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3 <title>MayaChemTools:Code:ModifyPDBFiles.pl</title>
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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: ModifyPDBFiles.pl,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
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18 5 <span class="c"># $Revision: 1.25 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></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 <http://www.gnu.org/licenses/> 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">"$FindBin::Bin/../lib"</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
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52 39 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span>
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53 40
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54 41 <span class="c"># Autoflush STDOUT</span>
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55 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
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56 43
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57 44 <span class="c"># Starting message...</span>
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58 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
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59 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
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60 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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61 48
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62 49 <span class="c"># Get the options and setup script...</span>
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63 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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64 51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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65 52 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span>
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66 53 <span class="s">}</span>
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67 54
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68 55 <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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69 56 <span class="i">@PDBFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"pdb"</span><span class="s">)</span><span class="sc">;</span>
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70 57
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71 58 <span class="c"># Process options...</span>
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72 59 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
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73 60 <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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74 61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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75 62
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76 63 <span class="c"># Setup information about input files...</span>
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77 64 <span class="k">print</span> <span class="q">"Checking input PDB file(s)...\n"</span><span class="sc">;</span>
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78 65 <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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79 66 <span class="i">RetrievePDBFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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80 67
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81 68 <span class="c"># Process input files..</span>
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82 69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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83 70 <span class="k">if</span> <span class="s">(</span><span class="i">@PDBFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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84 71 <span class="k">print</span> <span class="q">"\nProcessing PDB files...\n"</span><span class="sc">;</span>
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85 72 <span class="s">}</span>
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86 73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
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87 74 <span class="k">if</span> <span class="s">(</span><span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
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88 75 <span class="k">print</span> <span class="q">"\nProcessing file $PDBFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
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89 76 <span class="i">ModifyPDBFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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90 77 <span class="s">}</span>
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91 78 <span class="s">}</span>
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92 79 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
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93 80
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94 81 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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95 82 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span>
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96 83 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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97 84
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98 85 <span class="c">###############################################################################</span>
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99 86
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100 87 <span class="c"># Modify appropriate information...</span>
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101 <a name="ModifyPDBFiles-"></a> 88 <span class="k">sub </span><span class="m">ModifyPDBFiles</span> <span class="s">{</span>
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102 89 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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103 90 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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104 91
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105 92 <span class="c"># Get PDB data...</span>
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106 93 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
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107 94 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
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108 95
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109 96 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberAtoms$/i</span><span class="s">)</span> <span class="s">{</span>
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110 97 <span class="i">RenumberAtoms</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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111 98 <span class="s">}</span>
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112 99 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberResidues$/i</span><span class="s">)</span> <span class="s">{</span>
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113 100 <span class="i">RenumberResidues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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114 101 <span class="s">}</span>
