</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
598 585 <span class="i">$IgnoreRecord</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
599 586 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
600 587 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
601 588
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
602 589 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IgnoreRecord</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
603 590 <span class="i">$ChainRecordCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
604 591 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
605 592 <span class="i">$AtomNumber</span> = <span class="k">int</span> <span class="i">$AtomNumber</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
606 593 <span class="i">$AtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
607 594 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
608 595 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
609 596 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
610 597 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainRecordCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
611 598 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
612 599 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
613 600 <span class="i">$ChainRecordCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
614 601 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
615 602 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
616 603 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
617 604 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
618 605 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
619 606
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
620 607 <span class="c"># Write out appropriate CONECT records...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
621 608 <span class="i">$ConectRecordLinesRef</span> = <span class="i">GetConectRecordLines</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> \<span class="i">%AtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
622 609 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConectRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
623 610 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
624 611 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
625 612
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
626 613 <span class="c"># Write out END record...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
627 614 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
628 615
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
629 616 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
630 617 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
631 618
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
632 619 <span class="c"># Does record type correspond to the specified record type?</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
633 <a name="CheckRecordType-"></a> 620 <span class="k">sub </span><span class="m">CheckRecordType</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
634 621 <span class="k">my</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
635 622 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
636 623
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
637 624 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
638 625 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} =~ <span class="q">/^Atom$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
639 626 <span class="i">$Status</span> = <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
640 627 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
641 628 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} =~ <span class="q">/^Hetatm$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
642 629 <span class="i">$Status</span> = <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
643 630 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
644 631 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} =~ <span class="q">/^AtomAndHetatm$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
645 632 <span class="i">$Status</span> = <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
646 633 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
647 634
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
648 635 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
649 636 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
650 637
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
651 638 <span class="c"># Does record meets distance citerion specified by the user?</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
652 <a name="CheckResidueDistance-"></a> 639 <span class="k">sub </span><span class="m">CheckResidueDistance</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
653 640 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedResidueID</span><span class="cm">,</span> <span class="i">$StartingLineNum</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="i">$OriginCoordsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
654 641 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$RecordLineIndex</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$ResidueID</span><span class="cm">,</span> <span class="i">@Coords</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
655 642
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
656 643 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
657 644
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
658 645 <span class="j">RECORDLINE:</span> <span class="k">for</span> <span class="i">$RecordLineIndex</span> <span class="s">(</span><span class="s">(</span><span class="i">$StartingLineNum</span> - <span class="n">1</span><span class="s">)</span> .. <span class="i">$#</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
659 646 <span class="i">$RecordLine</span> = <span class="i">$PDBRecordLinesRef</span>-&gt;[<span class="i">$RecordLineIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
660 647 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
661 648 <span class="k">next</span> <span class="j">RECORDLINE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
662 649 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
663 650 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
664 651 <span class="i">$ResidueID</span> = <span class="q">&quot;${ResidueName}_${ResidueNumber}_${ChainID}&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
665 652
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
666 653 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueID</span> !~ <span class="q">/^$SpecifiedResidueID$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
667 654 <span class="c"># It&#39;s a new residue line...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
668 655 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
669 656 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
670 657
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
671 658 <span class="c"># Check distance...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
672 659 <span class="i">@Coords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">push</span> <span class="i">@Coords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
673 660 <span class="k">if</span> <span class="s">(</span><span class="i">CheckDistance</span><span class="s">(</span>\<span class="i">@Coords</span><span class="cm">,</span> <span class="i">$OriginCoordsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
674 661 <span class="c"># Distance criterion is met for at least one record in the residue...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
675 662 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
676 663 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
677 664 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
678 665 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
679 666 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
680 667 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
681 668
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
682 669 <span class="c"># Does record meets distance citerion specified by the user?</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
683 <a name="CheckDistance-"></a> 670 <span class="k">sub </span><span class="m">CheckDistance</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
684 671 <span class="k">my</span><span class="s">(</span><span class="i">$CoordsRef</span><span class="cm">,</span> <span class="i">$OriginCoordsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
685 672 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$DistanceSquare</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
686 673
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
687 674 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
688 675
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
689 676 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
690 677 <span class="c"># Go over coordinates of all the atoms in the residue...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
691 678 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueCoordsCount</span><span class="s">)</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$OriginCoordsRef</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
692 679 <span class="j">INDEX:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> &lt; <span class="i">$ResidueCoordsCount</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
693 680 <span class="i">$DistanceSquare</span> = <span class="s">(</span><span class="i">$CoordsRef</span>-&gt;[<span class="n">0</span>] - <span class="i">$OriginCoordsRef</span>-&gt;[<span class="i">$Index</span>]<span class="s">)</span>**<span class="n">2</span> + <span class="s">(</span><span class="i">$CoordsRef</span>-&gt;[<span class="n">1</span>] - <span class="i">$OriginCoordsRef</span>-&gt;[<span class="i">$Index</span> + <span class="n">1</span>]<span class="s">)</span>**<span class="n">2</span> + <span class="s">(</span><span class="i">$CoordsRef</span>-&gt;[<span class="n">2</span>] - <span class="i">$OriginCoordsRef</span>-&gt;[<span class="i">$Index</span> + <span class="n">2</span>]<span class="s">)</span>**<span class="n">2</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
694 681 <span class="i">$Distance</span> = <span class="k">sqrt</span> <span class="i">$DistanceSquare</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
695 682 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance</span> &lt;= <span class="i">$OptionsInfo</span>{<span class="w">MaxExtractionDistance</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
696 683 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
697 684 <span class="k">last</span> <span class="j">INDEX</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
698 685 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
699 686 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
700 687 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
701 688 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
702 689 <span class="i">$DistanceSquare</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
703 690 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
704 691 <span class="i">$DistanceSquare</span> += <span class="s">(</span><span class="i">$CoordsRef</span>-&gt;[<span class="i">$Index</span>] - <span class="i">$OriginCoordsRef</span>-&gt;[<span class="i">$Index</span>]<span class="s">)</span>**<span class="n">2</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
705 692 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
