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3 <title>MayaChemTools:Code:TopologicalPharmacophoreAtomTripletsFingerprints.pl</title>
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13 <pre>
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14 1 #!/usr/bin/perl -w
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: TopologicalPharmacophoreAtomTripletsFingerprints.pl,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:46:23 $</span>
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18 5 <span class="c"># $Revision: 1.34 $</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">SDFileUtil</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">MoleculeFileIO</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">FileIO::FingerprintsSDFileIO</span><span class="sc">;</span>
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53 40 <span class="k">use</span> <span class="w">FileIO::FingerprintsTextFileIO</span><span class="sc">;</span>
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54 41 <span class="k">use</span> <span class="w">FileIO::FingerprintsFPFileIO</span><span class="sc">;</span>
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55 42 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
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56 43 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="sc">;</span>
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57 44
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58 45 <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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59 46
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60 47 <span class="c"># Autoflush STDOUT</span>
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61 48 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
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62 49
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63 50 <span class="c"># Starting message...</span>
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64 51 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
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65 52 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
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66 53 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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67 54
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68 55 <span class="c"># Get the options and setup script...</span>
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69 56 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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70 57 <span class="k">if</span> <span class="s">(</span><span class="i">$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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71 58 <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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72 59 <span class="s">}</span>
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73 60
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74 61 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
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75 62 <span class="i">@SDFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"sdf sd"</span><span class="s">)</span><span class="sc">;</span>
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76 63
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77 64 <span class="c"># Process options...</span>
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78 65 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
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79 66 <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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80 67 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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81 68
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82 69 <span class="c"># Setup information about input files...</span>
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83 70 <span class="k">print</span> <span class="q">"Checking input SD file(s)...\n"</span><span class="sc">;</span>
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84 71 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
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85 72 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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86 73
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87 74 <span class="c"># Process input files..</span>
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88 75 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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89 76 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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90 77 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span>
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91 78 <span class="s">}</span>
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92 79 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
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93 80 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
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94 81 <span class="k">print</span> <span class="q">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
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95 82 <span class="i">GenerateTopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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96 83 <span class="s">}</span>
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97 84 <span class="s">}</span>
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98 85 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
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99 86
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100 87 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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101 88 <span class="i">$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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102 89 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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103 90
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104 91 <span class="c">###############################################################################</span>
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105 92
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106 93 <span class="c"># Generate fingerprints for a SD file...</span>
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107 94 <span class="c">#</span>
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108 <a name="GenerateTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 95 <span class="k">sub </span><span class="m">GenerateTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span>
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109 96 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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110 97 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$MoleculeFileIO</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="cm">,</span> <span class="i">$SetupOutputFiles</span><span class="s">)</span><span class="sc">;</span>
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111 98
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112 99 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
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113 100
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114 101 <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
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115 102 <span class="i">$SetupOutputFiles</span> = <span class="n">1</span><span class="sc">;</span>
