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1 <html>
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3 <title>MayaChemTools:Code:SimilaritySearchingFingerprints.pl</title>
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12 <br/>
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13 <pre>
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14 1 #!/usr/bin/perl -w
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: SimilaritySearchingFingerprints.pl,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:46:21 $</span>
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18 5 <span class="c"># $Revision: 1.18 $</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">StatisticsUtil</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">PseudoHeap</span><span class="sc">;</span>
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53 40 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsFileUtil</span><span class="sc">;</span>
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54 41 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsBitVector</span><span class="sc">;</span>
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55 42 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsVector</span><span class="sc">;</span>
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56 43
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57 44 <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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58 45
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59 46 <span class="c"># Autoflush STDOUT</span>
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60 47 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
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61 48
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62 49 <span class="c"># Starting message...</span>
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63 50 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
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64 51 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
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65 52 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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66 53
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67 54 <span class="c"># Get the options and setup script...</span>
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68 55 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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69 56 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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70 57 <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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71 58 <span class="s">}</span>
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72 59
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73 60 <span class="c"># Process reference and database file names...</span>
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74 61 <span class="k">my</span><span class="s">(</span><span class="i">@FingerprintsFilesList</span><span class="s">)</span><span class="sc">;</span>
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75 62 <span class="i">ProcessFingerprintsFileNames</span><span class="s">(</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 fingerprints inut and SD/text output files...</span>
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83 70 <span class="k">my</span><span class="s">(</span><span class="i">%FingerprintsFilesInfo</span><span class="cm">,</span> <span class="i">%OutputFilesInfo</span><span class="cm">,</span> <span class="i">%SimilaritySearchInfo</span><span class="s">)</span><span class="sc">;</span>
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84 71 <span class="k">print</span> <span class="q">"Checking and retrieving information from reference and database fingerprints files...\n"</span><span class="sc">;</span>
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85 72 <span class="i">RetrieveFingerprintsFilesInfo</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"># Perform similarity search...</span>
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88 75 <span class="k">print</span> <span class="q">"Performing similarity search...\n"</span><span class="sc">;</span>
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89 76 <span class="k">my</span><span class="s">(</span><span class="i">%SimilaritySearchResults</span><span class="cm">,</span> <span class="i">%DatabaseFingerprintsFileData</span><span class="s">)</span><span class="sc">;</span>
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90 77 <span class="i">PerformSimilaritySearch</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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91 78
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92 79 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
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93 80
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94 81 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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95 82 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span>
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96 83 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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97 84
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98 85 <span class="c">###############################################################################</span>
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99 86
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100 87 <span class="c"># Perform similarity search using fingerprints data in reference and database text files...</span>
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101 88 <span class="c">#</span>
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102 <a name="PerformSimilaritySearch-"></a> 89 <span class="k">sub </span><span class="m">PerformSimilaritySearch</span> <span class="s">{</span>
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103 90
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104 91 <span class="k">print</span> <span class="q">"\nProcessing fingerprints data for reference molecules...\n"</span><span class="sc">;</span>
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105 92 <span class="i">ReadReferenceFingerprintsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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106 93
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107 94 <span class="i">InitializeSimilaritySearchResults</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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108 95 <span class="i">GenerateSimilaritySearchResults</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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109 96 <span class="i">WriteSimilaritySearchResultFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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110 97 <span class="s">}</span>
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111 98
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112 99 <span class="c"># Find similar molecules from database molecules for individual or multiple reference molecules...</span>
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113 100 <span class="c">#</span>
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114 <a name="GenerateSimilaritySearchResults-"></a> 101 <span class="k">sub </span><span class="m">GenerateSimilaritySearchResults</span> <span class="s">{</span>
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115 102 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseFingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FingerprintsCount</span><span class="cm">,</span> <span class="i">$IgnoredFingerprintsCount</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsObject</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ReferenceFingerprintsObject</span><span class="cm">,</span> <span class="i">$ReferenceIndex</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$FusedComparisonValue</span><span class="cm">,</span> <span class="i">@ComparisonValues</span><span class="s">)</span><span class="sc">;</span>
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116 103
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117 104 <span class="k">print</span> <span class="q">"Processing fingerprints data for database molecules...\n"</span><span class="sc">;</span>
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118 105
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119 106 <span class="s">(</span><span class="i">$FingerprintsCount</span><span class="cm">,</span> <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
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120 107
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121 108 <span class="i">$DatabaseFingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsFileIOParameters</span>}}<span class="s">)</span><span class="sc">;</span>
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122 109 <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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123 110
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124 111 <span class="i">@ComparisonValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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125 112
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126 113 <span class="j">DATABASEFP:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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127 114 <span class="i">$FingerprintsCount</span>++<span class="sc">;</span>
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128 115
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129 116 <span class="k">if</span> <span class="s">(</span>!<span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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130 117 <span class="i">$IgnoredFingerprintsCount</span>++<span class="sc">;</span>
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131 118 <span class="k">next</span> <span class="j">DATABASEFP</span><span class="sc">;</span>
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132 119 <span class="s">}</span>
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133 120 <span class="i">$DatabaseFingerprintsObject</span> = <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->GetFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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134 121 <span class="i">$DatabaseCmpdID</span> = <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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135 122