706 693 <span class="i">$Distance</span> = <span class="k">sqrt</span> <span class="i">$DistanceSquare</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
707 694 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$Distance</span> &lt;= <span class="i">$OptionsInfo</span>{<span class="w">MaxExtractionDistance</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
708 695 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
709 696
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
710 697 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
711 698 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
712 699
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
713 700 <span class="c"># Write out modifed header and other older records...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
714 <a name="WriteHeaderAndOlderRecords-"></a> 701 <span class="k">sub </span><span class="m">WriteHeaderAndOlderRecords</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
715 702 <span class="k">my</span><span class="s">(</span><span class="i">$OutFileRef</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
716 703
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
717 704 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
718 705 <span class="c"># Write out modified HEADER record...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
719 706 <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="i">GetHeaderRecordInformation</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
720 707 <span class="i">$Classification</span> = <span class="q">&#39;Data extracted using MayaChemTools&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
721 708 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">GenerateHeaderRecordLine</span><span class="s">(</span><span class="i">$IDCode</span><span class="cm">,</span> <span class="i">$Classification</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
722 709 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
723 710 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
724 711 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">$PDBRecordLinesRef</span>-&gt;[<span class="n">0</span>]<span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
725 712 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
726 713
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
727 714 <span class="c"># Write out any old records...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
728 715 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
729 716 <span class="k">my</span><span class="s">(</span><span class="i">$RecordLineIndex</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
730 717 <span class="c"># Skip HEADER record and write out older records all the way upto first MODEL/ATOM/HETATM records from input file...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
731 718 <span class="j">RECORDLINE:</span> <span class="k">for</span> <span class="i">$RecordLineIndex</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
732 719 <span class="i">$RecordLine</span> = <span class="i">$PDBRecordLinesRef</span>-&gt;[<span class="i">$RecordLineIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
733 720 <span class="k">if</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
734 721 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
735 722 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
736 723 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="q">&quot;$RecordLine\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
737 724 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
738 725 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
739 726 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
740 727
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
741 728 <span class="c"># Get header record information assuming it&#39;s the first record...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
742 <a name="GetHeaderRecordInformation-"></a> 729 <span class="k">sub </span><span class="m">GetHeaderRecordInformation</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
743 730 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
744 731 <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="cm">,</span> <span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
745 732
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
746 733 <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="s">(</span><span class="q">&#39;&#39;</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
747 734 <span class="i">$HeaderRecordLine</span> = <span class="i">$PDBRecordLinesRef</span>-&gt;[<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
748 735 <span class="k">if</span> <span class="s">(</span><span class="i">IsHeaderRecordType</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
749 736 <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="i">ParseHeaderRecordLine</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
750 737 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
751 738 <span class="k">return</span> <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
752 739 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
753 740
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
754 741 <span class="c"># Get one letter residue code...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
755 <a name="GetResidueCode-"></a> 742 <span class="k">sub </span><span class="m">GetResidueCode</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
756 743 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
757 744 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
758 745
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
759 746 <span class="i">$ResidueCode</span> = <span class="i">$OptionsInfo</span>{<span class="w">NonStandardSequenceCode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
760 747 <span class="i">$StandardResidue</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
761 748
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
762 749 <span class="k">if</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
763 750 <span class="c"># Assume it&#39;s an amino acid...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
764 751 <span class="k">if</span> <span class="s">(</span><span class="i">AminoAcids::IsAminoAcid</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
765 752 <span class="c"># Standard amino acid...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
766 753 <span class="i">$ResidueCode</span> = <span class="i">AminoAcids::GetAminoAcidOneLetterCode</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
767 754 <span class="i">$StandardResidue</span> = <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
768 755 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
769 756 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
770 757 <span class="k">elsif</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
771 758 <span class="c"># Assume it&#39;s a nucleic acid...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
772 759 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueName</span> =~ <span class="q">/^(A|G|T|U|C)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
773 760 <span class="i">$ResidueCode</span> = <span class="i">$ResidueName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
774 761 <span class="i">$StandardResidue</span> = <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
775 762 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
776 763 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
777 764
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
778 765 <span class="k">return</span> <span class="s">(</span><span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">$StandardResidue</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
779 766 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
780 767
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
781 768 <span class="c"># Process option values...</span>
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deepakjadmin
parents:
diff changeset
782 <a name="ProcessOptions-"></a> 769 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
783 770 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
784 771 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
785 772
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parents:
diff changeset
786 773 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedChains</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
787 774 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">chains</span>} =~ <span class="q">/^(First|All)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
788 775 <span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} = <span class="i">$Options</span>{<span class="w">chains</span>}<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
789 776 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
790 777 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
791 778 <span class="i">@SpecifiedChains</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">chains</span>}<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
792 779 <span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} = <span class="q">&#39;Specified&#39;</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
793 780 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
794 781 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedChains</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
795 782 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedChains</span>}}<span class="cm">,</span> <span class="i">@SpecifiedChains</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
796 783
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deepakjadmin
parents:
diff changeset
797 784 <span class="i">$OptionsInfo</span>{<span class="w">CombineChains</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">combinechains</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
798 785
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
799 786 <span class="i">$OptionsInfo</span>{<span class="w">CombineChainSequences</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">combinechains</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
800 787
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deepakjadmin
parents:
diff changeset
801 788 <span class="i">ProcessResiduesOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
802 789 <span class="i">ProcessAtomsOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
803 790 <span class="i">ProcessDistanceOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
804 791
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deepakjadmin
parents:
diff changeset
805 792 <span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} = <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
806 793 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
807 794 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
808 795
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
809 796 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
810 797 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
811 798
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
812 799 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^NonWater$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
813 800 <span class="k">my</span><span class="s">(</span><span class="i">$WaterResidueName</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
814 801 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} =~ <span class="q">/Automatic/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