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116 103
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117 104 <span class="i">$MoleculeFileIO</span> = <span class="w">new</span> <span class="i">MoleculeFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
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118 105 <span class="i">$MoleculeFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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119 106
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120 107 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
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121 108 <span class="i">$IgnoredCmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
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122 109
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123 110 <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Molecule</span> = <span class="i">$MoleculeFileIO</span><span class="i">->ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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124 111 <span class="i">$CmpdCount</span>++<span class="sc">;</span>
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125 112
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126 113 <span class="c"># Filter compound data before calculating fingerprints...</span>
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127 114 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Filter</span>}<span class="s">)</span> <span class="s">{</span>
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128 115 <span class="k">if</span> <span class="s">(</span><span class="i">CheckAndFilterCompound</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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129 116 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
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130 117 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
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131 118 <span class="s">}</span>
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132 119 <span class="s">}</span>
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133 120
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134 121 <span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span> = <span class="i">GenerateMoleculeFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
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135 122 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">)</span> <span class="s">{</span>
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136 123 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
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137 124 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'FingerprintsGenerationFailed'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
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138 125 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
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139 126 <span class="s">}</span>
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140 127
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141 128 <span class="k">if</span> <span class="s">(</span><span class="i">$SetupOutputFiles</span><span class="s">)</span> <span class="s">{</span>
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142 129 <span class="i">$SetupOutputFiles</span> = <span class="n">0</span><span class="sc">;</span>
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143 130 <span class="i">SetupFingerprintsLabelValueIDs</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">)</span><span class="sc">;</span>
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144 131 <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="i">SetupAndOpenOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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145 132 <span class="s">}</span>
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146 133
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147 134 <span class="i">WriteDataToOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
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148 135 <span class="s">}</span>
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149 136 <span class="i">$MoleculeFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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150 137
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151 138 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
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152 139 <span class="i">$NewFPSDFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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153 140 <span class="s">}</span>
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154 141 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
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155 142 <span class="i">$NewFPTextFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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156 143 <span class="s">}</span>
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157 144 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
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158 145 <span class="i">$NewFPFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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159 146 <span class="s">}</span>
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160 147
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161 148 <span class="i">WriteFingerprintsGenerationSummaryStatistics</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="s">)</span><span class="sc">;</span>
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162 149 <span class="s">}</span>
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163 150
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164 151 <span class="c"># Process compound being ignored due to problems in fingerprints geneation...</span>
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165 152 <span class="c">#</span>
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166 <a name="ProcessIgnoredCompound-"></a> 153 <span class="k">sub </span><span class="m">ProcessIgnoredCompound</span> <span class="s">{</span>
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167 154 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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168 155 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
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169 156
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170 157 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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171 158 <span class="i">$CmpdID</span> = <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
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172 159
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173 160 <span class="j">MODE:</span> <span class="s">{</span>
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174 161 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNonElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
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175 162 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n"</span><span class="sc">;</span>
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176 163 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
|
|
|
177 164 <span class="s">}</span>
|
|
|
178 165
|
|
|
179 166 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNoElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
180 167 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n"</span><span class="sc">;</span>