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115 102 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenumberWaters$/i</span><span class="s">)</span> <span class="s">{</span>
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116 103 <span class="i">RenumberWaters</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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117 104 <span class="s">}</span>
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118 105 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^RenameChainIDs$/i</span><span class="s">)</span> <span class="s">{</span>
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119 106 <span class="i">RenameChainsIDs</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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120 107 <span class="s">}</span>
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121 108 <span class="s">}</span>
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122 109
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123 110 <span class="c"># Renumber atom and hetro atom numbers...</span>
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124 <a name="RenumberAtoms-"></a> 111 <span class="k">sub </span><span class="m">RenumberAtoms</span> <span class="s">{</span>
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125 112 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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126 113 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="cm">,</span> <span class="i">$NewAtomNumber</span><span class="cm">,</span> <span class="i">$RecordType</span><span class="cm">,</span> <span class="i">%OldToNewAtomNumbersMap</span><span class="s">)</span><span class="sc">;</span>
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127 114
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128 115 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
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129 116 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span>
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130 117 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span>
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131 118
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132 119 <span class="c"># Write out header and other older recors...</span>
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133 120 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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134 121
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135 122 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span>
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136 123 <span class="c"># chains and multiple models..</span>
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137 124 <span class="i">%OldToNewAtomNumbersMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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138 125 <span class="i">$NewAtomNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>}<span class="sc">;</span>
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139 126 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
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140 127 <span class="k">if</span> <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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141 128 <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
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142 129
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143 130 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
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144 131
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145 132 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$NewAtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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146 133
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147 134 <span class="i">$OldToNewAtomNumbersMap</span>{<span class="i">$AtomNumber</span>} = <span class="i">$NewAtomNumber</span><span class="sc">;</span>
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148 135 <span class="i">$NewAtomNumber</span>++<span class="sc">;</span>
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149 136 <span class="s">}</span>
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150 137 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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151 138 <span class="i">$NewAtomNumber</span>++<span class="sc">;</span>
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152 139 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$NewAtomNumber</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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153 140 <span class="s">}</span>
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154 141 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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155 142 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
156 143 <span class="s">}</span>
|
|
|
157 144 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
158 145 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
159 146 <span class="c"># Restart numbering...</span>
|
|
|
160 147 <span class="i">$NewAtomNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>}<span class="sc">;</span>
|
|
|
161 148 <span class="s">}</span>
|
|
|
162 149 <span class="s">}</span>
|
|
|
163 150
|
|
|
164 151 <span class="c"># Write out modified CONECT records...</span>
|
|
|
165 152 <span class="k">my</span><span class="s">(</span><span class="i">$ModifiedConectAtomNum</span><span class="cm">,</span> <span class="i">$ConectAtomNum</span><span class="cm">,</span> <span class="i">@ConectAtomNums</span><span class="cm">,</span> <span class="i">@ModifiedConectAtomNums</span><span class="s">)</span><span class="sc">;</span>
|
|
|
166 153 <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
167 154 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
168 155 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
|
|
|
169 156 <span class="s">}</span>
|
|
|
170 157 <span class="i">@ConectAtomNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
171 158 <span class="i">@ModifiedConectAtomNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
172 159 <span class="k">push</span> <span class="i">@ConectAtomNums</span><span class="cm">,</span> <span class="i">ParseConectRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
173 160 <span class="j">ATOMNUMBER:</span> <span class="k">for</span> <span class="i">$ConectAtomNum</span> <span class="s">(</span><span class="i">@ConectAtomNums</span><span class="s">)</span> <span class="s">{</span>
|
|
|
174 161 <span class="i">$ModifiedConectAtomNum</span> = <span class="i">$ConectAtomNum</span><span class="sc">;</span>
|
|
|
175 162 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ConectAtomNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
176 163 <span class="i">$AtomNumber</span> = <span class="i">$ConectAtomNum</span><span class="sc">;</span>
|
|
|
177 164 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
178 165 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OldToNewAtomNumbersMap</span>{<span class="i">$AtomNumber</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
179 166 <span class="i">$ModifiedConectAtomNum</span> = <span class="i">$OldToNewAtomNumbersMap</span>{<span class="i">$AtomNumber</span>}<span class="sc">;</span>
|
|
|
180 167 <span class="s">}</span>
|
|