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136 123 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span>
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137 124 <span class="i">@ComparisonValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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138 125 <span class="s">}</span>
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139 126
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140 127 <span class="j">REFERENCEFP:</span> <span class="k">for</span> <span class="i">$ReferenceIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceCmpdIDsRef</span>}}<span class="s">)</span> <span class="s">{</span>
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141 128 <span class="i">$ReferenceCmpdID</span> = <span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceCmpdIDsRef</span>}->[<span class="i">$ReferenceIndex</span>]<span class="sc">;</span>
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142 129 <span class="i">$ReferenceFingerprintsObject</span> = <span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceFingerprintsObjectsRef</span>}->[<span class="i">$ReferenceIndex</span>]<span class="sc">;</span>
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143 130
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144 131 <span class="i">$ComparisonValue</span> = <span class="i">CompareReferenceAndDatabaseFingerprintsPair</span><span class="s">(</span><span class="i">$ReferenceFingerprintsObject</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsObject</span><span class="s">)</span><span class="sc">;</span>
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145 132 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ComparisonValue</span><span class="s">)</span> <span class="s">{</span>
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146 133 <span class="k">next</span> <span class="j">REFERENCEFP</span><span class="sc">;</span>
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147 134 <span class="s">}</span>
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148 135
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149 136 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>}<span class="s">)</span> <span class="s">{</span>
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150 137 <span class="i">CollectSimilaritySearchResults</span><span class="s">(</span><span class="i">$DatabaseFingerprintsFileIO</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span><span class="sc">;</span>
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151 138 <span class="s">}</span>
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152 139 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span>
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153 140 <span class="k">push</span> <span class="i">@ComparisonValues</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="sc">;</span>
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154 141 <span class="s">}</span>
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155 142 <span class="s">}</span>
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156 143
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157 144 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span>
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158 145 <span class="i">$FusedComparisonValue</span> = <span class="i">CalculateGroupFusionComparisonValue</span><span class="s">(</span>\<span class="i">@ComparisonValues</span><span class="s">)</span><span class="sc">;</span>
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159 146 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$FusedComparisonValue</span><span class="s">)</span> <span class="s">{</span>
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160 147 <span class="k">next</span> <span class="j">DATABASEFP</span><span class="sc">;</span>
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161 148 <span class="s">}</span>
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162 149 <span class="i">CollectSimilaritySearchResults</span><span class="s">(</span><span class="i">$DatabaseFingerprintsFileIO</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$FusedComparisonValue</span><span class="s">)</span><span class="sc">;</span>
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163 150 <span class="s">}</span>
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164 151 <span class="s">}</span>
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165 152 <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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166 153
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167 154 <span class="k">print</span> <span class="q">"Number of fingerprints data entries in database fingerprints file: $FingerprintsCount\n"</span><span class="sc">;</span>
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168 155 <span class="k">print</span> <span class="q">"Number of fingerprints date entries processed successfully: "</span><span class="cm">,</span> <span class="s">(</span><span class="i">$FingerprintsCount</span> - <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> <span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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169 156 <span class="k">print</span> <span class="q">"Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n"</span><span class="sc">;</span>
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170 157 <span class="s">}</span>
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171 158
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172 159 <span class="c"># Compare a pair of reference and database fingerprints objects corresponding to bit-vector or</span>
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173 160 <span class="c"># vectors using specified comparison method and comparison cutoff...</span>
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174 161 <span class="c">#</span>
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175 <a name="CompareReferenceAndDatabaseFingerprintsPair-"></a> 162 <span class="k">sub </span><span class="m">CompareReferenceAndDatabaseFingerprintsPair</span> <span class="s">{</span>
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176 163 <span class="k">my</span><span class="s">(</span><span class="i">$ReferenceFingerprintsObject</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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177 164 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMethod</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="s">)</span><span class="sc">;</span>
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178 165
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179 166 <span class="i">$ComparisonMethod</span> = <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethod</span>}<span class="sc">;</span>
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180 167 <span class="i">$ComparisonValue</span> = <span class="i">$ReferenceFingerprintsObject</span><span class="i">->$ComparisonMethod</span><span class="s">(</span><span class="i">$DatabaseFingerprintsObject</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethodParameters</span>}}<span class="s">)</span><span class="sc">;</span>
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181 168
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182 169 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ComparisonValue</span><span class="s">)</span> <span class="s">{</span>
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183 170 <span class="k">warn</span> <span class="q">"Warning: Ignoring fingerprints data for reference compound ID "</span><span class="cm">,</span> <span class="i">$ReferenceFingerprintsObject</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">": Its comparison with database compound ID, "</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsObject</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">", failed.\n"</span><span class="sc">;</span>
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184 171 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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185 172 <span class="s">}</span>
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186 173
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187 174 <span class="i">$ComparisonValue</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="s">)</span><span class="sc">;</span>
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188 175
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189 176 <span class="c"># Apply any comparison cutoff...</span>
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190 177 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyComparisonCutoff</span>}<span class="s">)</span> <span class="s">{</span>
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191 178 <span class="k">return</span> <span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} ? <span class="s">(</span><span class="i">$ComparisonValue</span> >= <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonCutoff</span>} ? <span class="i">$ComparisonValue</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$ComparisonValue</span> <= <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonCutoff</span>} ? <span class="i">$ComparisonValue</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
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192 179 <span class="s">}</span>
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193 180 <span class="k">else</span> <span class="s">{</span>
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194 181 <span class="k">return</span> <span class="i">$ComparisonValue</span><span class="sc">;</span>
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195 182 <span class="s">}</span>
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196 183 <span class="s">}</span>
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197 184
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198 185 <span class="c"># Calculate group fusion comparison value...</span>
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199 186 <span class="c">#</span>
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200 <a name="CalculateGroupFusionComparisonValue-"></a> 187 <span class="k">sub </span><span class="m">CalculateGroupFusionComparisonValue</span> <span class="s">{</span>