815 802 <span class="k">push</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="cm">,</span> <span class="s">(</span><span class="q">&#39;HOH&#39;</span><span class="cm">,</span> <span class="q">&#39;WAT&#39;</span><span class="cm">,</span> <span class="q">&#39;H2O&#39;</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
816 803 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
817 804 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
818 805 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
819 806 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
820 807 <span class="k">for</span> <span class="i">$WaterResidueName</span> <span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
821 808 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$WaterResidueName</span>} = <span class="i">$WaterResidueName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
822 809 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
823 810 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
824 811 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
825 812
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
826 813 <span class="i">$OptionsInfo</span>{<span class="w">RecordMode</span>} = <span class="i">$Options</span>{<span class="w">recordmode</span>} ? <span class="i">$Options</span>{<span class="w">recordmode</span>} <span class="co">:</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^(Atoms|CAlphas|AtomNums|AtomsRange|AtomNames)$/i</span> ? <span class="q">&quot;Atom&quot;</span> <span class="co">:</span> <span class="q">&quot;AtomAndHetatm&quot;</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
827 814
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
828 815 <span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
829 816
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
830 817 <span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
831 818
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
832 819 <span class="i">$OptionsInfo</span>{<span class="w">KeepNonStandardSequences</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">nonstandardkeep</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
833 820 <span class="i">$OptionsInfo</span>{<span class="w">NonStandardSequenceCode</span>} = <span class="i">$Options</span>{<span class="w">nonstandardcode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
834 821 <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>} = <span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
835 822 <span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} = <span class="i">$Options</span>{<span class="w">sequencerecords</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
836 823 <span class="i">$OptionsInfo</span>{<span class="w">SequenceIDPrefixSource</span>} = <span class="i">$Options</span>{<span class="w">sequenceidprefix</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
837 824
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
838 825 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
839 826 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
840 827 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
841 828
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
842 829 <span class="c"># Process specified residue options...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
843 <a name="ProcessResiduesOptions-"></a> 830 <span class="k">sub </span><span class="m">ProcessResiduesOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
844 831 <span class="k">my</span><span class="s">(</span><span class="i">$ResidueNum</span><span class="cm">,</span> <span class="i">$StartResidueNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">@SpecifiedResidueNumsList</span><span class="cm">,</span> <span class="i">@SpecifiedResidueNamesList</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
845 832
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
846 833 <span class="i">@SpecifiedResidueNumsList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
847 834 <span class="s">(</span><span class="i">$StartResidueNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
848 835
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
849 836 <span class="i">@SpecifiedResidueNamesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
850 837
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
851 838 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(ResidueNums|ResiduesRange|ResidueNames)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
852 839 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">residues</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
853 840 <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--Residues\&quot; option in \&quot;ResidueNums, ResiduesRange, or ResidueNames\&quot; \&quot;-m, --mode\&quot;. \n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
854 841 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
855 842 <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>} = <span class="i">$Options</span>{<span class="w">residues</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
856 843 <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>} =~ <span class="q">s/ //g</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
857 844
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
858 845 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResidueNames$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
859 846 <span class="i">@SpecifiedResidueNamesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
860 847 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
861 848 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
862 849 <span class="i">@SpecifiedResidueNumsList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Residues</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
863 850 <span class="k">for</span> <span class="i">$ResidueNum</span> <span class="s">(</span><span class="i">@SpecifiedResidueNumsList</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
864 851 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$ResidueNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
865 852 <span class="k">die</span> <span class="q">&quot;Error: Invalid residue number value, $ResidueNum, for \&quot;--Residues\&quot; option during \&quot;ResidueNumes\&quot; or \&quot;ResiduesRange\&quot;value of \&quot;-m --mode\&quot; option: Residue number must be a positive integer.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
866 853 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
867 854 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
868 855 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ResiduesRange$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
869 856 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedResidueNumsList</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
870 857 <span class="k">die</span> <span class="q">&quot;Error: Invalid number of residue number values, &quot;</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedResidueNumsList</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;, for \&quot;--Residues\&quot; option during \&quot;ResiduesRange\&quot; value of \&quot;-m --mode\&quot; option: The number of values must be 2 corresponding to start and end residue numbers.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
871 858 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
872 859 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedResidueNumsList</span>[<span class="n">0</span>] &gt; <span class="i">$SpecifiedResidueNumsList</span>[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
873 860 <span class="k">die</span> <span class="q">&quot;Error: Invalid residue number values, @SpecifiedResidueNumsList, for \&quot;--Residues\&quot; option during \&quot;ResiduesRange\&quot; value of \&quot;-m --mode\&quot; option: The start residue number must be less than end residue number.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
874 861 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
875 862 <span class="s">(</span><span class="i">$StartResidueNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="s">)</span> = <span class="i">@SpecifiedResidueNumsList</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
876 863 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
877 864 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
878 865 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
879 866
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
880 867 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
881 868 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedResidueNumsList</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
882 869
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
883 870 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartResidueNum</span>} = <span class="i">$StartResidueNum</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
884 871 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndResidueNum</span>} = <span class="i">$EndResNum</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
885 872
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
886 873 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
887 874 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedResidueNamesList</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
888 875
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
889 876 <span class="c"># Set up a specified residue numbers map...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
890 877 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
891 878 <span class="k">for</span> <span class="i">$ResidueNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsList</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
892 879 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNumsMap</span>}{<span class="i">$ResidueNum</span>} = <span class="i">$ResidueNum</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
893 880 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
894 881
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
895 882 <span class="c"># Set up a specified residue names map...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
896 883 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
897 884 <span class="k">for</span> <span class="i">$ResidueName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesList</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
898 885 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedResidueNamesMap</span>}{<span class="k">lc</span> <span class="i">$ResidueName</span>} = <span class="k">lc</span> <span class="i">$ResidueName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
899 886 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
900 887
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
901 888 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
902 889
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
903 890 <span class="c"># Process specified atom options...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
904 <a name="ProcessAtomsOptions-"></a> 891 <span class="k">sub </span><span class="m">ProcessAtomsOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
905 892 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNum</span><span class="cm">,</span> <span class="i">$StartAtomNum</span><span class="cm">,</span> <span class="i">$EndAtomNum</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">@SpecifiedAtomNumsList</span><span class="cm">,</span> <span class="i">@SpecifiedAtomNamesList</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