|
|
|
181 168 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
|
|
|
182 169 <span class="s">}</span>
|
|
|
183 170
|
|
|
184 171 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^FingerprintsGenerationFailed$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
185 172 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"</span><span class="sc">;</span>
|
|
|
186 173 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
|
|
|
187 174 <span class="s">}</span>
|
|
|
188 175 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"</span><span class="sc">;</span>
|
|
|
189 176 <span class="s">}</span>
|
|
|
190 177 <span class="s">}</span>
|
|
|
191 178
|
|
|
192 179 <span class="c"># Check and filter compounds....</span>
|
|
|
193 180 <span class="c">#</span>
|
|
|
194 <a name="CheckAndFilterCompound-"></a> 181 <span class="k">sub </span><span class="m">CheckAndFilterCompound</span> <span class="s">{</span>
|
|
|
195 182 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
196 183 <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
197 184
|
|
|
198 185 <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfElementsAndNonElements</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
199 186
|
|
|
200 187 <span class="k">if</span> <span class="s">(</span><span class="i">$NonElementCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
201 188 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'ContainsNonElementalData'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
202 189 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
203 190 <span class="s">}</span>
|
|
|
204 191
|
|
|
205 192 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ElementCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
206 193 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'ContainsNoElementalData'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
207 194 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
208 195 <span class="s">}</span>
|
|
|
209 196
|
|
|
210 197 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
211 198 <span class="s">}</span>
|
|
|
212 199
|
|
|
213 200 <span class="c"># Write out compounds fingerprints generation summary statistics...</span>
|
|
|
214 201 <span class="c">#</span>
|
|
|
215 <a name="WriteFingerprintsGenerationSummaryStatistics-"></a> 202 <span class="k">sub </span><span class="m">WriteFingerprintsGenerationSummaryStatistics</span> <span class="s">{</span>
|
|
|
216 203 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
217 204 <span class="k">my</span><span class="s">(</span><span class="i">$ProcessedCmpdCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
218 205
|
|
|
219 206 <span class="i">$ProcessedCmpdCount</span> = <span class="i">$CmpdCount</span> - <span class="i">$IgnoredCmpdCount</span><span class="sc">;</span>
|
|
|
220 207
|
|
|
221 208 <span class="k">print</span> <span class="q">"\nNumber of compounds: $CmpdCount\n"</span><span class="sc">;</span>
|
|
|
222 209 <span class="k">print</span> <span class="q">"Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n"</span><span class="sc">;</span>
|
|
|
223 210 <span class="k">print</span> <span class="q">"Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n"</span><span class="sc">;</span>
|
|
|
224 211 <span class="s">}</span>
|
|
|
225 212
|
|
|
226 213 <span class="c"># Append atom pair value IDs to fingerprint label...</span>
|
|
|
227 214 <span class="c">#</span>
|
|
|
228 <a name="SetupFingerprintsLabelValueIDs-"></a> 215 <span class="k">sub </span><span class="m">SetupFingerprintsLabelValueIDs</span> <span class="s">{</span>
|
|
|
229 216 <span class="k">my</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
230 217
|
|
|
231 218 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomTripletsSetSizeToUse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> ||
|
|
|
232 219 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabelMode</span>} !~ <span class="q">/^FingerprintsLabelWithIDs$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
233 220 <span class="k">return</span><span class="sc">;</span>
|
|
|
234 221 <span class="s">}</span>
|
|
|
235 222 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>} .= <span class="q">"; Value IDs: "</span> . <span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="i">->GetFingerprintsVector</span><span class="i">->GetValueIDsString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
236 223 <span class="s">}</span>
|
|
|
237 224
|
|
|
238 225 <span class="c"># Open output files...</span>
|
|
|
239 226 <span class="c">#</span>
|
|
|
240 <a name="SetupAndOpenOutputFiles-"></a> 227 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span>
|
|
|
241 228 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
242 229 <span class="k">my</span><span class="s">(</span><span class="i">$NewFPSDFile</span><span class="cm">,</span> <span class="i">$NewFPFile</span><span class="cm">,</span> <span class="i">$NewFPTextFile</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
|
|
|
243 230
|
|
|
244 231 <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
|
|
|
245 232
|
|
|
246 233 <span class="c"># Setup common parameters for fingerprints file IO objects...</span>
|
|
|
247 234 <span class="c">#</span>
|
|
|
248 235 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Write'</span><span class="cm">,</span> <span class="q">'Overwrite'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="q">'FingerprintsVectorString'</span><span class="cm">,</span> <span class="q">'VectorStringFormat'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
249 236
|
|
|
250 237 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
251 238 <span class="i">$NewFPSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
|
|
|
252 239 <span class="k">print</span> <span class="q">"Generating SD file $NewFPSDFile...\n"</span><span class="sc">;</span>
|
|
|
253 240 <span class="i">$NewFPSDFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsSDFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$NewFPSDFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">'FingerprintsFieldLabel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
254 241 <span class="i">$NewFPSDFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
255 242 <span class="s">}</span>
|
|
|
256 243
|
|
|
257 244 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
258 245 <span class="i">$NewFPFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
|
|
|
259 246 <span class="k">print</span> <span class="q">"Generating FP file $NewFPFile...\n"</span><span class="sc">;</span>
|
|
|
260 247 <span class="i">$NewFPFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsFPFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$NewFPFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
|
|
|
261 248 <span class="i">$NewFPFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
262 249 <span class="s">}</span>
|
|
|
263 250
|
|
|
264 251 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
265 252 <span class="k">my</span><span class="s">(</span><span class="i">$ColLabelsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
266 253
|
|
|
267 254 <span class="i">$NewFPTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
|
|
|
268 255 <span class="i">$ColLabelsRef</span> = <span class="i">SetupFPTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
269 256
|
|
|
270 257 <span class="k">print</span> <span class="q">"Generating text file $NewFPTextFile...\n"</span><span class="sc">;</span>
|
|
|
271 258 <span class="i">$NewFPTextFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsTextFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$NewFPTextFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">'DataColLabels'</span> <span class="cm">=></span> <span class="i">$ColLabelsRef</span><span class="cm">,</span> <span class="q">'OutDelim'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="q">'OutQuote'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