|
181 168 <span class="s">}</span>
|
|
|
182 169 <span class="s">}</span>
|
|
|
183 170 <span class="k">push</span> <span class="i">@ModifiedConectAtomNums</span><span class="cm">,</span> <span class="i">$ModifiedConectAtomNum</span><span class="sc">;</span>
|
|
|
184 171 <span class="s">}</span>
|
|
|
185 172 <span class="c"># Write out the record...</span>
|
|
|
186 173 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateConectRecordLine</span><span class="s">(</span><span class="i">@ModifiedConectAtomNums</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
187 174 <span class="s">}</span>
|
|
|
188 175
|
|
|
189 176 <span class="c"># Write out END record...</span>
|
|
|
190 177 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
191 178
|
|
|
192 179 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
|
|
|
193 180 <span class="s">}</span>
|
|
|
194 181
|
|
|
195 182 <span class="c"># Renumber residues...</span>
|
|
|
196 <a name="RenumberResidues-"></a> 183 <span class="k">sub </span><span class="m">RenumberResidues</span> <span class="s">{</span>
|
|
|
197 184 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
198 185 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="cm">,</span> <span class="i">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$NewHetatmResidueNumber</span><span class="cm">,</span> <span class="i">$TERCount</span><span class="cm">,</span> <span class="i">$TotalTERCount</span><span class="cm">,</span> <span class="i">$PreviousResidueNumber</span><span class="cm">,</span> <span class="i">$PreviousHetatmResidueNumber</span><span class="cm">,</span> <span class="i">$RecordType</span><span class="s">)</span><span class="sc">;</span>
|
|
|
199 186
|
|
|
200 187 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
|
|
|
201 188 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span>
|
|
|
202 189 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span>
|
|
|
203 190
|
|
|
204 191 <span class="c"># Write out header and other older recors...</span>
|
|
|
205 192 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
206 193
|
|
|
207 194 <span class="c"># Do a quick count of all TER records...</span>
|
|
|
208 195 <span class="i">$TotalTERCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
209 196 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
210 197 <span class="k">if</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
211 198 <span class="i">$TotalTERCount</span>++<span class="sc">;</span>
|
|
|
212 199 <span class="s">}</span>
|
|
|
213 200 <span class="s">}</span>
|
|
|
214 201
|
|
|
215 202 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span>
|
|
|
216 203 <span class="c"># chains and multiple models..</span>
|
|
|
217 204 <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>}<span class="sc">;</span>
|
|
|
218 205 <span class="i">$NewHetatmResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingHetatmResidueNumber</span>}<span class="sc">;</span>
|
|
|
219 206
|
|
|
220 207 <span class="i">$TERCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
221 208 <span class="i">$PreviousResidueNumber</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
222 209 <span class="i">$PreviousHetatmResidueNumber</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
223 210
|
|
|
224 211 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
225 212 <span class="k">if</span> <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="s">(</span><span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> && <span class="s">(</span><span class="i">$TERCount</span> < <span class="i">$TotalTERCount</span> || <span class="i">$OptionsInfo</span>{<span class="w">HetatmResidueNumberMode</span>} =~ <span class="q">/^Automatic$/i</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
226 213 <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
227 214 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
228 215
|
|
|
229 216 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousResidueNumber</span> && <span class="i">$PreviousResidueNumber</span> != <span class="i">$ResidueNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
230 217 <span class="i">$PreviousResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span>
|
|
|
231 218 <span class="i">$NewResidueNumber</span>++<span class="sc">;</span>
|
|
|
232 219 <span class="s">}</span>
|
|
|
233 220 <span class="k">else</span> <span class="s">{</span>
|
|
|
234 221 <span class="c"># First residue in a chain...</span>
|
|
|
235 222 <span class="i">$PreviousResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span>
|
|
|
236 223 <span class="s">}</span>
|
|
|
237 224 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
238 225
|
|
|
239 226 <span class="s">}</span>
|
|
|
240 227 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
241 228 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
242 229
|
|
|
243 230 <span class="c"># User HETATM residue numbers...</span>
|
|
|
244 231 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousHetatmResidueNumber</span> && <span class="i">$PreviousHetatmResidueNumber</span> != <span class="i">$ResidueNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
245 232 <span class="i">$PreviousHetatmResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span>
|
|
|
246 233 <span class="i">$NewHetatmResidueNumber</span>++<span class="sc">;</span>
|
|
|
247 234 <span class="s">}</span>
|
|
|
248 235 <span class="k">else</span> <span class="s">{</span>
|
|
|
249 236 <span class="c"># First HETATM residue outside a chain...</span>
|
|
|
250 237 <span class="i">$PreviousHetatmResidueNumber</span> = <span class="i">$ResidueNumber</span><span class="sc">;</span>
|
|
|
251 238 <span class="s">}</span>
|
|
|
252 239
|
|
|
253 240 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateHetatmRecordLine</span><span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$NewHetatmResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
254 241 <span class="s">}</span>
|
|
|
255 242 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
256 243 <span class="i">$TERCount</span>++<span class="sc">;</span>
|
|
|
257 244 <span class="i">$AtomNumber</span>++<span class="sc">;</span>
|
|
|
258 245 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
259 246 <span class="c"># For per chain numbering, start over again...</span>
|
|
|
260 247 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ResidueNumberMode</span>} =~ <span class="q">/^PerChain$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
261 248 <span class="k">if</span> <span class="s">(</span><span class="i">$TERCount</span> < <span class="i">$TotalTERCount</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
262 249 <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>}<span class="sc">;</span>
|
|
|
263 250 <span class="s">}</span>
|
|
|
264 251 <span class="i">$PreviousResidueNumber</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
265 252 <span class="s">}</span>
|
|
|
266 253 <span class="s">}</span>
|
|
|
267 254 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
268 255 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
269 256 <span class="s">}</span>
|
|
|
270 257 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
271 258 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
272 259 <span class="s">}</span>
|
|
|
273 260 <span class="s">}</span>
|
|
|
274 261
|
|
|
275 262 <span class="c"># Write out CONECT records...</span>
|
|
|
276 263 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
277 264 <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