906 893
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
907 894 <span class="i">@SpecifiedAtomNumsList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
908 895 <span class="s">(</span><span class="i">$StartAtomNum</span><span class="cm">,</span> <span class="i">$EndAtomNum</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
909 896
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
910 897 <span class="i">@SpecifiedAtomNamesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
911 898
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
912 899 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(AtomNums|AtomsRange|AtomNames)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
913 900 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">atoms</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
914 901 <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--Atoms\&quot; option in \&quot;AtomNums, AtomsRange, or AtomNames\&quot; \&quot;-m, --mode\&quot;. \n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
915 902 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
916 903 <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>} = <span class="i">$Options</span>{<span class="w">atoms</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
917 904 <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>} =~ <span class="q">s/ //g</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
918 905
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
919 906 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomNames$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
920 907 <span class="i">@SpecifiedAtomNamesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
921 908 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
922 909 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
923 910 <span class="i">@SpecifiedAtomNumsList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Atoms</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
924 911 <span class="k">for</span> <span class="i">$AtomNum</span> <span class="s">(</span><span class="i">@SpecifiedAtomNumsList</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
925 912 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$AtomNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
926 913 <span class="k">die</span> <span class="q">&quot;Error: Invalid atom number value, $AtomNum, for \&quot;--Atoms\&quot; option during \&quot;AtomNums\&quot; or \&quot;AtomsRange\&quot;value of \&quot;-m --mode\&quot; option: Atom number must be a positive integer.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
927 914 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
928 915 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
929 916 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^AtomsRange$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
930 917 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedAtomNumsList</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
931 918 <span class="k">die</span> <span class="q">&quot;Error: Invalid number of atom number values, &quot;</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedAtomNumsList</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;, for \&quot;--Atoms\&quot; option during \&quot;AtomsRange\&quot; value of \&quot;-m --mode\&quot; option: The number of values must be 2 corresponding to start and end atom numbers.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
932 919 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
933 920 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedAtomNumsList</span>[<span class="n">0</span>] &gt; <span class="i">$SpecifiedAtomNumsList</span>[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
934 921 <span class="k">die</span> <span class="q">&quot;Error: Invalid atom number values, @SpecifiedAtomNumsList, for \&quot;--Atoms\&quot; option during \&quot;AtomsRange\&quot; value of \&quot;-m --mode\&quot; option: The start atom number must be less than end atom number.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
935 922 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
936 923 <span class="s">(</span><span class="i">$StartAtomNum</span><span class="cm">,</span> <span class="i">$EndAtomNum</span><span class="s">)</span> = <span class="i">@SpecifiedAtomNumsList</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
937 924 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
938 925 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
939 926 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
940 927 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^CAlphas$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
941 928 <span class="i">@SpecifiedAtomNamesList</span> = <span class="s">(</span><span class="q">&quot;CA&quot;</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
942 929 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
943 930
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
944 931 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
945 932 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedAtomNumsList</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
946 933
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
947 934 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedStartAtomNum</span>} = <span class="i">$StartAtomNum</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
948 935 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedEndAtomNum</span>} = <span class="i">$EndAtomNum</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
949 936
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
950 937 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
951 938 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedAtomNamesList</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
952 939
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
953 940 <span class="c"># Set up a specified residue numbers map...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
954 941 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
955 942 <span class="k">for</span> <span class="i">$AtomNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsList</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
956 943 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNumsMap</span>}{<span class="i">$AtomNum</span>} = <span class="i">$AtomNum</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
957 944 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
958 945
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
959 946 <span class="c"># Set up a specified residue names map...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
960 947 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
961 948 <span class="k">for</span> <span class="i">$AtomName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesList</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
962 949 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAtomNamesMap</span>}{<span class="k">lc</span> <span class="i">$AtomName</span>} = <span class="k">lc</span> <span class="i">$AtomName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
963 950 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
964 951
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
965 952 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
966 953
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
967 954 <span class="c"># Process specified distance options...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
968 <a name="ProcessDistanceOptions-"></a> 955 <span class="k">sub </span><span class="m">ProcessDistanceOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
969 956 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
970 957
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
971 958 <span class="i">$OptionsInfo</span>{<span class="w">MaxExtractionDistance</span>} = <span class="i">$Options</span>{<span class="w">distance</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
972 959 <span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} = <span class="i">$Options</span>{<span class="w">distancemode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
973 960 <span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceOrigin</span>} = <span class="i">$Options</span>{<span class="w">distanceorigin</span>} ? <span class="i">$Options</span>{<span class="w">distanceorigin</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
974 961 <span class="i">$OptionsInfo</span>{<span class="w">DistanceSelectionMode</span>} = <span class="i">$Options</span>{<span class="w">distanceselectionmode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
975 962
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
976 963 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Distance$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
977 964 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">distanceorigin</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
978 965 <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--distanceorigin\&quot; option in \&quot;Distance\&quot; \&quot;-m, --mode\&quot;. \n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
979 966 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
980 967 <span class="i">@SpecifiedDistanceOrigin</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">distanceorigin</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
981 968 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Atom$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
982 969 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
983 970 <span class="k">die</span> <span class="q">&quot;Error: Invalid number of values, &quot;</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot; for option \&quot;distanceorigin\&quot; option during \&quot;Atom\&quot; value of \&quot;--distancemode\&quot; : The number of values must be 2.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
984 971 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
985 972 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
986 973 <span class="k">die</span> <span class="q">&quot;Error: Invalid atom number value, &quot;</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">&quot;, for option \&quot;distanceorigin\&quot; option during \&quot;Atom\&quot; value of \&quot;--distancemode\&quot;. Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
987 974 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
988 975 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
989 976 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Hetatm$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
990 977 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
991 978 <span class="k">die</span> <span class="q">&quot;Error: Invalid number of values, &quot;</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot; for option \&quot;distanceorigin\&quot; option during \&quot;Hetatm\&quot; value of \&quot;--distancemode\&quot; : The number of values must be 2.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
992 979 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
993 980 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
994 981 <span class="k">die</span> <span class="q">&quot;Error: Invalid hetatm number value, &quot;</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">&quot;, for option \&quot;distanceorigin\&quot; option during \&quot;Hetatm\&quot; value of \&quot;--distancemode\&quot;. Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