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201 188 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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202 189 <span class="k">my</span><span class="s">(</span><span class="i">$FusedComparisonValue</span><span class="cm">,</span> <span class="i">@ComparisonValues</span><span class="s">)</span><span class="sc">;</span>
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203 190
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204 191 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$ComparisonValuesRef</span>}<span class="s">)</span> <span class="s">{</span>
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205 192 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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206 193 <span class="s">}</span>
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207 194
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208 195 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">SortComparisonValues</span>}<span class="s">)</span> <span class="s">{</span>
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209 196 <span class="i">@ComparisonValues</span> = <span class="k">sort</span> <span class="s">{</span> <span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} ? <span class="s">(</span><span class="i">$b</span> <=> <span class="i">$a</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$a</span> <=> <span class="i">$b</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$ComparisonValuesRef</span>}<span class="sc">;</span>
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210 197 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">UsekNN</span>} && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">kNN</span>} < <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$ComparisonValuesRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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211 198 <span class="c"># Keep only top kNN values for group fusion...</span>
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212 199 <span class="k">splice</span> <span class="i">@ComparisonValues</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">kNN</span>}<span class="sc">;</span>
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213 200 <span class="s">}</span>
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214 201 <span class="i">$ComparisonValuesRef</span> = \<span class="i">@ComparisonValues</span><span class="sc">;</span>
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|
|
215 202 <span class="s">}</span>
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216 203
|
|
|
217 204 <span class="i">$FusedComparisonValue</span> = <span class="i">&</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>}}<span class="s">(</span><span class="i">$ComparisonValuesRef</span><span class="s">)</span><span class="sc">;</span>
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218 205 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>}<span class="s">)</span> <span class="s">{</span>
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|
219 206 <span class="i">$FusedComparisonValue</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$FusedComparisonValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
220 207 <span class="s">}</span>
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|
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221 208
|
|
|
222 209 <span class="k">return</span> <span class="i">$FusedComparisonValue</span><span class="sc">;</span>
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|
|
223 210 <span class="s">}</span>
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224 211
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|
225 212 <span class="c"># Collect similarity results for individual reference and multiple references search...</span>
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|
226 213 <span class="c">#</span>
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|
227 <a name="CollectSimilaritySearchResults-"></a> 214 <span class="k">sub </span><span class="m">CollectSimilaritySearchResults</span> <span class="s">{</span>
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228 215 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseFingerprintsFileIO</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
229 216
|
|
|
230 217 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span> <span class="s">{</span>
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|
|
231 218 <span class="i">$SimilaritySearchResults</span>{<span class="i">$ReferenceCmpdID</span>}<span class="i">->AddKeyValuePair</span><span class="s">(</span><span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
232 219 <span class="s">}</span>
|
|
|
233 220 <span class="k">else</span> <span class="s">{</span>
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|
234 221 <span class="i">$SimilaritySearchResults</span>{<span class="w">ResultsPseudoHeap</span>}<span class="i">->AddKeyValuePair</span><span class="s">(</span><span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
235 222 <span class="s">}</span>
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236 223
|
|
|
237 224 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectInputFileData</span>}<span class="s">)</span> <span class="s">{</span>
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|
|
238 225 <span class="i">CollectDatabaseFileData</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsFileIO</span><span class="s">)</span><span class="sc">;</span>
|
|
|
239 226 <span class="s">}</span>
|
|
|
240 227 <span class="s">}</span>
|
|
|
241 228
|
|
|
242 229 <span class="c"># Initialize similarity results for individual or multiple reference molecules...</span>
|
|
|
243 230 <span class="c">#</span>
|
|
|
244 <a name="InitializeSimilaritySearchResults-"></a> 231 <span class="k">sub </span><span class="m">InitializeSimilaritySearchResults</span> <span class="s">{</span>
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|
|
245 232 <span class="k">my</span><span class="s">(</span><span class="i">$ReferenceCmpdID</span><span class="s">)</span><span class="sc">;</span>
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|
246 233
|
|
|
247 234 <span class="i">%SimilaritySearchResults</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
248 235
|
|
|
249 236 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
250 237 <span class="k">for</span> <span class="i">$ReferenceCmpdID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceCmpdIDsRef</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
251 238 <span class="i">$SimilaritySearchResults</span>{<span class="i">$ReferenceCmpdID</span>} = <span class="w">new</span> <span class="i">PseudoHeap</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} ? <span class="q">'KeepTopN'</span> <span class="co">:</span> <span class="q">'KeepBottomN'</span><span class="s">)</span><span class="cm">,</span> <span class="q">'KeyType'</span> <span class="cm">=></span> <span class="q">'Numeric'</span><span class="cm">,</span> <span class="q">'MaxSize'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSimilarMolecules</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
252 239 <span class="s">}</span>
|
|
|
253 240 <span class="s">}</span>
|
|
|
254 241 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
255 242 <span class="i">$SimilaritySearchResults</span>{<span class="w">ResultsPseudoHeap</span>} = <span class="w">new</span> <span class="i">PseudoHeap</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} ? <span class="q">'KeepTopN'</span> <span class="co">:</span> <span class="q">'KeepBottomN'</span><span class="s">)</span><span class="cm">,</span> <span class="q">'KeyType'</span> <span class="cm">=></span> <span class="q">'Numeric'</span><span class="cm">,</span> <span class="q">'MaxSize'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSimilarMolecules</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
256 243 <span class="s">}</span>
|
|
|
257 244
|
|
|
258 245 <span class="i">%DatabaseFingerprintsFileData</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
259 246 <span class="s">}</span>
|
|
|
260 247
|
|
|
261 248 <span class="c"># Write out results SD and/or CSV/TSV text files for individual or multiple reference molecules...</span>
|
|
|
262 249 <span class="c">#</span>
|
|
|
263 <a name="WriteSimilaritySearchResultFiles-"></a> 250 <span class="k">sub </span><span class="m">WriteSimilaritySearchResultFiles</span> <span class="s">{</span>
|
|
|
264 251 <span class="k">my</span><span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
265 252
|
|
|
266 253 <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">SetupAndOpenOutputFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
267 254
|
|
|
268 255 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
269 256 <span class="k">for</span> <span class="i">$ReferenceCmpdID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceCmpdIDsRef</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
270 257 <span class="k">for</span> <span class="i">$ComparisonValue</span> <span class="s">(</span><span class="i">$SimilaritySearchResults</span>{<span class="i">$ReferenceCmpdID</span>}<span class="i">->GetSortedKeys</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
271 258 <span class="k">for</span> <span class="i">$DatabaseCmpdID</span> <span class="s">(</span><span class="i">$SimilaritySearchResults</span>{<span class="i">$ReferenceCmpdID</span>}<span class="i">->GetKeyValues</span><span class="s">(</span><span class="i">$ComparisonValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
272 259 <span class="i">WriteDataToOutputFiles</span><span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
273 260 <span class="s">}</span>
|
|
|
274 261 <span class="s">}</span>
|
|
|
275 262 <span class="s">}</span>
|
|
|
276 263 <span class="s">}</span>
|
|
|
277 264 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
278 265 <span class="k">for</span> <span class="i">$ComparisonValue</span> <span class="s">(</span><span class="i">$SimilaritySearchResults</span>{<span class="w">ResultsPseudoHeap</span>}<span class="i">->GetSortedKeys</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
279 266 <span class="k">for</span> <span class="i">$DatabaseCmpdID</span> <span class="s">(</span><span class="i">$SimilaritySearchResults</span>{<span class="w">ResultsPseudoHeap</span>}<span class="i">->GetKeyValues</span><span class="s">(</span><span class="i">$ComparisonValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
280 267 <span class="i">WriteDataToOutputFiles</span><span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
281 268 <span class="s">}</span>
|
|
|
282 269 <span class="s">}</span>
|
|
|
283 270 <span class="s">}</span>
|
|
|
284 271
|
|
|