278 265 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
279 266 <span class="s">}</span>
|
|
|
280 267 <span class="s">}</span>
|
|
|
281 268
|
|
|
282 269 <span class="c"># Write out END record...</span>
|
|
|
283 270 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
284 271
|
|
|
285 272 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
|
|
|
286 273 <span class="s">}</span>
|
|
|
287 274
|
|
|
288 275 <span class="c"># Renumber water residues...</span>
|
|
|
289 <a name="RenumberWaters-"></a> 276 <span class="k">sub </span><span class="m">RenumberWaters</span> <span class="s">{</span>
|
|
|
290 277 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
291 278 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="cm">,</span> <span class="i">$NewResidueNumber</span><span class="cm">,</span> <span class="i">$RecordType</span><span class="s">)</span><span class="sc">;</span>
|
|
|
292 279
|
|
|
293 280 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
|
|
|
294 281 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span>
|
|
|
295 282 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span>
|
|
|
296 283
|
|
|
297 284 <span class="c"># Write out header and other older recors...</span>
|
|
|
298 285 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
299 286
|
|
|
300 287 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span>
|
|
|
301 288 <span class="c"># chains and multiple models..</span>
|
|
|
302 289 <span class="i">$NewResidueNumber</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingWaterResidueNumber</span>}<span class="sc">;</span>
|
|
|
303 290 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
304 291 <span class="k">if</span> <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
305 292 <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
306 293
|
|
|
307 294 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
308 295
|
|
|
309 296 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$ResidueName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
310 297 <span class="i">$ResidueNumber</span> = <span class="i">$NewResidueNumber</span><span class="sc">;</span>
|
|
|
311 298 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
312 299 <span class="i">$NewResidueNumber</span>++<span class="sc">;</span>
|
|
|
313 300 <span class="s">}</span>
|
|
|
314 301 <span class="k">else</span> <span class="s">{</span>
|
|
|
315 302 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
316 303 <span class="s">}</span>
|
|
|
317 304 <span class="s">}</span>
|
|
|
318 305 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
319 306 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
320 307 <span class="s">}</span>
|
|
|
321 308 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
322 309 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
323 310 <span class="s">}</span>
|
|
|
324 311 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
325 312 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
326 313 <span class="s">}</span>
|
|
|
327 314 <span class="s">}</span>
|
|
|
328 315
|
|
|
329 316 <span class="c"># Write out CONECT records...</span>
|
|
|
330 317 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
331 318 <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
332 319 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
333 320 <span class="s">}</span>
|
|
|
334 321 <span class="s">}</span>
|
|
|
335 322
|
|
|
336 323 <span class="c"># Write out END record...</span>
|
|
|
337 324 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
338 325
|
|
|
339 326 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
|
|
|
340 327 <span class="s">}</span>
|
|
|
341 328
|
|
|
342 329 <span class="c"># Rename chain IDs...</span>
|
|
|
343 <a name="RenameChainsIDs-"></a> 330 <span class="k">sub </span><span class="m">RenameChainsIDs</span> <span class="s">{</span>
|
|
|
344 331 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
345 332 <span class="k">my</span><span class="s">(</span><span class="i">$PDBFileName</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="cm">,</span> <span class="i">$ConectRecordLinesRef</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="cm">,</span> <span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$PreviousChainID</span><span class="cm">,</span> <span class="i">$FirstChainID</span><span class="cm">,</span> <span class="i">$NewChainID</span><span class="cm">,</span> <span class="i">$NewChainIDCounter</span><span class="cm">,</span> <span class="i">%OldToNewChainIDsMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
346 333
|
|
|
347 334 <span class="i">$PDBFileName</span> = <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$FileIndex</span>][<span class="n">0</span>]<span class="sc">;</span>
|
|
|
348 335 <span class="k">print</span> <span class="q">"Generating PDBFileName file $PDBFileName...\n"</span><span class="sc">;</span>
|
|
|
349 336 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PDBFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PDBFileName: $! \n"</span><span class="sc">;</span>
|
|
|
350 337
|
|
|
351 338 <span class="c"># Write out header and other older recors...</span>
|
|
|
352 339 <span class="i">WriteHeaderAndOlderRecords</span><span class="s">(</span>\<span class="i">*OUTFILE</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
353 340
|
|
|
354 341 <span class="c"># Write out all ATOM records along with TER and model records to indicate</span>
|
|
|
355 342 <span class="c"># chains and multiple models..</span>
|
|
|
356 343 <span class="i">%OldToNewChainIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
357 344 <span class="i">$NewChainIDCounter</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartingChainID</span>}<span class="sc">;</span>
|
|
|
358 345 <span class="i">$FirstChainID</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
359 346 <span class="i">$PreviousChainID</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
360 347 <span class="j">LINE:</span> <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
361 348 <span class="k">if</span> <span class="s">(</span><span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
362 349 <span class="i">$RecordType</span> = <span class="i">GetPDBRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
363 350
|
|
|
364 351 <span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$ChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span> = <span class="i">ParseAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
365 352
|
|
|
366 353 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$ResidueName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
367 354 <span class="c"># Chain IDs are not assigned to water residues...</span>
|
|
|
368 355 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
369 356 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
|
|
|
370 357 <span class="s">}</span>
|
|
|
371 358
|
|
|
372 359 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstChainID</span><span class="s">)</span> <span class="s">{</span>
|
|
|
373 360 <span class="i">$FirstChainID</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
374 361 <span class="i">$PreviousChainID</span> = <span class="i">$ChainID</span><span class="sc">;</span>
|
|
|
375 362 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainID</span> || <span class="s">(</span>!<span class="i">$ChainID</span> && <span class="i">$OptionsInfo</span>{<span class="w">RenameEmptyChainIDs</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
376 363 <span class="i">$NewChainID</span> = <span class="i">$NewChainIDCounter</span><span class="sc">;</span>
|
