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