285 272 <span class="k">if</span> <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
286 273 <span class="k">close</span> <span class="i">$NewSDFileRef</span><span class="sc">;</span>
|
|
|
287 274 <span class="s">}</span>
|
|
|
288 275 <span class="k">if</span> <span class="s">(</span><span class="i">$NewTextFileRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
289 276 <span class="k">close</span> <span class="i">$NewTextFileRef</span><span class="sc">;</span>
|
|
|
290 277 <span class="s">}</span>
|
|
|
291 278 <span class="s">}</span>
|
|
|
292 279
|
|
|
293 280 <span class="c"># Write individual reference or multiple references similarity results along with any other data to output files...</span>
|
|
|
294 281 <span class="c">#</span>
|
|
|
295 <a name="WriteDataToOutputFiles-"></a> 282 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span>
|
|
|
296 283 <span class="k">my</span><span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="cm">,</span> <span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
297 284
|
|
|
298 285 <span class="k">if</span> <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
299 286 <span class="i">WriteMolStringDataToSDOutputFile</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
300 287 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span> <span class="s">{</span>
|
|
|
301 288 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <ReferenceCmpdID>\n$ReferenceCmpdID\n\n"</span><span class="sc">;</span>
|
|
|
302 289 <span class="s">}</span>
|
|
|
303 290 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <DatabaseCmpdID>\n$DatabaseCmpdID\n\n> <ComparisonValue>\n$ComparisonValue\n\n"</span><span class="sc">;</span>
|
|
|
304 291 <span class="i">WriteDatabaseDataToSDOutputFile</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
305 292 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"\$\$\$\$\n"</span><span class="sc">;</span>
|
|
|
306 293 <span class="s">}</span>
|
|
|
307 294
|
|
|
308 295 <span class="k">if</span> <span class="s">(</span><span class="i">$NewTextFileRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
309 296 <span class="k">my</span><span class="s">(</span><span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
|
|
|
310 297
|
|
|
311 298 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
312 299 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$ReferenceCmpdID</span><span class="s">)</span> <span class="s">{</span>
|
|
|
313 300 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$ReferenceCmpdID</span><span class="sc">;</span>
|
|
|
314 301 <span class="s">}</span>
|
|
|
315 302 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$ComparisonValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
316 303
|
|
|
317 304 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>} || <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
318 305 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">RetrieveDatabaseDataForTextOutputFile</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
319 306 <span class="s">}</span>
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|
|
320 307 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
321 308 <span class="s">}</span>
|
|
|
322 309 <span class="s">}</span>
|
|
|
323 310
|
|
|
324 311 <span class="c"># Open output files...</span>
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|
|
325 312 <span class="c">#</span>
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|
326 <a name="SetupAndOpenOutputFiles-"></a> 313 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span>
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|
|
327 314 <span class="k">my</span><span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$NewSDFile</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
328 315
|
|
|
329 316 <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">2</span><span class="sc">;</span>
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330 317
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|
331 318 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
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|
|
332 319 <span class="i">$NewSDFile</span> = <span class="i">$OutputFilesInfo</span>{<span class="w">SDOutFileName</span>}<span class="sc">;</span>
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|
|
333 320 <span class="k">print</span> <span class="q">"Generating SD file $NewSDFile...\n"</span><span class="sc">;</span>
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|
|
334 321 <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">">$NewSDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewSDFile: $! \n"</span><span class="sc">;</span>
|
|
|
335 322 <span class="i">$NewSDFileRef</span> = \<span class="i">*NEWSDFILE</span><span class="sc">;</span>
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|
|
336 323 <span class="s">}</span>
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|
337 324
|
|
|
338 325 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
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|
|
339 326 <span class="i">$NewTextFile</span> = <span class="i">$OutputFilesInfo</span>{<span class="w">TextOutFileName</span>}<span class="sc">;</span>
|
|
|
340 327 <span class="k">print</span> <span class="q">"Generating text file $NewTextFile...\n"</span><span class="sc">;</span>
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|
|
341 328 <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">">$NewTextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewTextFile: $! \n"</span><span class="sc">;</span>
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|
|
342 329 <span class="i">$NewTextFileRef</span> = \<span class="i">*NEWTEXTFILE</span><span class="sc">;</span>
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|
|
343 330
|
|
|
344 331 <span class="i">WriteTextFileCoulmnLabels</span><span class="s">(</span>\<span class="i">*NEWTEXTFILE</span><span class="s">)</span><span class="sc">;</span>
|
|
|
345 332 <span class="s">}</span>
|
|
|
346 333
|
|
|
347 334 <span class="k">return</span> <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
348 335 <span class="s">}</span>
|
|
|
349 336
|
|
|
350 337 <span class="c"># Write out approriate column labels to text file...</span>
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|
|
351 338 <span class="c">#</span>
|
|
|
352 <a name="WriteTextFileCoulmnLabels-"></a> 339 <span class="k">sub </span><span class="m">WriteTextFileCoulmnLabels</span> <span class="s">{</span>
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|
|
353 340 <span class="k">my</span><span class="s">(</span><span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
354 341 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
|
|
|
355 342
|
|
|
356 343 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
357 344
|
|
|
358 345 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
359 346 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">qw(ReferenceCompoundID DatabaseCompoundID ComparisonValue)</span><span class="sc">;</span>
|
|
|
360 347 <span class="s">}</span>
|
|
|
361 348 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
362 349 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">qw(DatabaseCompoundID ComparisonValue)</span><span class="sc">;</span>
|
|
|
363 350 <span class="s">}</span>
|
|
|
364 351
|
|
|
365 352 <span class="c"># Add columns for other database fingerprints file data to be written to output file...</span>
|
|
|
366 353 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
367 354 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataFieldsToOutput</span>}}<span class="sc">;</span>
|
|
|
368 355 <span class="s">}</span>
|
|
|
369 356 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
370 357 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabelsToOutput</span>}}<span class="sc">;</span>
|
|
|
371 358 <span class="s">}</span>
|
|
|
372 359
|
|
|
373 360 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
374 361 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
|
|
|
375 362 <span class="s">}</span>
|
|
|
376 363
|
|
|
377 364 <span class="c"># Write molecule string data to SD output file...</span>
|
|
|
378 365 <span class="c">#</span>
|
|
|
379 <a name="WriteMolStringDataToSDOutputFile-"></a> 366 <span class="k">sub </span><span class="m">WriteMolStringDataToSDOutputFile</span> <span class="s">{</span>
|
|
|
380 367 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
381 368
|
|
|
382 369 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectCmpdStringData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
383 370 <span class="k">my</span><span class="s">(</span><span class="i">$MolString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
384 371
|
|
|
385 372 <span class="s">(</span><span class="i">$MolString</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/M END/</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}<span class="sc">;</span>
|
|
|
386 373 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"$MolString\nM END\n"</span><span class="sc">;</span>
|
|
|
387 374 <span class="s">}</span>
|
|
|
388 375 <span class="k">else</span> <span class="s">{</span>
|
|
|
389 376 <span class="c"># Just write out an empty molecule data string...</span>
|
|
|
390 377 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="i">SDFileUtil::GenerateEmptyCtabBlockLines</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
391 378 <span class="s">}</span>
|
|
|
392 379 <span class="s">}</span>
|
|
|
393 380
|
|
|
394 381 <span class="c"># Write database data from SD or Text database file to SD output file...</span>
|
|
|
395 382 <span class="c">#</span>
|
|
|
396 <a name="WriteDatabaseDataToSDOutputFile-"></a> 383 <span class="k">sub </span><span class="m">WriteDatabaseDataToSDOutputFile</span> <span class="s">{</span>
|
|
|
397 384 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
398 385
|
|
|
399 386 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
400 387 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabel</span><span class="cm">,</span> <span class="i">$DataFieldValue</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldLabelAndValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
401 388
|
|
|
402 389 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">/\n/</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}<span class="sc">;</span>
|
|
|
403 390 <span class="i">%DataFieldLabelAndValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
|
|
|
404 391
|
|
|
405 392 <span class="k">for</span> <span class="i">$DataFieldLabel</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputCurrentDataFields</span>} ? <span class="i">GetCmpdDataHeaderLabels</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span> <span class="co">:</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataFieldsToOutput</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