|
|
377 364 <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>} = <span class="i">$NewChainID</span><span class="sc">;</span>
|
|
|
378 365 <span class="s">}</span>
|
|
|
379 366 <span class="k">else</span> <span class="s">{</span>
|
|
|
380 367 <span class="i">$NewChainID</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
381 368 <span class="s">}</span>
|
|
|
382 369 <span class="s">}</span>
|
|
|
383 370 <span class="k">elsif</span> <span class="s">(</span><span class="i">$PreviousChainID</span> <span class="k">ne</span> <span class="i">$ChainID</span><span class="s">)</span> <span class="s">{</span>
|
|
|
384 371 <span class="k">if</span> <span class="s">(</span><span class="i">$ChainID</span> || <span class="s">(</span>!<span class="i">$ChainID</span> && <span class="i">$OptionsInfo</span>{<span class="w">RenameEmptyChainIDs</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
385 372 <span class="i">$PreviousChainID</span> = <span class="i">$ChainID</span><span class="sc">;</span>
|
|
|
386 373 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
387 374 <span class="i">$NewChainID</span> = <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>}<span class="sc">;</span>
|
|
|
388 375 <span class="s">}</span>
|
|
|
389 376 <span class="k">else</span> <span class="s">{</span>
|
|
|
390 377 <span class="i">$NewChainIDCounter</span>++<span class="sc">;</span>
|
|
|
391 378 <span class="i">$NewChainID</span> = <span class="i">$NewChainIDCounter</span><span class="sc">;</span>
|
|
|
392 379 <span class="i">$OldToNewChainIDsMap</span>{<span class="i">$ChainID</span>} = <span class="i">$NewChainID</span><span class="sc">;</span>
|
|
|
393 380 <span class="s">}</span>
|
|
|
394 381 <span class="s">}</span>
|
|
|
395 382 <span class="k">else</span> <span class="s">{</span>
|
|
|
396 383 <span class="i">$NewChainID</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
397 384 <span class="s">}</span>
|
|
|
398 385 <span class="s">}</span>
|
|
|
399 386
|
|
|
400 387 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateAtomOrHetatmRecordLine</span><span class="s">(</span><span class="i">$RecordType</span><span class="cm">,</span> <span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AlternateLocation</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$NewChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="cm">,</span> <span class="i">$X</span><span class="cm">,</span> <span class="i">$Y</span><span class="cm">,</span> <span class="i">$Z</span><span class="cm">,</span> <span class="i">$Occupancy</span><span class="cm">,</span> <span class="i">$TemperatureFactor</span><span class="cm">,</span> <span class="i">$SegmentID</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$AtomCharge</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
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|
401 388 <span class="s">}</span>
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|
402 389 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsTerRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
403 390 <span class="i">$AtomNumber</span>++<span class="sc">;</span>
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|
404 391 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateTerRecordLine</span><span class="s">(</span><span class="i">$AtomNumber</span><span class="cm">,</span> <span class="i">$ResidueName</span><span class="cm">,</span> <span class="i">$NewChainID</span><span class="cm">,</span> <span class="i">$ResidueNumber</span><span class="cm">,</span> <span class="i">$InsertionCode</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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|
405 392 <span class="s">}</span>
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|
406 393 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
407 394 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
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|
408 395 <span class="s">}</span>
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|
409 396 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEndmdlRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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410 397 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
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|
411 398 <span class="s">}</span>
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|
412 399 <span class="s">}</span>
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413 400
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414 401 <span class="c"># Write out CONECT records...</span>
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415 402 <span class="k">for</span> <span class="i">$RecordLine</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
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416 403 <span class="k">if</span> <span class="s">(</span><span class="i">IsConectRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
417 404 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
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|
418 405 <span class="s">}</span>
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|
419 406 <span class="s">}</span>
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420 407
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421 408 <span class="c"># Write out END record...</span>
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422 409 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="i">GenerateEndRecordLine</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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423 410
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|
424 411 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
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|
425 412 <span class="s">}</span>
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426 413
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427 414
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428 415 <span class="c"># Write out modifed header and other older records...</span>
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|
429 <a name="WriteHeaderAndOlderRecords-"></a> 416 <span class="k">sub </span><span class="m">WriteHeaderAndOlderRecords</span> <span class="s">{</span>
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430 417 <span class="k">my</span><span class="s">(</span><span class="i">$OutFileRef</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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431 418
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|
432 419 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>}<span class="s">)</span> <span class="s">{</span>
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|
433 420 <span class="c"># Write out modified HEADER record...</span>
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|
434 421 <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="i">GetHeaderRecordInformation</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
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|
435 422 <span class="i">$Classification</span> = <span class="q">'Data modified using MayaChemTools'</span><span class="sc">;</span>
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|
436 423 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">GenerateHeaderRecordLine</span><span class="s">(</span><span class="i">$IDCode</span><span class="cm">,</span> <span class="i">$Classification</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
437 424 <span class="s">}</span>
|
|
|