272 259 <span class="i">$NewFPTextFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
273 260 <span class="s">}</span>
|
|
|
274 261
|
|
|
275 262 <span class="k">return</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
|
|
|
276 263 <span class="s">}</span>
|
|
|
277 264
|
|
|
278 265 <span class="c"># Write fingerpritns and other data to appropriate output files...</span>
|
|
|
279 266 <span class="c">#</span>
|
|
|
280 <a name="WriteDataToOutputFiles-"></a> 267 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span>
|
|
|
281 268 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
282 269 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
283 270
|
|
|
284 271 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
285 272 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span> || <span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
|
|
|
286 273 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
287 274 <span class="s">}</span>
|
|
|
288 275
|
|
|
289 276 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
|
|
|
290 277 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
291 278
|
|
|
292 279 <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">->GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
293 280 <span class="i">$NewFPSDFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
294 281 <span class="s">}</span>
|
|
|
295 282
|
|
|
296 283 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
|
|
|
297 284 <span class="k">my</span><span class="s">(</span><span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
298 285
|
|
|
299 286 <span class="i">$ColValuesRef</span> = <span class="i">SetupFPTextFileCoulmnValues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
300 287 <span class="i">$NewFPTextFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="cm">,</span> <span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
301 288 <span class="s">}</span>
|
|
|
302 289
|
|
|
303 290 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
|
|
|
304 291 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
305 292
|
|
|
306 293 <span class="i">$CompoundID</span> = <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
307 294 <span class="i">$NewFPFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="cm">,</span> <span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
308 295 <span class="s">}</span>
|
|
|
309 296 <span class="s">}</span>
|
|
|
310 297
|
|
|
311 298 <span class="c"># Generate approriate column labels for FPText output file...</span>
|
|
|
312 299 <span class="c">#</span>
|
|
|
313 <a name="SetupFPTextFileCoulmnLabels-"></a> 300 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnLabels</span> <span class="s">{</span>
|
|
|
314 301 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
315 302 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
|
|
|
316 303
|
|
|
317 304 <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
318 305 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
319 306 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
|
|
|
320 307 <span class="s">}</span>
|
|
|
321 308 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
322 309 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
|
|
|
323 310 <span class="s">}</span>
|
|
|
324 311 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
325 312 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
|
|
|
326 313 <span class="s">}</span>
|
|
|
327 314 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
328 315 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span>
|
|
|
329 316 <span class="s">}</span>
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|
330 317 <span class="c"># Add fingerprints label...</span>
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|
|
331 318 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="sc">;</span>
|
|
|
332 319
|
|
|
333 320 <span class="k">return</span> \<span class="i">@ColLabels</span><span class="sc">;</span>
|
|
|
334 321 <span class="s">}</span>
|
|
|
335 322
|
|
|
336 323 <span class="c"># Generate column values FPText output file..</span>
|
|
|
337 324 <span class="c">#</span>
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|
338 <a name="SetupFPTextFileCoulmnValues-"></a> 325 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnValues</span> <span class="s">{</span>
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|
339 326 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
340 327 <span class="k">my</span><span class="s">(</span><span class="i">@ColValues</span><span class="s">)</span><span class="sc">;</span>
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341 328
|
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|
342 329 <span class="i">@ColValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
343 330 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
344 331 <span class="k">push</span> <span class="i">@ColValues</span><span class="cm">,</span> <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
345 332 <span class="s">}</span>
|
|
|
346 333 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
347 334 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
|
|
|
348 335 <span class="s">}</span>
|
|
|
349 336 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
350 337 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
|
|
|
351 338 <span class="s">}</span>
|
|
|
352 339 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
353 340 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
|
|
|
354 341 <span class="s">}</span>
|
|
|
355 342
|
|
|
356 343 <span class="k">return</span> \<span class="i">@ColValues</span><span class="sc">;</span>
|
|
|
357 344 <span class="s">}</span>
|
|
|
358 345
|
|
|
359 346 <span class="c"># Generate compound ID for FP and FPText output files..</span>
|
|
|
360 347 <span class="c">#</span>
|
|
|
361 <a name="SetupCmpdIDForOutputFiles-"></a> 348 <span class="k">sub </span><span class="m">SetupCmpdIDForOutputFiles</span> <span class="s">{</span>
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|
362 349 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
363 350 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
364 351
|
|
|
365 352 <span class="i">$CmpdID</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
366 353 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolNameOrLabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
367 354 <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
368 355 <span class="i">$MolName</span> = <span class="i">$Molecule</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
369 356 <span class="i">$CmpdID</span> = <span class="i">$MolName</span> ? <span class="i">$MolName</span> <span class="co">:</span> <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span>
|
|
|
370 357 <span class="s">}</span>
|
|
|
371 358 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^LabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
372 359 <span class="i">$CmpdID</span> = <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span>
|
|
|
373 360 <span class="s">}</span>
|
|
|
374 361 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
375 362 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span>
|
|
|
376 363 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
|
|
|
377 364 <span class="i">$CmpdID</span> = <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$SpecifiedDataField</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$SpecifiedDataField</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
378 365 <span class="s">}</span>