406 393 <span class="i">$DataFieldValue</span> = <span class="k">exists</span> <span class="i">$DataFieldLabelAndValues</span>{<span class="i">$DataFieldLabel</span>} ? <span class="i">$DataFieldLabelAndValues</span>{<span class="i">$DataFieldLabel</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
407 394 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <$DataFieldLabel>\n$DataFieldValue\n\n"</span><span class="sc">;</span>
|
|
|
408 395 <span class="s">}</span>
|
|
|
409 396 <span class="s">}</span>
|
|
|
410 397 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
411 398 <span class="k">my</span><span class="s">(</span><span class="i">$DataColNum</span><span class="cm">,</span> <span class="i">$DataFieldLabel</span><span class="cm">,</span> <span class="i">$DataFieldValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
412 399
|
|
|
413 400 <span class="k">for</span> <span class="i">$DataColNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumsToOutput</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
414 401 <span class="i">$DataFieldLabel</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumToLabelMap</span>}{<span class="i">$DataColNum</span>}<span class="sc">;</span>
|
|
|
415 402 <span class="i">$DataFieldValue</span> = <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}->[<span class="i">$DataColNum</span>]<span class="sc">;</span>
|
|
|
416 403 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <$DataFieldLabel>\n$DataFieldValue\n\n"</span><span class="sc">;</span>
|
|
|
417 404 <span class="s">}</span>
|
|
|
418 405 <span class="s">}</span>
|
|
|
419 406 <span class="s">}</span>
|
|
|
420 407
|
|
|
421 408 <span class="c"># Retriebe database data from SD or Text database file for text output file...</span>
|
|
|
422 409 <span class="c">#</span>
|
|
|
423 <a name="RetrieveDatabaseDataForTextOutputFile-"></a> 410 <span class="k">sub </span><span class="m">RetrieveDatabaseDataForTextOutputFile</span> <span class="s">{</span>
|
|
|
424 411 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
425 412
|
|
|
426 413 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
427 414 <span class="k">my</span><span class="s">(</span><span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldLabelAndValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
428 415
|
|
|
429 416 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">/\n/</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}<span class="sc">;</span>
|
|
|
430 417 <span class="i">%DataFieldLabelAndValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
|
|
|
431 418
|
|
|
432 419 <span class="k">return</span> <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValues</span>{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValues</span>{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataFieldsToOutput</span>}}<span class="sc">;</span>
|
|
|
433 420 <span class="s">}</span>
|
|
|
434 421 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
435 422 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
436 423 <span class="k">return</span> <span class="k">map</span> <span class="s">{</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}->[<span class="i">$_</span>] <span class="s">}</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumsToOutput</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
437 424 <span class="s">}</span>
|
|
|
438 425 <span class="k">else</span> <span class="s">{</span>
|
|
|
439 426 <span class="k">return</span> <span class="s">(</span><span class="q">''</span><span class="s">)</span> x <span class="i">$#</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumsToOutput</span>}}<span class="sc">;</span>
|
|
|
440 427 <span class="s">}</span>
|
|
|
441 428 <span class="s">}</span>
|
|
|
442 429 <span class="s">}</span>
|
|
|
443 430
|
|
|
444 431 <span class="c"># Collect database file SD compound string or CSV/TSV data line for generating results</span>
|
|
|
445 432 <span class="c"># files..</span>
|
|
|
446 433 <span class="c">#</span>
|
|
|
447 <a name="CollectDatabaseFileData-"></a> 434 <span class="k">sub </span><span class="m">CollectDatabaseFileData</span> <span class="s">{</span>
|
|
|
448 435 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseCmpdID</span><span class="cm">,</span> <span class="i">$DatabaseFingerprintsFileIO</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
449 436
|
|
|
450 437 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
451 438 <span class="k">return</span><span class="sc">;</span>
|
|
|
452 439 <span class="s">}</span>
|
|
|
453 440
|
|
|
454 441 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectCmpdStringData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
455 442 <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>} = <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->GetCompoundString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
456 443 <span class="s">}</span>
|
|
|
457 444
|
|
|
458 445 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectDataLine</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
459 446 <span class="k">my</span><span class="s">(</span><span class="i">@DataLineWords</span><span class="s">)</span><span class="sc">;</span>
|
|
|
460 447 <span class="i">@DataLineWords</span> = <span class="i">$DatabaseFingerprintsFileIO</span><span class="i">->GetDataLineWords</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
461 448 <span class="i">$DatabaseFingerprintsFileData</span>{<span class="i">$DatabaseCmpdID</span>} = \<span class="i">@DataLineWords</span><span class="sc">;</span>
|
|
|
462 449 <span class="s">}</span>
|
|
|
463 450
|
|
|
464 451 <span class="s">}</span>
|
|
|
465 452
|
|
|
466 453 <span class="c"># Read fingerprints data from reference fingerprints file...</span>
|
|
|
467 454 <span class="c">#</span>
|
|
|
468 <a name="ReadReferenceFingerprintsData-"></a> 455 <span class="k">sub </span><span class="m">ReadReferenceFingerprintsData</span> <span class="s">{</span>
|
|
|
469 456 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="s">)</span><span class="sc">;</span>
|
|
|
470 457
|
|
|
471 458 <span class="i">$FingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsFileIOParameters</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
472 459 <span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceCmpdIDsRef</span>}<span class="cm">,</span> <span class="i">$SimilaritySearchInfo</span>{<span class="w">ReferenceFingerprintsObjectsRef</span>}<span class="s">)</span> = <span class="i">Fingerprints::FingerprintsFileUtil::ReadAndProcessFingerpritsData</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="s">)</span><span class="sc">;</span>
|
|
|
473 460
|
|
|
474 461 <span class="s">}</span>
|
|
|
475 462
|
|
|
476 463 <span class="c"># Retrieve information about fingerprints files...</span>
|
|
|
477 464 <span class="c">#</span>
|
|
|
478 <a name="RetrieveFingerprintsFilesInfo-"></a> 465 <span class="k">sub </span><span class="m">RetrieveFingerprintsFilesInfo</span> <span class="s">{</span>
|
|
|
479 466
|
|
|
480 467 <span class="i">%FingerprintsFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
481 468 <span class="i">%OutputFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
482 469 <span class="i">%SimilaritySearchInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
483 470
|
|
|
484 471 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
485 472 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
486 473
|
|
|
487 474 <span class="c"># Set up reference and database file names...</span>
|
|
|
488 475 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FileName</span>} = <span class="i">$FingerprintsFilesList</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
489 476 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FileName</span>} = <span class="i">$FingerprintsFilesList</span>[<span class="n">1</span>]<span class="sc">;</span>
|
|
|
490 477
|
|
|
491 478 <span class="c"># Retrieve information about reference and database fingerprints file...</span>
|
|
|
492 479 <span class="i">RetrieveReferenceFingerprintsFileInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
493 480 <span class="i">RetrieveDatabaseFingerprintsFileInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
494 481
|
|
|
495 482 <span class="c"># Setup fingerprints comparison method and associated method parameters...</span>
|
|
|
496 483 <span class="i">SetupReferenceAndDatabaseFingerprintsComparisonInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
497 484
|
|
|
498 485 <span class="c"># Retrieve information for output files...</span>
|
|
|
499 486 <span class="i">RetrieveOutputFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
500 487 <span class="s">}</span>
|
|
|
501 488
|
|
|
502 489 <span class="c"># Setup refrerence and database fingerprints comparison method and associated method parameters...</span>
|
|
|
503 490 <span class="c">#</span>
|
|
|
504 <a name="SetupReferenceAndDatabaseFingerprintsComparisonInfo-"></a> 491 <span class="k">sub </span><span class="m">SetupReferenceAndDatabaseFingerprintsComparisonInfo</span> <span class="s">{</span>
|
|
|
505 492
|
|
|
506 493 <span class="c"># Make sure reference and database fingerprints string match...</span>
|
|
|
507 494 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FirstFingerprintsStringType</span>} !~ <span class="q">/^$FingerprintsFilesInfo{Database}{FirstFingerprintsStringType}$/i</span><span class="s">)</span> ||
|
|
|
508 495 <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsBitVectorStringMode</span>} != <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsBitVectorStringMode</span>}<span class="s">)</span> ||
|
|
|
509 496 <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsVectorStringMode</span>} != <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsVectorStringMode</span>}<span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
510 497 <span class="k">die</span> <span class="q">"Error: First reference fingerprints string type, $FingerprintsFilesInfo{Reference}{FirstFingerprintsStringType}, must match first database fingerprints type, $FingerprintsFilesInfo{Database}{FirstFingerprintsStringType}.\n"</span><span class="sc">;</span>
|
|
|
511 498 <span class="s">}</span>
|
|
|
512 499
|
|
|
513 500 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FirstFingerprintsStringDescription</span>} !~ <span class="q">/^$FingerprintsFilesInfo{Database}{FirstFingerprintsStringDescription}$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