438 425 <span class="k">else</span> <span class="s">{</span>
|
|
|
439 426 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="i">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
440 427 <span class="s">}</span>
|
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|
441 428
|
|
|
442 429 <span class="c"># Write out any old records...</span>
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|
443 430 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>}<span class="s">)</span> <span class="s">{</span>
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|
|
444 431 <span class="k">my</span><span class="s">(</span><span class="i">$RecordLineIndex</span><span class="cm">,</span> <span class="i">$RecordLine</span><span class="s">)</span><span class="sc">;</span>
|
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|
445 432 <span class="c"># Skip HEADER record and write out older records all the way upto first MODEL/ATOM/HETATM records from input file...</span>
|
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|
446 433 <span class="j">RECORDLINE:</span> <span class="k">for</span> <span class="i">$RecordLineIndex</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$PDBRecordLinesRef</span>}<span class="s">)</span> <span class="s">{</span>
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|
|
447 434 <span class="i">$RecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="i">$RecordLineIndex</span>]<span class="sc">;</span>
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|
|
448 435 <span class="k">if</span> <span class="s">(</span><span class="i">IsModelRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsAtomRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span> || <span class="i">IsHetatmRecordType</span><span class="s">(</span><span class="i">$RecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
449 436 <span class="k">last</span> <span class="j">RECORDLINE</span><span class="sc">;</span>
|
|
|
450 437 <span class="s">}</span>
|
|
|
451 438 <span class="k">print</span> <span class="i">$OutFileRef</span> <span class="q">"$RecordLine\n"</span><span class="sc">;</span>
|
|
|
452 439 <span class="s">}</span>
|
|
|
453 440 <span class="s">}</span>
|
|
|
454 441 <span class="s">}</span>
|
|
|
455 442
|
|
|
456 443 <span class="c"># Get header record information assuming it's the first record...</span>
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|
|
457 <a name="GetHeaderRecordInformation-"></a> 444 <span class="k">sub </span><span class="m">GetHeaderRecordInformation</span> <span class="s">{</span>
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|
|
458 445 <span class="k">my</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
459 446 <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="cm">,</span> <span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
460 447
|
|
|
461 448 <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="s">(</span><span class="q">''</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
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|
|
462 449 <span class="i">$HeaderRecordLine</span> = <span class="i">$PDBRecordLinesRef</span>->[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
463 450 <span class="k">if</span> <span class="s">(</span><span class="i">IsHeaderRecordType</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
464 451 <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span> = <span class="i">ParseHeaderRecordLine</span><span class="s">(</span><span class="i">$HeaderRecordLine</span><span class="s">)</span><span class="sc">;</span>
|
|
|
465 452 <span class="s">}</span>
|
|
|
466 453 <span class="k">return</span> <span class="s">(</span><span class="i">$Classification</span><span class="cm">,</span> <span class="i">$DepositionDate</span><span class="cm">,</span> <span class="i">$IDCode</span><span class="s">)</span><span class="sc">;</span>
|
|
|
467 454 <span class="s">}</span>
|
|
|
468 455
|
|
|
469 456
|
|
|
470 457 <span class="c"># Process option values...</span>
|
|
|
471 <a name="ProcessOptions-"></a> 458 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
|
|
|
472 459 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
473 460 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
|
|
|
474 461
|
|
|
475 462 <span class="i">$OptionsInfo</span>{<span class="w">StartingAtomNumber</span>} = <span class="i">$Options</span>{<span class="w">atomnumberstart</span>}<span class="sc">;</span>
|
|
|
476 463 <span class="i">$OptionsInfo</span>{<span class="w">StartingChainID</span>} = <span class="i">$Options</span>{<span class="w">chainidstart</span>}<span class="sc">;</span>
|
|
|
477 464 <span class="i">$OptionsInfo</span>{<span class="w">RenameEmptyChainIDs</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidrenameempty</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
478 465
|
|
|
479 466 <span class="i">$OptionsInfo</span>{<span class="w">KeepOldRecords</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
480 467 <span class="i">$OptionsInfo</span>{<span class="w">ModifyHeaderRecord</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
481 468
|
|
|
482 469 <span class="i">$OptionsInfo</span>{<span class="w">ResidueNumberMode</span>} = <span class="i">$Options</span>{<span class="w">residuenumbermode</span>}<span class="sc">;</span>
|
|
|
483 470 <span class="i">$OptionsInfo</span>{<span class="w">StartingResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">residuenumberstart</span>}<span class="sc">;</span>
|
|
|
484 471
|
|
|
485 472 <span class="i">$OptionsInfo</span>{<span class="w">HetatmResidueNumberMode</span>} = <span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>}<span class="sc">;</span>
|
|
|
486 473 <span class="i">$OptionsInfo</span>{<span class="w">StartingHetatmResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>}<span class="sc">;</span>
|
|
|
487 474
|
|
|
488 475 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
489 476 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
490 477
|
|
|
491 478 <span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} = <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span>
|
|
|
492 479 <span class="i">$OptionsInfo</span>{<span class="w">StartingWaterResidueNumber</span>} = <span class="i">$Options</span>{<span class="w">waterresiduestart</span>}<span class="sc">;</span>
|
|
|
493 480 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
494 481 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
495 482
|
|
|
496 483 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span><span class="sc">;</span>
|
|
|
497 484 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
498 485 <span class="k">my</span><span class="s">(</span><span class="i">$WaterResidueName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
499 486 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WaterResidueNames</span>} =~ <span class="q">/Automatic/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
500 487 <span class="k">push</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="cm">,</span> <span class="s">(</span><span class="q">'HOH'</span><span class="cm">,</span> <span class="q">'WAT'</span><span class="cm">,</span> <span class="q">'H2O'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
501 488 <span class="s">}</span>
|
|
|
502 489 <span class="k">else</span> <span class="s">{</span>
|
|
|
503 490 <span class="i">@SpecifiedWaterResiduesList</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">waterresiduenames</span>}<span class="sc">;</span>
|
|
|
504 491 <span class="s">}</span>
|
|
|