995 982 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
996 983 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
997 984 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
998 985 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> == <span class="n">2</span> || <span class="i">@SpecifiedDistanceOrigin</span> == <span class="n">3</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
999 986 <span class="k">die</span> <span class="q">&quot;Error: Invalid number of values, &quot;</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot; for option \&quot;distanceorigin\&quot; option during \&quot;Residue\&quot; value of \&quot;--distancemode\&quot; : The number of values must be either 2 or 3.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1000 987 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1001 988 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1002 989 <span class="k">die</span> <span class="q">&quot;Error: Invalid residue number value, &quot;</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">&quot;, for option \&quot;distanceorigin\&quot; option during \&quot;Residue\&quot; value of \&quot;--distancemode\&quot;. Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1003 990 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1004 991 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1005 992 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^XYZ$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1006 993 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span> != <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1007 994 <span class="k">die</span> <span class="q">&quot;Error: Invalid number of values, &quot;</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot; for option \&quot;distanceorigin\&quot; option during \&quot;XYZ\&quot; value of \&quot;--distancemode\&quot; : The number of values must be 3.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1008 995 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1009 996 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1010 997 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="i">@SpecifiedDistanceOrigin</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1011 998 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsNumerical</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1012 999 <span class="k">die</span> <span class="q">&quot;Error: Invalid coordinate value, &quot;</span><span class="cm">,</span> <span class="i">$SpecifiedDistanceOrigin</span>[<span class="n">0</span>]<span class="cm">,</span> <span class="q">&quot;, for option \&quot;distanceorigin\&quot; option during \&quot;XYZ\&quot; value of \&quot;--distancemode\&quot;. Allowed values: numerical\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1013 1000 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1014 1001 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1015 1002 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1016 1003 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1017 1004 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1018 1005 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDistanceOrigin</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1019 1006
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1020 1007 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1021 1008
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1022 1009 <span class="c"># Retrieve information about PDB files...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1023 <a name="RetrievePDBFilesInfo-"></a>1010 <span class="k">sub </span><span class="m">RetrievePDBFilesInfo</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1024 1011 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$PDBFile</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">@ChainLabels</span><span class="cm">,</span> <span class="i">@ChainSequenceIDs</span><span class="cm">,</span> <span class="i">@ChainSequenceIDsPrefix</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1025 1012
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1026 1013 <span class="i">%PDBFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1027 1014 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1028 1015 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1029 1016 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1030 1017 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1031 1018 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1032 1019 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1033 1020 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1034 1021 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1035 1022
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1036 1023 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1037 1024 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1038 1025
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1039 1026 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1040 1027 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1041 1028 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1042 1029 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1043 1030 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1044 1031 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1045 1032 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1046 1033 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1047 1034
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1048 1035 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1049 1036 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$PDBFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1050 1037 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1051 1038 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1052 1039 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1053 1040 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="q">&quot;pdb&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1054 1041 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: It&#39;s not a PDB file\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1055 1042 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1056 1043 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1057 1044 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">PDBFILE</span><span class="cm">,</span> <span class="q">&quot;$PDBFile&quot;</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1058 1045 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1059 1046 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1060 1047 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1061 1048 <span class="k">close</span> <span class="w">PDBFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1062 1049
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1063 1050 <span class="c"># Get PDB data...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1064 1051 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1065 1052 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Sequences$/i</span> &amp;&amp; <span class="i">$OptionsInfo</span>{<span class="w">SequenceRecordSource</span>} =~ <span class="q">/^SeqRes$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1066 1053 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="q">&#39;SeqRes&#39;</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1067 1054 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1068 1055 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1069 1056 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1070 1057 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1071 1058 <span class="k">if</span> <span class="s">(</span>!<span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1072 1059 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: No chains found \n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1073 1060 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1074 1061 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1075 1062
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1076 1063 <span class="c"># Make sure specified chains exist in PDB file...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1077 1064 <span class="i">@SpecifiedChains</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1078 1065 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} =~ <span class="q">/^Specified$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1079 1066 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedChains</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1080 1067 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">Residues</span>}{<span class="i">$ChainID</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1081 1068 <span class="k">push</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1082 1069 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1083 1070 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1084 1071 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: Specified chain, $ChainID, in \&quot;-c, --chains\&quot; option doesn&#39;t exist.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1085 1072 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1086 1073 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1087 1074 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1088 1075 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1089 1076 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} =~ <span class="q">/^First$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1090 1077 <span class="k">push</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}[<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1091 1078 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1092 1079 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ChainsToExtract</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1093 1080 <span class="k">push</span> <span class="i">@SpecifiedChains</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>-&gt;{<span class="w">ChainIDs</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1094 1081 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1095 1082 <span class="c"># Setup chain labels to use for sequence IDs and generating output files...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1096 1083 <span class="i">@ChainLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1097 1084 <span class="k">for</span> <span class="i">$ChainID</span> <span class="s">(</span><span class="i">@SpecifiedChains</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1098 1085 <span class="i">$ChainLabel</span> = <span class="i">$ChainID</span><span class="sc">;</span> <span class="i">$ChainLabel</span> =~ <span class="q">s/^None//ig</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1099 1086 <span class="i">$ChainLabel</span> = <span class="q">&quot;Chain${ChainLabel}&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1100 1087 <span class="k">push</span> <span class="i">@ChainLabels</span><span class="cm">,</span> <span class="i">$ChainLabel</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1101 1088 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1102 1089