514 501 <span class="k">warn</span> <span class="q">"Warning: First reference fingerprints string description, $FingerprintsFilesInfo{Reference}{FirstFingerprintsStringDescription}, doesn't match first database fingerprints string description, $FingerprintsFilesInfo{Database}{FirstFingerprintsStringDescription}.\n"</span><span class="sc">;</span>
|
|
|
515 502 <span class="s">}</span>
|
|
|
516 503
|
|
|
517 504 <span class="c"># Setup individual reference and multiple references search mode...</span>
|
|
|
518 505 <span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
519 506 <span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
520 507
|
|
|
521 508 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^IndividualReference$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
522 509 <span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
523 510 <span class="s">}</span>
|
|
|
524 511 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^MultipleReferences$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
525 512 <span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
526 513 <span class="s">}</span>
|
|
|
527 514 <span class="k">else</span> <span class="s">{</span>
|
|
|
528 515 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: IndividualReference, MultipleReferences\n"</span><span class="sc">;</span>
|
|
|
529 516 <span class="s">}</span>
|
|
|
530 517
|
|
|
531 518 <span class="c"># Set up reference and database fingerprints similarity search method and paramaters...</span>
|
|
|
532 519 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="cm">,</span> <span class="i">$ComparisonMethod</span><span class="cm">,</span> <span class="i">$ApplyComparisonCutoff</span><span class="cm">,</span> <span class="i">$ComparisonCutoff</span><span class="cm">,</span> <span class="i">$KeepTop</span><span class="cm">,</span> <span class="i">@ComparisonMethodParameters</span><span class="s">)</span><span class="sc">;</span>
|
|
|
533 520
|
|
|
534 521 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethod</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
535 522 <span class="i">@</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethodParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
536 523
|
|
|
537 524 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonCutoff</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
538 525 <span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
539 526
|
|
|
540 527 <span class="i">$ComparisonMeasure</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$ComparisonMethod</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
541 528 <span class="i">@ComparisonMethodParameters</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
542 529
|
|
|
543 530 <span class="j">FINGERPRINTSTYPE:</span> <span class="s">{</span>
|
|
|
544 531 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsBitVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
545 532 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonMeasure</span>}<span class="sc">;</span>
|
|
|
546 533 <span class="i">$ComparisonMethod</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonMeasureMethod</span>}<span class="sc">;</span>
|
|
|
547 534
|
|
|
548 535 <span class="k">if</span> <span class="s">(</span><span class="i">$ComparisonMeasure</span> =~ <span class="q">/^TverskySimilarity$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
549 536 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>}<span class="sc">;</span>
|
|
|
550 537 <span class="s">}</span>
|
|
|
551 538 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ComparisonMeasure</span> =~ <span class="q">/^WeightedTverskySimilarity$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
552 539 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>}<span class="sc">;</span>
|
|
|
553 540 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>}<span class="sc">;</span>
|
|
|
554 541 <span class="s">}</span>
|
|
|
555 542 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ComparisonMeasure</span> =~ <span class="q">/^WeightedTanimotoSimilarity$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
556 543 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>}<span class="sc">;</span>
|
|
|
557 544 <span class="s">}</span>
|
|
|
558 545
|
|
|
559 546 <span class="k">last</span> <span class="j">FINGERPRINTSTYPE</span><span class="sc">;</span>
|
|
|
560 547 <span class="s">}</span>
|
|
|
561 548 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
562 549 <span class="k">my</span><span class="s">(</span><span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
563 550
|
|
|
564 551 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMeasure</span>}<span class="sc">;</span>
|
|
|
565 552 <span class="i">$ComparisonMethod</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMeasuresMethod</span>}<span class="sc">;</span>
|
|
|
566 553
|
|
|
567 554 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMode</span>}<span class="sc">;</span>
|
|
|
568 555
|
|
|
569 556 <span class="i">$SkipValuesCheck</span> = <span class="i">$OptionsInfo</span>{<span class="w">Fast</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
570 557 <span class="k">push</span> <span class="i">@ComparisonMethodParameters</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="sc">;</span>
|
|
|
571 558
|
|
|
572 559 <span class="k">last</span> <span class="j">FINGERPRINTSTYPE</span><span class="sc">;</span>
|
|
|
573 560 <span class="s">}</span>
|
|
|
574 561 <span class="k">die</span> <span class="q">"Error: Uknown fingerprints string type. Supported values: FingerprintsBitVectorString or FingerprintsVectorString.\n"</span><span class="sc">;</span>
|
|
|
575 562 <span class="s">}</span>
|
|
|
576 563
|
|
|
577 564 <span class="i">$ApplyComparisonCutoff</span> = <span class="i">$SimilaritySearchInfo</span>{<span class="w">IndividualReferenceMode</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$SimilaritySearchInfo</span>{<span class="w">MultipleReferencesMode</span>} && <span class="i">$OptionsInfo</span>{<span class="w">GroupFusionApplyCutoff</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
|
|
|
578 565
|
|
|
579 566 <span class="i">$ComparisonCutoff</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$KeepTop</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
580 567 <span class="k">if</span> <span class="s">(</span><span class="i">$ComparisonMethod</span> =~ <span class="q">/Distance/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
581 568 <span class="i">$ComparisonCutoff</span> = <span class="i">$OptionsInfo</span>{<span class="w">DistanceCutoff</span>}<span class="sc">;</span>
|
|
|
582 569 <span class="i">$KeepTop</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SearchMode</span>} =~ <span class="q">/^SimilaritySearch$/i</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
583 570 <span class="s">}</span>
|
|
|
584 571 <span class="k">else</span> <span class="s">{</span>
|
|
|
585 572 <span class="i">$ComparisonCutoff</span> = <span class="i">$OptionsInfo</span>{<span class="w">SimilarityCutoff</span>}<span class="sc">;</span>
|
|
|
586 573 <span class="i">$KeepTop</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SearchMode</span>} =~ <span class="q">/^SimilaritySearch$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
587 574 <span class="s">}</span>
|
|
|
588 575
|
|
|
589 576 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethod</span>} = <span class="i">$ComparisonMethod</span><span class="sc">;</span>
|
|
|
590 577 <span class="i">@</span>{<span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonMethodParameters</span>}} = <span class="i">@ComparisonMethodParameters</span><span class="sc">;</span>
|
|
|
591 578
|
|
|
592 579 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ComparisonCutoff</span>} = <span class="i">$ComparisonCutoff</span><span class="sc">;</span>
|
|
|
593 580 <span class="i">$SimilaritySearchInfo</span>{<span class="w">KeepTop</span>} = <span class="i">$KeepTop</span><span class="sc">;</span>
|
|
|
594 581 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyComparisonCutoff</span>} = <span class="i">$ApplyComparisonCutoff</span><span class="sc">;</span>
|
|
|
595 582
|
|
|
596 583 <span class="c"># Setup references to group fusion methods...</span>
|
|
|
597 584 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
598 585 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
599 586
|
|
|
600 587 <span class="j">FUSIONRULE:</span> <span class="s">{</span>
|
|
|
601 588 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Max$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
602 589 <span class="c"># It's always the first value in the appropriated sorted list using value of KeepTop...</span>
|
|
|
603 590 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = <span class="k">sub</span> <span class="s">{</span> <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> <span class="k">return</span> <span class="i">$ComparisonValuesRef</span>->[<span class="n">0</span>]<span class="sc">;</span> <span class="s">}</span><span class="sc">;</span>
|
|
|
604 591 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span>
|
|
|
605 592 <span class="s">}</span>
|
|
|
606 593 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Min$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
607 594 <span class="c"># It's always the last value in the appropriated sorted list using value of KeepTop...</span>
|
|
|
608 595 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = <span class="k">sub</span> <span class="s">{</span> <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> <span class="k">return</span> <span class="i">$ComparisonValuesRef</span>->[<span class="i">$#</span>{<span class="i">$ComparisonValuesRef</span>}]<span class="sc">;</span> <span class="s">}</span><span class="sc">;</span>
|
|
|
609 596 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span>
|
|
|
610 597 <span class="s">}</span>
|
|
|
611 598 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Mean$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
612 599 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = \<span class="i">&StatisticsUtil::Mean</span><span class="sc">;</span>
|
|
|
613 600 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
614 601 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span>
|
|
|
615 602 <span class="s">}</span>
|
|
|
616 603 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Median$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
617 604 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = \<span class="i">&StatisticsUtil::Median</span><span class="sc">;</span>
|
|
|
618 605 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