|
|
|
379 366 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolName$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
380 367 <span class="i">$CmpdID</span> = <span class="i">$Molecule</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
381 368 <span class="s">}</span>
|
|
|
382 369 <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span>
|
|
|
383 370 <span class="s">}</span>
|
|
|
384 371
|
|
|
385 372 <span class="c"># Generate fingerprints for molecule...</span>
|
|
|
386 373 <span class="c">#</span>
|
|
|
387 <a name="GenerateMoleculeFingerprints-"></a> 374 <span class="k">sub </span><span class="m">GenerateMoleculeFingerprints</span> <span class="s">{</span>
|
|
|
388 375 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
389 376 <span class="k">my</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">)</span><span class="sc">;</span>
|
|
|
390 377
|
|
|
391 378 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
392 379 <span class="i">$Molecule</span><span class="i">->KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
393 380 <span class="s">}</span>
|
|
|
394 381 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">->DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
395 382 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
396 383 <span class="s">}</span>
|
|
|
397 384 <span class="i">$Molecule</span><span class="i">->SetAromaticityModel</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
398 385 <span class="i">$Molecule</span><span class="i">->DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
399 386
|
|
|
400 387 <span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">'AtomTripletsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">AtomTripletsSetSizeToUse</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'DistanceBinSize'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">DistanceBinSize</span>}<span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">UseTriangleInequality</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
401 388
|
|
|
402 389 <span class="c"># Generate fingerprints...</span>
|
|
|
403 390 <span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="i">->GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
404 391
|
|
|
405 392 <span class="c"># Make sure fingerprints generation is successful...</span>
|
|
|
406 393 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="i">->IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
407 394 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
408 395 <span class="s">}</span>
|
|
|
409 396
|
|
|
410 397 <span class="k">return</span> <span class="i">$TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="sc">;</span>
|
|
|
411 398 <span class="s">}</span>
|
|
|
412 399
|
|
|
413 400 <span class="c"># Retrieve information about SD files...</span>
|
|
|
414 401 <span class="c">#</span>
|
|
|
415 <a name="RetrieveSDFilesInfo-"></a> 402 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
|
|
|
416 403 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$TextOutFileExt</span><span class="cm">,</span> <span class="i">$SDOutFileExt</span><span class="cm">,</span> <span class="i">$FPOutFileExt</span><span class="cm">,</span> <span class="i">$NewSDFileName</span><span class="cm">,</span> <span class="i">$NewFPFileName</span><span class="cm">,</span> <span class="i">$NewTextFileName</span><span class="cm">,</span> <span class="i">$CheckDataField</span><span class="cm">,</span> <span class="i">$CollectDataFields</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
417 404
|
|
|
418 405 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
419 406 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
420 407 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
421 408 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
422 409 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
423 410 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
424 411 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
425 412 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
426 413
|
|
|
427 414 <span class="i">$CheckDataField</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
428 415 <span class="i">$CollectDataFields</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^(All|Common)$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
429 416
|
|
|
430 417 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
|
|
|
431 418 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
432 419
|
|
|
433 420 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
434 421 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
|
|
|
435 422 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
|
|
|
436 423 <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
|
|
|
437 424 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
|
|
|
438 425
|
|
|
439 426 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
440 427 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
441 428 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span>
|
|
|
442 429 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
443 430 <span class="s">}</span>
|
|
|
444 431 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
445 432 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span>
|
|
|
446 433 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
447 434 <span class="s">}</span>
|
|
|
448 435
|
|
|
449 436 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span>
|
|
|
450 437 <span class="c"># Make sure data field exists in SD file..</span>
|
|
|
451 438 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$SpecifiedDataField</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
452 439
|
|
|
453 440 <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
454 441 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $SDFile: $! \n"</span><span class="sc">;</span>
|
|
|
455 442 <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
|
|
|
456 443 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
|
|
|
457 444 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
|
|
|
458 445 <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
|
|
|
459 446 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
|
|
|
460 447 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
461 448 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n"</span><span class="sc">;</span>
|
|
|
462 449 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
463 450 <span class="s">}</span>
|
|
|
464 451 <span class="s">}</span>
|
|
|
465 452
|
|
|
466 453 <span class="i">$AllDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
467 454 <span class="i">$CommonDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
468 455 <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span>
|
|
|
469 456 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
470 457 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $SDFile: $! \n"</span><span class="sc">;</span>
|
|
|
471 458 <span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span> = <span class="i">GetAllAndCommonCmpdDataHeaderLabels</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
|
|
|
472 459 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
|
|
|
473 460 <span class="s">}</span>
|
|
|
474 461
|
|
|
475 462 <span class="c"># Setup output file names...</span>
|
|
|
476 463 <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">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
477 464 <span class="s">(</span><span class="i">$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">$SDFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
478 465
|
|
|
479 466 <span class="i">$TextOutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span>
|
|
|
480 467 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