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1103 1090 <span class="c"># Make sure specified distance origin is valid...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1104 1091 <span class="i">@DistanceOrigin</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1105 1092 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Distance$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1106 1093 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^(Atom|Hetatm)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1107 1094 <span class="k">my</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$SpecifiedAtomName</span><span class="cm">,</span> <span class="i">$SpecifiedAtomNumber</span><span class="cm">,</span> <span class="i">$RecordFound</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1108 1095 <span class="i">$RecordType</span> = <span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1109 1096 <span class="s">(</span><span class="i">$SpecifiedAtomNumber</span><span class="cm">,</span> <span class="i">$SpecifiedAtomName</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1110 1097 <span class="i">$RecordFound</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1111 1098 <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1112 1099 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1113 1100 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1114 1101 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1115 1102 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1116 1103 <span class="i">$AtomName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$AtomName</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1117 1104 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$RecordType</span> =~ <span class="q">/^Atom$/i</span> &amp;&amp; <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> || <span class="s">(</span><span class="i">$RecordType</span> =~ <span class="q">/^Hetatm$/i</span> &amp;&amp; <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1118 1105 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNumber</span> == <span class="i">$SpecifiedAtomNumber</span> &amp;&amp; <span class="i">$AtomName</span> <span class="k">eq</span> <span class="i">$SpecifiedAtomName</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1119 1106 <span class="i">$RecordFound</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1120 1107 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1121 1108 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1122 1109 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1123 1110 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1124 1111 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RecordFound</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1125 1112 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: &quot;</span><span class="cm">,</span> <span class="k">uc</span><span class="s">(</span><span class="i">$RecordType</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot; record corresponding to \&quot;--distanceorigin\&quot; option value, $OptionsInfo{ExtractionDistanceOrigin}, doesn&#39;t exist.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1126 1113 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1127 1114 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1128 1115 <span class="k">push</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1129 1116 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1130 1117 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1131 1118 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedResidueNumber</span><span class="cm">,</span> <span class="i">$SpecifiedResidueName</span><span class="cm">,</span> <span class="i">$SpecifiedChainID</span><span class="cm">,</span> <span class="i">$RecordFound</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1132 1119 <span class="i">$SpecifiedChainID</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1133 1120 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}} == <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1134 1121 <span class="s">(</span><span class="i">$SpecifiedResidueNumber</span><span class="cm">,</span> <span class="i">$SpecifiedResidueName</span><span class="cm">,</span> <span class="i">$SpecifiedChainID</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1135 1122 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1136 1123 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1137 1124 <span class="s">(</span><span class="i">$SpecifiedResidueNumber</span><span class="cm">,</span> <span class="i">$SpecifiedResidueName</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1138 1125 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1139 1126 <span class="i">$RecordFound</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1140 1127 <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1141 1128 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1142 1129 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1143 1130 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1144 1131 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span> = <span class="i">ParseAtomRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1145 1132 <span class="i">$ResidueName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ResidueName</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1146 1133 <span class="i">$ChainID</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ChainID</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1147 1134 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedChainID</span> &amp;&amp; <span class="s">(</span><span class="i">$SpecifiedChainID</span> <span class="k">ne</span> <span class="i">$ChainID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1148 1135 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1149 1136 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1150 1137 <span class="k">if</span> <span class="s">(</span><span class="i">$ResidueNumber</span> == <span class="i">$SpecifiedResidueNumber</span> &amp;&amp; <span class="i">$ResidueName</span> <span class="k">eq</span> <span class="i">$SpecifiedResidueName</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1151 1138 <span class="c"># Store coordinates for all the atoms...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1152 1139 <span class="i">$RecordFound</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1153 1140 <span class="k">push</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="s">(</span><span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1154 1141 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1155 1142 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1156 1143 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1157 1144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RecordFound</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1158 1145 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: ATOM/HETATM record corresponding to \&quot;--distanceorigin\&quot; option value, $OptionsInfo{ExtractionDistanceOrigin}, doesn&#39;t exist.\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1159 1146 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1160 1147 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1161 1148 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1162 1149 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^XYZ$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1163 1150 <span class="k">push</span> <span class="i">@DistanceOrigin</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedExtractionDistanceOrigin</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1164 1151 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1165 1152 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1166 1153 <span class="c"># Setup output file names...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1167 1154 <span class="i">@OutFileNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1168 1155 <span class="i">$FileDir</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1169 1156 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1170 1157 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@PDBFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1171 1158 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1172 1159 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1173 1160 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1174 1161 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1175 1162 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1176 1163 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1177 1164 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1178 1165 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1179 1166 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1180 1167 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1181 1168 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1182 1169 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1183 1170 <span class="i">$Mode</span> = <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1184 1171 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(Atoms|CAlphas|AtomNums|AtomsRange|AtomNames|ResidueNums|ResiduesRange|ResidueNames|Distance|NonWater|NonHydrogens)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1185 1172 <span class="i">$OutFileName</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1186 1173 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^CAlphas$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1187 1174 <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}CAlphas.pdb&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1188 1175 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1189 1176 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Atoms$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1190 1177 <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}Atoms.pdb&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1191 1178 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1192 1179 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomNums$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1193 1180 <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}AtomNums.pdb&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1194 1181 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1195 1182 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomsRange$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1196 1183 <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}AtomsRange.pdb&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1197 1184 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1198 1185 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomNames$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1199 1186 <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}AtomNames.pdb&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1200 1187 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1201 1188 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ResidueNums$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1202 1189 <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}ResidueNums.pdb&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1203 1190 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1204 1191 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ResiduesRange$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1205 1192 <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}ResiduesRange.pdb&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1206 1193 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1207 1194 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ResidueNames$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1208 1195 <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}ResidueNames.pdb&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1209 1196 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1210 1197 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^NonWater$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1211 