619 606 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span>
|
|
|
620 607 <span class="s">}</span>
|
|
|
621 608 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Sum$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
622 609 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = \<span class="i">&StatisticsUtil::Sum</span><span class="sc">;</span>
|
|
|
623 610 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
624 611 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span>
|
|
|
625 612 <span class="s">}</span>
|
|
|
626 613 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^Euclidean$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
627 614 <span class="i">$SimilaritySearchInfo</span>{<span class="w">GroupFusionMethodRef</span>} = \<span class="i">&StatisticsUtil::Euclidean</span><span class="sc">;</span>
|
|
|
628 615 <span class="i">$SimilaritySearchInfo</span>{<span class="w">ApplyPrecisionDuringFusion</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
629 616 <span class="k">last</span> <span class="j">FUSIONRULE</span><span class="sc">;</span>
|
|
|
630 617 <span class="s">}</span>
|
|
|
631 618 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{groupfusionrule}, for option \"-g, --GroupFusionRule\" is not valid. Allowed values: Max, Min, Mean, Median, Sum, Euclidean\n"</span><span class="sc">;</span>
|
|
|
632 619 <span class="s">}</span>
|
|
|
633 620
|
|
|
634 621 <span class="i">$SimilaritySearchInfo</span>{<span class="w">UsekNN</span>} = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">kNN</span>} !~ <span class="q">/^All$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
635 622 <span class="i">$SimilaritySearchInfo</span>{<span class="w">SortComparisonValues</span>} = <span class="s">(</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} =~ <span class="q">/^(Max|Min)$/i</span><span class="s">)</span> || <span class="i">$SimilaritySearchInfo</span>{<span class="w">UsekNN</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
636 623 <span class="s">}</span>
|
|
|
637 624
|
|
|
638 625 <span class="c"># Retrieve information about reference fingerprints file...</span>
|
|
|
639 626 <span class="c">#</span>
|
|
|
640 <a name="RetrieveReferenceFingerprintsFileInfo-"></a> 627 <span class="k">sub </span><span class="m">RetrieveReferenceFingerprintsFileInfo</span> <span class="s">{</span>
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|
|
641 628 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span><span class="sc">;</span>
|
|
|
642 629
|
|
|
643 630 <span class="i">$FingerprintsFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FileName</span>}<span class="sc">;</span>
|
|
|
644 631 <span class="s">(</span><span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span> = <span class="i">RetrieveFingerprintsFileInfo</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
645 632
|
|
|
646 633 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FileType</span>} = <span class="i">$FileType</span><span class="sc">;</span>
|
|
|
647 634 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">InDelim</span>} = <span class="i">$InDelim</span><span class="sc">;</span>
|
|
|
648 635
|
|
|
649 636 <span class="c"># Setup reference FingerprintsFileIO parameters...</span>
|
|
|
650 637 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsFileIOParameters</span>}} = <span class="i">RetrieveFingerprintsFileIOParameters</span><span class="s">(</span><span class="q">'Reference'</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
651 638
|
|
|
652 639 <span class="c"># Make sure reference fingerprints data file contains valid and retrieve fingerprints string mode information...</span>
|
|
|
653 640 <span class="s">(</span><span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span> = <span class="i">RetrieveFingerprintsFileFingerprintsStringInfo</span><span class="s">(</span><span class="q">'Reference'</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
654 641 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsStringMode</span>} = <span class="i">$FingerprintsStringMode</span><span class="sc">;</span>
|
|
|
655 642 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="i">$FingerprintsBitVectorStringMode</span><span class="sc">;</span>
|
|
|
656 643 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FingerprintsVectorStringMode</span>} = <span class="i">$FingerprintsVectorStringMode</span><span class="sc">;</span>
|
|
|
657 644 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FirstFingerprintsStringType</span>} = <span class="i">$FirstFingerprintsStringType</span><span class="sc">;</span>
|
|
|
658 645 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FirstFingerprintsStringDescription</span>} = <span class="i">$FirstFingerprintsStringDescription</span><span class="sc">;</span>
|
|
|
659 646
|
|
|
660 647 <span class="s">}</span>
|
|
|
661 648
|
|
|
662 649 <span class="c"># Retrieve information about database fingerprints file...</span>
|
|
|
663 650 <span class="c">#</span>
|
|
|
664 <a name="RetrieveDatabaseFingerprintsFileInfo-"></a> 651 <span class="k">sub </span><span class="m">RetrieveDatabaseFingerprintsFileInfo</span> <span class="s">{</span>
|
|
|
665 652 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span><span class="sc">;</span>
|
|
|
666 653
|
|
|
667 654 <span class="i">$FingerprintsFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FileName</span>}<span class="sc">;</span>
|
|
|
668 655 <span class="s">(</span><span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span> = <span class="i">RetrieveFingerprintsFileInfo</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
669 656
|
|
|
670 657 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FileType</span>} = <span class="i">$FileType</span><span class="sc">;</span>
|
|
|
671 658 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">InDelim</span>} = <span class="i">$InDelim</span><span class="sc">;</span>
|
|
|
672 659
|
|
|
673 660 <span class="c"># Setup reference FingerprintsFileIO parameters...</span>
|
|
|
674 661 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsFileIOParameters</span>}} = <span class="i">RetrieveFingerprintsFileIOParameters</span><span class="s">(</span><span class="q">'Database'</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
675 662
|
|
|
676 663 <span class="c"># Make sure database fingerprints data file contains valid and retrieve fingerprints string mode information...</span>
|
|
|
677 664 <span class="s">(</span><span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span> = <span class="i">RetrieveFingerprintsFileFingerprintsStringInfo</span><span class="s">(</span><span class="q">'Database'</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
678 665 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsStringMode</span>} = <span class="i">$FingerprintsStringMode</span><span class="sc">;</span>
|
|
|
679 666 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="i">$FingerprintsBitVectorStringMode</span><span class="sc">;</span>
|
|
|
680 667 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FingerprintsVectorStringMode</span>} = <span class="i">$FingerprintsVectorStringMode</span><span class="sc">;</span>
|
|
|
681 668 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FirstFingerprintsStringType</span>} = <span class="i">$FirstFingerprintsStringType</span><span class="sc">;</span>
|
|
|
682 669 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FirstFingerprintsStringDescription</span>} = <span class="i">$FirstFingerprintsStringDescription</span><span class="sc">;</span>
|
|
|
683 670
|
|
|
684 671 <span class="c"># Retrieve database fingerprints data field information for output file...</span>
|
|
|
685 672 <span class="c">#</span>
|
|
|
686 673 <span class="i">RetrieveDatabaseFingerprintsDataFieldsInfo</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span>
|
|
|
687 674
|
|
|
688 675 <span class="c"># Retrieve database fingerprints text file data columns information for output file...</span>
|
|
|
689 676 <span class="c">#</span>
|
|
|
690 677 <span class="i">RetrieveDatabaseFingerprintsDataColsInfo</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span>
|
|
|
691 678
|
|
|
692 679 <span class="c"># Any need to collect database compound string or data line for generation of results files...</span>
|
|
|
693 680 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectCmpdStringData</span>} = <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
694 681 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectDataLine</span>} = <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^Text$/i</span> && <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataColsMode</span>} =~ <span class="q">/^(All|Specify)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
695 682 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectInputFileData</span>} = <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectCmpdStringData</span>} || <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CollectDataLine</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
696 683
|
|
|
697 684 <span class="c"># Set maximum number of similar compounds to find for individual reference of set of multiple</span>
|
|
|
698 685 <span class="c"># reference compounds...</span>
|
|
|
699 686 <span class="c">#</span>
|
|
|
700 687 <span class="i">SetMaximumSimilarMoleculesToRetrieve</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span>
|
|
|
701 688 <span class="s">}</span>
|
|
|
702 689
|
|
|
703 690 <span class="c"># Retrieve database fingerprints data field information...</span>
|
|
|
704 691 <span class="c">#</span>
|
|
|
705 <a name="RetrieveDatabaseFingerprintsDataFieldsInfo-"></a> 692 <span class="k">sub </span><span class="m">RetrieveDatabaseFingerprintsDataFieldsInfo</span> <span class="s">{</span>
|
|
|
706 693 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
707 694 <span class="k">my</span><span class="s">(</span><span class="i">$CollectDataFields</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="cm">,</span> <span class="i">@DataFieldsToOutput</span><span class="s">)</span><span class="sc">;</span>
|
|
|
708 695
|
|
|
709 696 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
710 697 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataFieldsToOutput</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
711 698
|
|
|
712 699 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputCurrentDataFields</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
713 700
|
|
|
714 701 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">AllDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