481 468 <span class="i">$TextOutFileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span>
|
|
|
482 469 <span class="s">}</span>
|
|
|
483 470 <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span>
|
|
|
484 471 <span class="i">$FPOutFileExt</span> = <span class="q">"fpf"</span><span class="sc">;</span>
|
|
|
485 472
|
|
|
486 473 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
487 474 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
488 475 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
|
|
|
489 476 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
|
|
|
490 477 <span class="s">}</span>
|
|
|
491 478 <span class="k">else</span> <span class="s">{</span>
|
|
|
492 479 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
|
|
|
493 480 <span class="s">}</span>
|
|
|
494 481 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
|
|
|
495 482 <span class="s">}</span>
|
|
|
496 483 <span class="k">else</span> <span class="s">{</span>
|
|
|
497 484 <span class="i">$OutFileRoot</span> = <span class="q">"${FileName}TopologicalPharmacophoreAtomTripletsFP"</span><span class="sc">;</span>
|
|
|
498 485 <span class="s">}</span>
|
|
|
499 486
|
|
|
500 487 <span class="i">$NewSDFileName</span> = <span class="q">"${OutFileRoot}.${SDOutFileExt}"</span><span class="sc">;</span>
|
|
|
501 488 <span class="i">$NewFPFileName</span> = <span class="q">"${OutFileRoot}.${FPOutFileExt}"</span><span class="sc">;</span>
|
|
|
502 489 <span class="i">$NewTextFileName</span> = <span class="q">"${OutFileRoot}.${TextOutFileExt}"</span><span class="sc">;</span>
|
|
|
503 490
|
|
|
504 491 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
505 492 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
506 493 <span class="k">warn</span> <span class="q">"Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n"</span><span class="sc">;</span>
|
|
|
507 494 <span class="k">print</span> <span class="q">"Specify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span>
|
|
|
508 495 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
509 496 <span class="s">}</span>
|
|
|
510 497 <span class="s">}</span>
|
|
|
511 498
|
|
|
512 499 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
513 500 <span class="c"># Check SD and text outout files...</span>
|
|
|
514 501 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
515 502 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span>
|
|
|
516 503 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n"</span><span class="sc">;</span>
|
|
|
517 504 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
518 505 <span class="s">}</span>
|
|
|
519 506 <span class="s">}</span>
|
|
|
520 507 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
521 508 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewFPFileName</span><span class="s">)</span> <span class="s">{</span>
|
|
|
522 509 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n"</span><span class="sc">;</span>
|
|
|
523 510 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
524 511 <span class="s">}</span>
|
|
|
525 512 <span class="s">}</span>
|
|
|
526 513 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
527 514 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewTextFileName</span><span class="s">)</span> <span class="s">{</span>
|
|
|
528 515 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n"</span><span class="sc">;</span>
|
|
|
529 516 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
530 517 <span class="s">}</span>
|
|
|
531 518 <span class="s">}</span>
|
|
|
532 519 <span class="s">}</span>
|
|
|
533 520
|
|
|
534 521 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
|
|
|
535 522
|
|
|
536 523 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
|
|
|
537 524 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span>
|
|
|
538 525 <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewFPFileName</span><span class="sc">;</span>
|
|
|
539 526 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span>
|
|
|
540 527
|
|
|
541 528 <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span>
|
|
|
542 529 <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span>
|
|
|
543 530 <span class="s">}</span>
|
|
|
544 531 <span class="s">}</span>
|
|
|
545 532
|
|
|
546 533 <span class="c"># Process option values...</span>
|
|
|
547 <a name="ProcessOptions-"></a> 534 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
|
|
|
548 535 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
549 536
|
|
|
550 537 <span class="i">ProcessAtomTypesToUseOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
551 538
|
|
|
552 539 <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span>
|
|
|
553 540
|
|
|
554 541 <span class="i">$OptionsInfo</span>{<span class="w">AtomTripletsSetSizeToUse</span>} = <span class="i">$Options</span>{<span class="w">atomtripletssetsizetouse</span>}<span class="sc">;</span>
|
|
|
555 542
|
|
|
556 543 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span>
|
|
|
557 544 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span>
|
|
|
558 545 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span>
|
|
|
559 546
|
|
|
560 547 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span>
|
|
|
561 548 <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
562 549
|
|
|
563 550 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
564 551 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
565 552
|
|
|
566 553 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
567 554 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
568 555 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
569 556 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n"</span><span class="sc">;</span>
|
|
|
570 557 <span class="s">}</span>
|
|
|
571 558 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span>
|
|
|
572 559 <span class="s">}</span>
|
|
|
573 560 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^(LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
574 561 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>} ? <span class="i">$Options</span>{<span class="w">compoundid</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span>
|
|
|
575 562 <span class="s">}</span>
|
|
|
576 563 <span class="s">}</span>
|
|
|
577 564 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
578 565 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
579 566 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n"</span><span class="sc">;</span>
|
|
|
580 567 <span class="s">}</span>
|
|
|
581 568 <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span>
|
|
|
582 569 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span>
|
|
|
583 570 <span class="s">}</span>
|
|
|
584 571
|
|
|
585 572 <span class="i">$OptionsInfo</span>{<span class="w">Filter</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
586 573
|
|
|
587 574 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabelMode</span>} = <span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>}<span class="sc">;</span>
|
|
|
588 575 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>} = <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} ? <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} <span class="co">:</span> <span class="q">'TopologicalPharmacophoreAtomTripletsFingerprints'</span><span class="sc">;</span>
|
|
|
589 576
|
|
|
590 577 <span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
591 578
|
|
|
592 579 <span class="i">$OptionsInfo</span>{<span class="w">DistanceBinSize</span>} = <span class="i">$Options</span>{<span class="w">distancebinsize</span>}<span class="sc">;</span>
|
|
|
593 580
|
|
|
594 581 <span class="i">$OptionsInfo</span>{<span class="w">MinDistance</span>} = <span class="i">$Options</span>{<span class="w">mindistance</span>}<span class="sc">;</span>