505 492 <span class="k">for</span> <span class="i">$WaterResidueName</span> <span class="s">(</span><span class="i">@SpecifiedWaterResiduesList</span><span class="s">)</span> <span class="s">{</span>
|
|
|
506 493 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesMap</span>}{<span class="i">$WaterResidueName</span>} = <span class="i">$WaterResidueName</span><span class="sc">;</span>
|
|
|
507 494 <span class="s">}</span>
|
|
|
508 495 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedWaterResiduesList</span>}}<span class="cm">,</span> <span class="i">@SpecifiedWaterResiduesList</span><span class="sc">;</span>
|
|
|
509 496 <span class="s">}</span>
|
|
|
510 497
|
|
|
511 498 <span class="c"># Retrieve information about PDB files...</span>
|
|
|
512 <a name="RetrievePDBFilesInfo-"></a> 499 <span class="k">sub </span><span class="m">RetrievePDBFilesInfo</span> <span class="s">{</span>
|
|
|
513 500 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$PDBFile</span><span class="cm">,</span> <span class="i">$PDBRecordLinesRef</span><span class="cm">,</span> <span class="i">$ChainsAndResiduesInfoRef</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$OutFileMode</span><span class="cm">,</span> <span class="i">@OutFileNames</span><span class="s">)</span><span class="sc">;</span>
|
|
|
514 501
|
|
|
515 502 <span class="i">%PDBFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
516 503 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
517 504 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
518 505 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
519 506
|
|
|
520 507 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#PDBFilesList</span><span class="s">)</span> <span class="s">{</span>
|
|
|
521 508 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
522 509
|
|
|
523 510 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
|
|
|
524 511 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
525 512 <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
526 513
|
|
|
527 514 <span class="i">$PDBFile</span> = <span class="i">$PDBFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
528 515 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$PDBFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
529 516 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It doesn't exist\n"</span><span class="sc">;</span>
|
|
|
530 517 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
531 518 <span class="s">}</span>
|
|
|
532 519 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$PDBFile</span><span class="cm">,</span> <span class="q">"pdb"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
533 520 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: It's not a PDB file\n"</span><span class="sc">;</span>
|
|
|
534 521 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
535 522 <span class="s">}</span>
|
|
|
536 523 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">PDBFILE</span><span class="cm">,</span> <span class="q">"$PDBFile"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
537 524 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: Couldn't open it: $! \n"</span><span class="sc">;</span>
|
|
|
538 525 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
539 526 <span class="s">}</span>
|
|
|
540 527 <span class="k">close</span> <span class="w">PDBFILE</span><span class="sc">;</span>
|
|
|
541 528
|
|
|
542 529 <span class="c"># Get PDB data...</span>
|
|
|
543 530 <span class="i">$PDBRecordLinesRef</span> = <span class="i">ReadPDBFile</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
544 531 <span class="i">$ChainsAndResiduesInfoRef</span> = <span class="i">GetChainsAndResidues</span><span class="s">(</span><span class="i">$PDBRecordLinesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
545 532 <span class="k">if</span> <span class="s">(</span>!<span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ChainsAndResiduesInfoRef</span>->{<span class="w">ChainIDs</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
546 533 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $PDBFile: No chains found \n"</span><span class="sc">;</span>
|
|
|
547 534 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
548 535 <span class="s">}</span>
|
|
|
549 536
|
|
|
550 537 <span class="c"># Setup output file names...</span>
|
|
|
551 538 <span class="i">@OutFileNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
552 539 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
553 540 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$PDBFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
554 541 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@PDBFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
555 542 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
556 543 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
|
|
|
557 544 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
|
|
|
558 545 <span class="s">}</span>
|
|
|
559 546 <span class="k">else</span> <span class="s">{</span>
|
|
|
560 547 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
|
|
|
561 548 <span class="s">}</span>
|
|
|
562 549 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
|
|
|
563 550 <span class="s">}</span>
|
|
|
564 551 <span class="k">else</span> <span class="s">{</span>
|
|
|
565 552 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
|
|
|
566 553 <span class="s">}</span>
|
|
|
567 554 <span class="i">$Mode</span> = <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="sc">;</span>
|
|
|
568 555 <span class="j">MODE:</span> <span class="s">{</span>
|
|
|
569 556 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenumberAtoms$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">'RenumberAtoms'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
|
|
|
570 557 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenumberResidues$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">'RenumberResidues'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
|
|
|
571 558 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenumberWaters$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">'RenumberWaters'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
|
|
|
572 559 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RenameChainIDs$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">'RenameChainIDs'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
|
|
|
573 560 <span class="i">$OutFileMode</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
574 561 <span class="s">}</span>
|
|
|
575 562 <span class="i">$OutFileName</span> = <span class="q">"${OutFileRoot}${OutFileMode}.pdb"</span><span class="sc">;</span>
|
|
|
576 563 <span class="k">push</span> <span class="i">@OutFileNames</span><span class="cm">,</span> <span class="i">$OutFileName</span><span class="sc">;</span>
|
|
|
577 564
|
|
|
578 565 <span class="i">$PDBFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
|
|
|
579 566 <span class="i">$PDBFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
|
|
|
580 567
|
|
|
581 568 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PDBFilesInfo</span>{<span class="w">OutFileNames</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@OutFileNames</span><span class="sc">;</span>
|
|
|
582 569 <span class="s">}</span>
|
|
|
583 570 <span class="s">}</span>
|
|
|
584 571
|
|
|
585 572 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
|
|
|
586 <a name="SetupScriptUsage-"></a> 573 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
|
|
|
587 574
|
|
|
588 575 <span class="c"># Retrieve all the options...</span>
|
|
|