1198 <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}NonWater.pdb&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1212 1199 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1213 1200 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^NonHydrogens$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1214 1201 <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}NonHydrogens.pdb&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1215 1202 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1216 1203 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Distance$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1217 1204 <span class="k">my</span><span class="s">(</span><span class="i">$DistanceMode</span><span class="s">)</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1218 1205 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Atom$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1219 1206 <span class="i">$DistanceMode</span> = <span class="q">&#39;Atom&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1220 1207 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1221 1208 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Hetatm$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1222 1209 <span class="i">$DistanceMode</span> = <span class="q">&#39;Hetatm&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1223 1210 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1224 1211 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^Residue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1225 1212 <span class="i">$DistanceMode</span> = <span class="q">&#39;Residue&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1226 1213 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1227 1214 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ExtractionDistanceMode</span>} =~ <span class="q">/^XYZ$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1228 1215 <span class="i">$DistanceMode</span> = <span class="q">&#39;XYZ&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1229 1216 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1230 1217 <span class="i">$OutFileName</span> = <span class="q">&quot;${OutFileRoot}DistanceBy${DistanceMode}.pdb&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1231 1218 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1232 1219 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1233 1220 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} &amp;&amp; <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1234 1221 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1235 1222 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1236 1223 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1237 1224 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1238 1225 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(Chains|Sequences)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1239 1226 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CombineChainSequences</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1240 1227 <span class="i">$OutFileName</span> = <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Chains$/i</span><span class="s">)</span> ? <span class="q">&quot;${OutFileRoot}ExtractedChains.pdb&quot;</span> <span class="co">:</span> <span class="q">&quot;${OutFileRoot}SequencesChainsCombined.fasta&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1241 1228 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1242 1229 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} &amp;&amp; <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1243 1230 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1244 1231 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1245 1232 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1246 1233 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1247 1234 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1248 1235 <span class="k">for</span> <span class="i">$ChainLabel</span> <span class="s">(</span><span class="i">@ChainLabels</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1249 1236 <span class="i">$OutFileName</span> = <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Chains$/i</span><span class="s">)</span> ? <span class="q">&quot;${OutFileRoot}${ChainLabel}.pdb&quot;</span> <span class="co">:</span> <span class="q">&quot;${OutFileRoot}Sequences${ChainLabel}.fasta&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1250 1237 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1251 1238 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} &amp;&amp; <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFileName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1252 1239 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $PDBFile: The file $OutFileName already exists\n&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1253 1240 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1254 1241 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1255 1242 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1256 1243 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1257 1244 <span class="s">}</span>
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parents:
diff changeset
1258 1245 <span class="i">@ChainSequenceIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1259 1246 <span class="i">@ChainSequenceIDsPrefix</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1260 1247 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Sequences$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1261 1248 <span class="k">my</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="cm">,</span> <span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="cm">,</span> <span class="i">$IDPrefix</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1262 1249 <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="i">GetHeaderRecordInformation</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1263 1250
73ae111cf86f Uploaded
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diff changeset
1264 1251 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceIDPrefixSource</span>} =~ <span class="q">/^FileName$/i</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
1265 1252 <span class="i">$IDPrefix</span> = <span class="i">$FileName</span><span class="sc">;</span>
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parents:
diff changeset
1266 1253 <span class="s">}</span>
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parents:
diff changeset
1267 1254 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SequenceIDPrefixSource</span>} =~ <span class="q">/^HeaderRecord$/i</span><span class="s">)</span> <span class="s">{</span>
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1268 1255 <span class="i">$IDPrefix</span> = <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$IDCode</span><span class="s">)</span> ? <span class="i">$IDCode</span> <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
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parents:
diff changeset
1269 1256 <span class="s">}</span>
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parents:
diff changeset
1270 1257 <span class="k">else</span> <span class="s">{</span>
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diff changeset
1271 1258 <span class="i">$IDPrefix</span> = <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$IDCode</span><span class="s">)</span> ? <span class="i">$IDCode</span> <span class="co">:</span> <span class="i">$FileName</span><span class="sc">;</span>
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parents:
diff changeset
1272 1259 <span class="s">}</span>
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1273 1260
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1274 1261 <span class="k">for</span> <span class="i">$ChainLabel</span> <span class="s">(</span><span class="i">@ChainLabels</span><span class="s">)</span> <span class="s">{</span>
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1275 1262 <span class="k">push</span> <span class="i">@ChainSequenceIDsPrefix</span><span class="cm">,</span> <span class="i">$IDPrefix</span><span class="sc">;</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1276 1263 <span class="k">push</span> <span class="i">@ChainSequenceIDs</span><span class="cm">,</span> <span class="q">&quot;${IDPrefix}_${ChainLabel}|PDB&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1277 1264 <span class="s">}</span>
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parents:
diff changeset
1278 1265 <span class="s">}</span>
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parents:
diff changeset
1279 1266
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diff changeset
1280 1267 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
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parents:
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1281 1268 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
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parents:
diff changeset
1282 1269
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parents:
diff changeset
1283 1270 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@OutFileNames</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1284 1271 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainLabels</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@ChainLabels</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1285 1272 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDsPrefix</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@ChainSequenceIDsPrefix</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1286 1273 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">ChainSequenceIDs</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@ChainSequenceIDs</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1287 1274 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">SpecifiedChains</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@SpecifiedChains</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1288 1275 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">DistanceOrigin</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@DistanceOrigin</span><span class="sc">;</span>
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parents:
diff changeset
1289 1276 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
1290 1277 <span class="s">}</span>
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parents:
diff changeset
1291 1278
73ae111cf86f Uploaded
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diff changeset
1292 1279
73ae111cf86f Uploaded
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diff changeset
1293 1280 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1294 <a name="SetupScriptUsage-"></a>1281 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
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parents:
diff changeset
1295 1282
73ae111cf86f Uploaded
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diff changeset
1296 1283 <span class="c"># Retrieve all the options...</span>
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diff changeset
1297 1284 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1298 1285 <span class="i">$Options</span>{<span class="w">chains</span>} = <span class="q">&#39;First&#39;</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1299 1286 <span class="i">$Options</span>{<span class="w">combinechains</span>} = <span class="q">&#39;no&#39;</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1300 1287 <span class="i">$Options</span>{<span class="w">distance</span>} = <span class="n">10.0</span><span class="sc">;</span>