|
|
|
595 582 <span class="i">$OptionsInfo</span>{<span class="w">MaxDistance</span>} = <span class="i">$Options</span>{<span class="w">maxdistance</span>}<span class="sc">;</span>
|
|
|
596 583
|
|
|
597 584 <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
|
|
|
598 585 <span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(SD|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
599 586 <span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(FP|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
600 587 <span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(Text|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
601 588
|
|
|
602 589 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="i">$Options</span>{<span class="w">outdelim</span>}<span class="sc">;</span>
|
|
|
603 590 <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
604 591
|
|
|
605 592 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
606 593 <span class="i">$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>
|
|
|
607 594
|
|
|
608 595 <span class="i">$OptionsInfo</span>{<span class="w">UseTriangleInequality</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">usetriangleinequality</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
609 596
|
|
|
610 597 <span class="c"># Setup default vector string format...</span>
|
|
|
611 598 <span class="k">my</span><span class="s">(</span><span class="i">$VectorStringFormat</span><span class="s">)</span><span class="sc">;</span>
|
|
|
612 599 <span class="i">$VectorStringFormat</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
613 600
|
|
|
614 601 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
615 602 <span class="i">$VectorStringFormat</span> = <span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="sc">;</span>
|
|
|
616 603
|
|
|
617 604 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomtripletssetsizetouse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> && <span class="i">$VectorStringFormat</span> =~ <span class="q">/^ValuesString$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
618 605 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid for $Options{atomtripletssetsizetouse} value of \"--AtomTripletsSetSizeToUse\" option. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"</span><span class="sc">;</span>
|
|
|
619 606 <span class="s">}</span>
|
|
|
620 607 <span class="s">}</span>
|
|
|
621 608 <span class="k">else</span> <span class="s">{</span>
|
|
|
622 609 <span class="i">$VectorStringFormat</span> = <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomtripletssetsizetouse</span>} =~ <span class="q">/^FixedSize$/</span><span class="s">)</span> ? <span class="q">"ValuesString"</span> <span class="co">:</span> <span class="q">"IDsAndValuesString"</span><span class="sc">;</span>
|
|
|
623 610 <span class="s">}</span>
|
|
|
624 611 <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>} = <span class="i">$VectorStringFormat</span><span class="sc">;</span>
|
|
|
625 612 <span class="s">}</span>
|
|
|
626 613
|
|
|
627 614 <span class="c"># Process atom type to use option...</span>
|
|
|
628 615 <span class="c">#</span>
|
|
|
629 <a name="ProcessAtomTypesToUseOption-"></a> 616 <span class="k">sub </span><span class="m">ProcessAtomTypesToUseOption</span> <span class="s">{</span>
|
|
|
630 617 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypesToUse</span><span class="cm">,</span> <span class="i">@AtomTypesWords</span><span class="s">)</span><span class="sc">;</span>
|
|
|
631 618
|
|
|
632 619 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
633 620 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomtypestouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
634 621 <span class="k">die</span> <span class="q">"Error: Atom types value specified using \"-a, --AtomTypesToUse\" option is empty\n"</span><span class="sc">;</span>
|
|
|
635 622 <span class="s">}</span>
|
|
|
636 623
|
|
|
637 624 <span class="i">$SpecifiedAtomTypesToUse</span> = <span class="i">$Options</span>{<span class="w">atomtypestouse</span>}<span class="sc">;</span>
|
|
|
638 625 <span class="i">$SpecifiedAtomTypesToUse</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
639 626 <span class="i">@AtomTypesWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypesToUse</span><span class="sc">;</span>
|
|
|
640 627
|
|
|
641 628 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypesWords</span><span class="s">)</span> <span class="s">{</span>
|
|
|
642 629 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$AtomType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
643 630 <span class="k">die</span> <span class="q">"Error: Atom type specified, $AtomType, using \"-a, --AtomTypesToUse\" option is not valid...\n "</span><span class="sc">;</span>
|
|
|
644 631 <span class="s">}</span>
|
|
|
645 632 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span>
|
|
|
646 633 <span class="s">}</span>
|
|
|
647 634 <span class="s">}</span>
|
|
|
648 635
|
|
|
649 636 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
|
|
|
650 <a name="SetupScriptUsage-"></a> 637 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
|
|
|
651 638
|
|
|
652 639 <span class="c"># Retrieve all the options...</span>
|
|
|
653 640 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
654 641
|
|
|
655 642 <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span>
|
|
|
656 643
|
|
|
657 644 <span class="i">$Options</span>{<span class="w">atomtripletssetsizetouse</span>} = <span class="q">'ArbitrarySize'</span><span class="sc">;</span>
|
|
|
658 645
|
|
|
659 646 <span class="i">$Options</span>{<span class="w">atomtypestouse</span>} = <span class="q">'HBD,HBA,PI,NI,H,Ar'</span><span class="sc">;</span>
|
|
|
660 647
|
|
|
661 648 <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span>
|
|
|
662 649 <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span>
|
|
|
663 650 <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span>
|
|
|
664 651
|
|
|
665 652 <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">'Yes'</span><span class="sc">;</span>
|
|
|
666 653
|
|
|
667 654 <span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>} = <span class="q">'FingerprintsLabelOnly'</span><span class="sc">;</span>
|
|
|
668 655
|
|
|
669 656 <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">'Yes'</span><span class="sc">;</span>
|
|
|
670 657
|
|
|
671 658 <span class="i">$Options</span>{<span class="w">mindistance</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
672 659 <span class="i">$Options</span>{<span class="w">maxdistance</span>} = <span class="n">10</span><span class="sc">;</span>
|
|
|
673 660
|
|
|
674 661 <span class="i">$Options</span>{<span class="w">distancebinsize</span>} = <span class="n">2</span><span class="sc">;</span>
|
|
|
675 662
|
|
|
676 663 <span class="i">$Options</span>{<span class="w">usetriangleinequality</span>} = <span class="q">'Yes'</span><span class="sc">;</span>
|
|
|
677 664
|
|
|
678 665 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">'text'</span><span class="sc">;</span>
|
|
|
679 666 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span>
|
|
|
680 667 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span>
|
|
|
681 668
|
|
|
682 669 <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
683 670
|
|
|