589 576 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
590 577 <span class="i">$Options</span>{<span class="w">atomnumberstart</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
591 578 <span class="i">$Options</span>{<span class="w">chainidstart</span>} = <span class="q">'A'</span><span class="sc">;</span>
|
|
|
592 579 <span class="i">$Options</span>{<span class="w">chainidrenameempty</span>} = <span class="q">'No'</span><span class="sc">;</span>
|
|
|
593 580 <span class="i">$Options</span>{<span class="w">keepoldrecords</span>} = <span class="q">'no'</span><span class="sc">;</span>
|
|
|
594 581 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'RenumberResidues'</span><span class="sc">;</span>
|
|
|
595 582 <span class="i">$Options</span>{<span class="w">modifyheader</span>} = <span class="q">'yes'</span><span class="sc">;</span>
|
|
|
596 583 <span class="i">$Options</span>{<span class="w">residuenumbermode</span>} = <span class="q">'PerChain'</span><span class="sc">;</span>
|
|
|
597 584 <span class="i">$Options</span>{<span class="w">residuenumberstart</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
598 585 <span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>} = <span class="q">'Automatic'</span><span class="sc">;</span>
|
|
|
599 586 <span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>} = <span class="n">6000</span><span class="sc">;</span>
|
|
|
600 587 <span class="i">$Options</span>{<span class="w">waterresiduenames</span>} = <span class="q">'Automatic'</span><span class="sc">;</span>
|
|
|
601 588 <span class="i">$Options</span>{<span class="w">waterresiduestart</span>} = <span class="n">8000</span><span class="sc">;</span>
|
|
|
602 589
|
|
|
603 590 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"atomnumberstart|a=i"</span><span class="cm">,</span> <span class="q">"chainidstart|c=s"</span><span class="cm">,</span> <span class="q">"chainidrenameempty=s"</span><span class="cm">,</span> <span class="q">"keepoldrecords|k=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"modifyheader=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"residuenumbermode=s"</span><span class="cm">,</span> <span class="q">"residuenumberstart=i"</span><span class="cm">,</span> <span class="q">"residuenumberhetatmmode=s"</span><span class="cm">,</span> <span class="q">"residuenumberstarthetatm=i"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"sequencelength=i"</span><span class="cm">,</span> <span class="q">"waterresiduenames=s"</span><span class="cm">,</span> <span class="q">"waterresiduestart=i"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
604 591 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
|
|
|
605 592 <span class="s">}</span>
|
|
|
606 593 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
607 594 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
608 595 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
|
|
|
609 596 <span class="s">}</span>
|
|
|
610 597 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span>
|
|
|
611 598 <span class="s">}</span>
|
|
|
612 599 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomnumberstart</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
613 600 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{atomnumberstart}, for option \"-a, --AtomNumberStart\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span>
|
|
|
614 601 <span class="s">}</span>
|
|
|
615 602 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidstart</span>}<span class="s">)</span> > <span class="n">1</span><span class="s">)</span> || <span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidstart</span>} !~ <span class="q">/[A-Z]/i</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
616 603 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{chainidstart}, for option \"-c, --ChainIDStart\" is not valid. Allowed values: a single character from A to Z\n"</span><span class="sc">;</span>
|
|
|
617 604 <span class="s">}</span>
|
|
|
618 605 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">chainidrenameempty</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
619 606 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{chainidrenameempty}, for option \"--chainidrenameempty\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
|
|
|
620 607 <span class="s">}</span>
|
|
|
621 608 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keepoldrecords</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
622 609 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keepoldrecords}, for option \"--KeepOldRecords\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
|
|
|
623 610 <span class="s">}</span>
|
|
|
624 611 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(RenumberAtoms|RenumberResidues|RenumberWaters|RenameChainIDs)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
625 612 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: RenumberAtoms, RenumberResidues, RenumberWaters or RenameChainIDs\n"</span><span class="sc">;</span>
|
|
|
626 613 <span class="s">}</span>
|
|
|
627 614 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">modifyheader</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
628 615 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{modifyheader}, for option \"--ModifyHeader\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
|
|
|
629 616 <span class="s">}</span>
|
|
|
630 617 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumbermode</span>} !~ <span class="q">/^(Sequential|PerChain)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
631 618 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumbermode}, for option \"--ResidueNumberMode\" is not valid. Allowed values: Sequential or PerChain\n"</span><span class="sc">;</span>
|
|
|
632 619 <span class="s">}</span>
|
|
|
633 620 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberstart</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
634 621 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumberstart}, for option \"--ResidueNumberStart\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span>
|
|
|
635 622 <span class="s">}</span>
|
|
|
636 623 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberhetatmmode</span>} !~ <span class="q">/^(automatic|specify)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
637 624 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumberhetatmmode}, for option \"--residuenumbermode\" is not valid. Allowed values: automatic or specify\n"</span><span class="sc">;</span>
|
|
|
638 625 <span class="s">}</span>
|
|
|
639 626 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">residuenumberstarthetatm</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
640 627 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{residuenumberstarthetatm}, for option \"--residuenumberstartHetatm\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span>
|
|
|
641 628 <span class="s">}</span>
|
|
|
642 629 <span class="k">if</span> <span class="s">(</span>!<span class="w">IsPositiveInteger</span> <span class="i">$Options</span>{<span class="w">waterresiduestart</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
643 630 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{waterresiduestart}, for option \"--waterresiduestart\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span>
|
|
|
644 631 <span class="s">}</span>
|
|
|
645 632 <span class="s">}</span>
|
|
|
646 633
|
|
|
647 <a name="EOF-"></a></pre>
|
|
|
648 <p> </p>
|
|
|
649 <br />
|
|
|
650 <center>
|
|
|
651 <img src="../../../images/h2o2.png">
|
|
|
652 </center>
|
|
|
653 </body>
|
|
|
654 </html>
|