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parents:
diff changeset
1301 1288 <span class="i">$Options</span>{<span class="w">distancemode</span>} = <span class="q">&#39;XYZ&#39;</span><span class="sc">;</span>
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parents:
diff changeset
1302 1289 <span class="i">$Options</span>{<span class="w">distanceselectionmode</span>} = <span class="q">&#39;ByAtom&#39;</span><span class="sc">;</span>
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parents:
diff changeset
1303 1290 <span class="i">$Options</span>{<span class="w">keepoldrecords</span>} = <span class="q">&#39;no&#39;</span><span class="sc">;</span>
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parents:
diff changeset
1304 1291 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;NonWater&#39;</span><span class="sc">;</span>
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parents:
diff changeset
1305 1292 <span class="i">$Options</span>{<span class="w">modifyheader</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
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parents:
diff changeset
1306 1293 <span class="i">$Options</span>{<span class="w">nonstandardkeep</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1307 1294 <span class="i">$Options</span>{<span class="w">nonstandardcode</span>} = <span class="q">&#39;X&#39;</span><span class="sc">;</span>
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parents:
diff changeset
1308 1295 <span class="i">$Options</span>{<span class="w">sequencelength</span>} = <span class="n">80</span><span class="sc">;</span>
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parents:
diff changeset
1309 1296 <span class="i">$Options</span>{<span class="w">sequenceidprefix</span>} = <span class="q">&#39;Automatic&#39;</span><span class="sc">;</span>
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parents:
diff changeset
1310 1297 <span class="i">$Options</span>{<span class="w">sequencerecords</span>} = <span class="q">&#39;Atom&#39;</span><span class="sc">;</span>
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parents:
diff changeset
1311 1298 <span class="i">$Options</span>{<span class="w">waterresiduenames</span>} = <span class="q">&#39;Automatic&#39;</span><span class="sc">;</span>
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diff changeset
1312 1299
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diff changeset
1313 1300 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;atoms|a=s&quot;</span><span class="cm">,</span> <span class="q">&quot;chains|c=s&quot;</span><span class="cm">,</span> <span class="q">&quot;combinechains=s&quot;</span><span class="cm">,</span> <span class="q">&quot;distance|d=f&quot;</span><span class="cm">,</span> <span class="q">&quot;distancemode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;distanceorigin=s&quot;</span><span class="cm">,</span> <span class="q">&quot;distanceselectionmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;keepoldrecords|k=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;modifyheader=s&quot;</span><span class="cm">,</span> <span class="q">&quot;nonstandardkeep=s&quot;</span><span class="cm">,</span> <span class="q">&quot;nonstandardcode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;recordmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;residues=s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequencelength=i&quot;</span><span class="cm">,</span> <span class="q">&quot;sequenceidprefix=s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequencerecords=s&quot;</span><span class="cm">,</span> <span class="q">&quot;waterresiduenames=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1314 1301 <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1315 1302 <span class="s">}</span>
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diff changeset
1316 1303 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1317 1304 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1318 1305 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1319 1306 <span class="s">}</span>
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diff changeset
1320 1307 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1321 1308 <span class="s">}</span>
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diff changeset
1322 1309 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">combinechains</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1323 1310 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{combinechains}, for option \&quot;--CombineChains\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1324 1311 <span class="s">}</span>
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parents:
diff changeset
1325 1312 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">distancemode</span>} !~ <span class="q">/^(Atom|Hetatm|Residue|XYZ)$/i</span><span class="s">)</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
1326 1313 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{distancemode}, for option \&quot;--DistanceMode\&quot; is not valid. Allowed values: Atom, Hetatm, Residue, or XYZ\n&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1327 1314 <span class="s">}</span>
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parents:
diff changeset
1328 1315 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">distanceselectionmode</span>} !~ <span class="q">/^(ByAtom|ByResidue)$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1329 1316 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{distanceselectionmode}, for option \&quot;--DistanceSelectionMode\&quot; is not valid. Allowed values: ByAtom or ByResidue\n&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1330 1317 <span class="s">}</span>
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diff changeset
1331 1318 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1332 1319 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{keepoldrecords}, for option \&quot;--KeepOldRecords\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1333 1320 <span class="s">}</span>
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parents:
diff changeset
1334 1321 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(Chains|Sequences|Atoms|CAlphas|AtomNums|AtomsRange|AtomNames|ResidueNums|ResidueNames|ResiduesRange|Distance|NonWater|NonHydrogens)$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1335 1322 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;m, --mode\&quot; is not valid. Allowed values: Chains, Sequences, Atoms, CAlphas, AtomNums, AtomsRange, AtomNames, ResidueNums, ResiduesRange, ResidueNames, Distance, NonWater, NonHydrogens\n&quot;</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1336 1323 <span class="s">}</span>
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parents:
diff changeset
1337 1324 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1338 1325 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{modifyheader}, for option \&quot;--ModifyHeader\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1339 1326 <span class="s">}</span>
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parents:
diff changeset
1340 1327 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">nonstandardkeep</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1341 1328 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{nonstandardkeep}, for option \&quot;--NonStandardKeep\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1342 1329 <span class="s">}</span>
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diff changeset
1343 1330 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">nonstandardcode</span>} !~ <span class="q">/^(\?|\-|X)$/i</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
1344 1331 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{nonstandardcode}, for option \&quot;--NonStandardCode\&quot; is not valid. Allowed values: ?, -, or X\n&quot;</span><span class="sc">;</span>
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parents:
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1345 1332 <span class="s">}</span>
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parents:
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1346 1333 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">recordmode</span>} &amp;&amp; <span class="i">$Options</span>{<span class="w">recordmode</span>} !~ <span class="q">/^(Atom|Hetatm|AtomAndHetatm)$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
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1347 1334 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{recordmode}, for option \&quot;--RecordMode\&quot; is not valid. Allowed values: Atom, Hetatm, AtomAndHetatm\n&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1348 1335 <span class="s">}</span>
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parents:
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1349 1336 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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parents:
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1350 1337 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{sequencelength}, for option \&quot;--SequenceLength\&quot; is not valid. Allowed values: &gt;0\n&quot;</span><span class="sc">;</span>
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parents:
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1351 1338 <span class="s">}</span>
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1352 1339 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequencerecords</span>} !~ <span class="q">/^(Atom|SeqRes)$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1353 1340 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{sequencerecords}, for option \&quot;--SequenceRecords\&quot; is not valid. Allowed values: Atom or SeqRes\n&quot;</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1354 1341 <span class="s">}</span>
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1355 1342 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequenceidprefix</span>} !~ <span class="q">/^(FileName|HeaderRecord|Automatic)$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
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1356 1343 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{sequenceidprefix}, for option \&quot;--SequenceIDPrefix\&quot; is not valid. Allowed values: FileName, HeaderRecord, or AutomaticAtom\n&quot;</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1357 1344 <span class="s">}</span>
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deepakjadmin
parents:
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1358 1345 <span class="s">}</span>
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parents:
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1359 1346
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1360 <a name="EOF-"></a></pre>
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1361 <p>&nbsp;</p>
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1362 <br />
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1363 <center>
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1364 <img src="../../../images/h2o2.png">
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1365 </center>
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parents:
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1366 </body>
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1367 </html>