684 671 <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">"aromaticitymodel=s"</span><span class="cm">,</span> <span class="q">"atomtripletssetsizetouse=s"</span><span class="cm">,</span> <span class="q">"atomtypestouse|a=s"</span><span class="cm">,</span> <span class="q">"compoundid=s"</span><span class="cm">,</span> <span class="q">"compoundidlabel=s"</span><span class="cm">,</span> <span class="q">"compoundidmode=s"</span><span class="cm">,</span> <span class="q">"datafields=s"</span><span class="cm">,</span> <span class="q">"datafieldsmode|d=s"</span><span class="cm">,</span> <span class="q">"distancebinsize=s"</span><span class="cm">,</span> <span class="q">"filter|f=s"</span><span class="cm">,</span> <span class="q">"fingerprintslabelmode=s"</span><span class="cm">,</span> <span class="q">"fingerprintslabel=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"keeplargestcomponent|k=s"</span><span class="cm">,</span> <span class="q">"mindistance=s"</span><span class="cm">,</span> <span class="q">"maxdistance=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"output=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"usetriangleinequality|u=s"</span><span class="cm">,</span> <span class="q">"vectorstringformat|v=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>
|
|
|
685 672 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
|
|
|
686 673 <span class="s">}</span>
|
|
|
687 674 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
688 675 <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>
|
|
|
689 676 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
|
|
|
690 677 <span class="s">}</span>
|
|
|
691 678 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span>
|
|
|
692 679 <span class="s">}</span>
|
|
|
693 680 <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
694 681 <span class="k">my</span><span class="s">(</span><span class="i">@SupportedModels</span><span class="s">)</span> = <span class="i">Molecule::GetSupportedAromaticityModels</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
695 682 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"</span><span class="sc">;</span>
|
|
|
696 683 <span class="s">}</span>
|
|
|
697 684 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomtripletssetsizetouse</span>} !~ <span class="q">/^(ArbitrarySize|FixedSize)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
698 685 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{atomtripletssetsizetouse}, for option \"--AtomTripletsSetSizeToUse\" is not valid. Allowed values: ArbitrarySize or FixedSize\n"</span><span class="sc">;</span>
|
|
|
699 686 <span class="s">}</span>
|
|
|
700 687 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
701 688 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span>
|
|
|
702 689 <span class="s">}</span>
|
|
|
703 690 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
704 691 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"</span><span class="sc">;</span>
|
|
|
705 692 <span class="s">}</span>
|
|
|
706 693 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">distancebinsize</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
707 694 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{distancebinsize}, for option \"--DistanceBinSize\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
|
|
|
708 695 <span class="s">}</span>
|
|
|
709 696 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
710 697 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
|
|
|
711 698 <span class="s">}</span>
|
|
|
712 699 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>} !~ <span class="q">/^(FingerprintsLabelOnly|FingerprintsLabelWithIDs)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
713 700 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{fingerprintslabelmode}, for option \"--FingerprintsLabelMode\" is not valid. Allowed values: FingerprintsLabelOnly or FingerprintsLabelWithIDs\n"</span><span class="sc">;</span>
|
|
|
714 701 <span class="s">}</span>
|
|
|
715 702 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
716 703 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
|
|
|
717 704 <span class="s">}</span>
|
|
|
718 705 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">mindistance</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
719 706 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mindistance}, for option \"--MinDistance\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
|
|
|
720 707 <span class="s">}</span>
|
|
|
721 708 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">maxdistance</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
722 709 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{maxdistance}, for option \"--MaxDistance\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
|
|
|
723 710 <span class="s">}</span>
|
|
|
724 711 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mindistance</span>} > <span class="i">$Options</span>{<span class="w">maxdistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
725 712 <span class="k">die</span> <span class="q">"Error: The value specified, specified, $Options{mindistance}, for option \"--MinDistance\" must be less than the value specified, $Options{maxdistance}, for option \"--MaxDistance\" \n"</span><span class="sc">;</span>
|
|
|
726 713 <span class="s">}</span>
|
|
|
727 714 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|FP|text|all)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
728 715 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n"</span><span class="sc">;</span>
|
|
|
729 716 <span class="s">}</span>
|
|
|
730 717 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
731 718 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span>
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732 719 <span class="s">}</span>
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733 720 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
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734 721 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
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735 722 <span class="s">}</span>
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736 723 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span> && <span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^No$/i</span><span class="s">)</span> <span class="s">{</span>
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737 724 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"</span><span class="sc">;</span>
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738 725 <span class="s">}</span>
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739 726 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">usetriangleinequality</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
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740 727 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{usetriangleinequality}, for option \"-u, --UseTriangleInequality\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
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741 728 <span class="s">}</span>
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|
742 729 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>} && <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} !~ <span class="q">/^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
743 730 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"</span><span class="sc">;</span>
|
|
|
744 731 <span class="s">}</span>
|
|
|
745 732 <span class="s">}</span>
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|
|
746 733
|
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747 <a name="EOF-"></a></pre>
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748 <p> </p>
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749 <br />
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750 <center>
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751 <img src="../../../images/h2o2.png">
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752 </center>
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753 </body>
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754 </html>
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