715 702 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CommonDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
716 703 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">SpecifiedDatabaseDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
717 704
|
|
|
718 705 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> !~ <span class="q">/^SD$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
719 706 <span class="k">return</span><span class="sc">;</span>
|
|
|
720 707 <span class="s">}</span>
|
|
|
721 708
|
|
|
722 709 <span class="c"># No need to go over SD file and collect data fields for SD file during All DatabaseDataFieldsMode as</span>
|
|
|
723 710 <span class="c"># they would be retrieved from database SD file compound string during generation of output files...</span>
|
|
|
724 711 <span class="c">#</span>
|
|
|
725 712 <span class="i">$CollectDataFields</span> = <span class="s">(</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} =~ <span class="q">/^(All|Common)$/i</span><span class="s">)</span> || <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} && <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} =~ <span class="q">/^Common$/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>
|
|
|
726 713
|
|
|
727 714 <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">$CommonDataFieldsRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">2</span><span class="sc">;</span>
|
|
|
728 715
|
|
|
729 716 <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span>
|
|
|
730 717 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$FingerprintsFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $FingerprintsFile: $! \n"</span><span class="sc">;</span>
|
|
|
731 718 <span class="s">(</span><span class="i">$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>
|
|
|
732 719 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
|
|
|
733 720 <span class="s">}</span>
|
|
|
734 721
|
|
|
735 722 <span class="i">@DataFieldsToOutput</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
736 723 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
737 724 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AllDataFieldsRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
738 725 <span class="k">push</span> <span class="i">@DataFieldsToOutput</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AllDataFieldsRef</span>}<span class="sc">;</span>
|
|
|
739 726 <span class="k">push</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">AllDataFields</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$AllDataFieldsRef</span>}<span class="sc">;</span>
|
|
|
740 727 <span class="s">}</span>
|
|
|
741 728 <span class="k">else</span> <span class="s">{</span>
|
|
|
742 729 <span class="c"># Retrieve and output data fields and values dynamically...</span>
|
|
|
743 730 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputCurrentDataFields</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
744 731 <span class="s">}</span>
|
|
|
745 732 <span class="s">}</span>
|
|
|
746 733 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
747 734 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
748 735 <span class="k">push</span> <span class="i">@DataFieldsToOutput</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$CommonDataFieldsRef</span>}<span class="sc">;</span>
|
|
|
749 736 <span class="k">push</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">CommonDataFields</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$CommonDataFieldsRef</span>}<span class="sc">;</span>
|
|
|
750 737 <span class="s">}</span>
|
|
|
751 738 <span class="s">}</span>
|
|
|
752 739 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
753 740 <span class="k">push</span> <span class="i">@DataFieldsToOutput</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataFields</span>}}<span class="sc">;</span>
|
|
|
754 741 <span class="k">push</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">SpecifiedDatabaseDataFields</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataFields</span>}}<span class="sc">;</span>
|
|
|
755 742 <span class="s">}</span>
|
|
|
756 743
|
|
|
757 744 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} !~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
758 745 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataFields</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
759 746 <span class="s">}</span>
|
|
|
760 747
|
|
|
761 748 <span class="k">push</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataFieldsToOutput</span>}}<span class="cm">,</span> <span class="i">@DataFieldsToOutput</span><span class="sc">;</span>
|
|
|
762 749
|
|
|
763 750 <span class="s">}</span>
|
|
|
764 751
|
|
|
765 752 <span class="c"># Retrieve database fingerprints data columns information...</span>
|
|
|
766 753 <span class="c">#</span>
|
|
|
767 <a name="RetrieveDatabaseFingerprintsDataColsInfo-"></a> 754 <span class="k">sub </span><span class="m">RetrieveDatabaseFingerprintsDataColsInfo</span> <span class="s">{</span>
|
|
|
768 755 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
769 756 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="cm">,</span> <span class="i">$ColLabel</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">@DataColLabels</span><span class="cm">,</span> <span class="i">@DataColLabelsToOutput</span><span class="cm">,</span> <span class="i">@DataColNumsToOutput</span><span class="cm">,</span> <span class="i">%DataColLabelToNumMap</span><span class="cm">,</span> <span class="i">%DataColNumToLabelMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
770 757
|
|
|
771 758 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
772 759
|
|
|
773 760 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
774 761 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabelToNumMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
775 762 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumToLabelMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
776 763
|
|
|
777 764 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumsToOutput</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
778 765 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabelsToOutput</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
779 766
|
|
|
780 767 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> !~ <span class="q">/^Text$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
781 768 <span class="k">return</span><span class="sc">;</span>
|
|
|
782 769 <span class="s">}</span>
|
|
|
783 770
|
|
|
784 771 <span class="i">@DataColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
785 772 <span class="i">@DataColLabelsToOutput</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
786 773 <span class="i">@DataColNumsToOutput</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
787 774
|
|
|
788 775 <span class="i">%DataColLabelToNumMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
789 776 <span class="i">%DataColNumToLabelMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
790 777
|
|
|
791 778 <span class="c"># Get column label line...</span>
|
|
|
792 779 <span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">"$FingerprintsFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $FingerprintsFile: $! \n"</span><span class="sc">;</span>
|
|
|
793 780 <span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span>
|
|
|
794 781 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span>
|
|
|
795 782
|
|
|
796 783 <span class="i">$InDelim</span> = <span class="s">(</span><span class="i">$InDelim</span> =~ <span class="q">/^Tab$/i</span><span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="i">$InDelim</span> =~ <span class="q">/semicolon/i</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
797 784
|
|
|
798 785 <span class="i">@DataColLabels</span> = <span class="i">TextUtil::SplitWords</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span>
|
|
|
799 786 <span class="i">$NumOfCols</span> = <span class="k">scalar</span> <span class="i">@DataColLabels</span><span class="sc">;</span>
|
|
|
800 787
|
|
|
801 788 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#DataColLabels</span><span class="s">)</span> <span class="s">{</span>
|
|
|
802 789 <span class="i">$ColLabel</span> = <span class="i">$DataColLabels</span>[<span class="i">$ColNum</span>]<span class="sc">;</span>
|
|
|
803 790 <span class="i">$DataColLabelToNumMap</span>{<span class="i">$ColLabel</span>} = <span class="i">$ColNum</span><span class="sc">;</span>
|
|
|
804 791 <span class="i">$DataColNumToLabelMap</span>{<span class="i">$ColNum</span>} = <span class="i">$ColLabel</span><span class="sc">;</span>
|
|
|
805 792 <span class="s">}</span>
|
|
|
806 793
|
|
|
807 794 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataColsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
808 795 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseColMode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
809 796 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataCols</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
810 797 <span class="k">if</span> <span class="s">(</span><span class="i">$ColNum</span> > <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span>
|
|
|
811 798 <span class="k">die</span> <span class="q">"Error: Column number, $ColNum, specified using \"--DatabaseDataCols\" is not valid: It must be <= $NumOfCols\n"</span><span class="sc">;</span>
|
|
|
812 799 <span class="s">}</span>
|
|
|
813 800 <span class="k">push</span> <span class="i">@DataColNumsToOutput</span><span class="cm">,</span> <span class="s">(</span><span class="i">$ColNum</span> - <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
814 801 <span class="s">}</span>
|
|
|
815 802 <span class="s">}</span>
|
|
|
816 803 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseColMode</span>} =~ <span class="q">/^ColLabel$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
817 804 <span class="k">for</span> <span class="i">$ColLabel</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataCols</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
818 805 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataColLabelToNumMap</span>{<span class="i">$ColLabel</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
819 806 <span class="k">die</span> <span class="q">"Error: Column label, $ColLabel, specified using \"--DatabaseDataCols\" is not valid: It doesn't exist\n"</span><span class="sc">;</span>
|
|
|
820 807 <span class="s">}</span>
|
|
|
821 808 <span class="k">push</span> <span class="i">@DataColNumsToOutput</span><span class="cm">,</span> <span class="i">$DataColLabelToNumMap</span>{<span class="i">$ColLabel</span>}<span class="sc">;</span>
|
|
|
822 809 <span class="s">}</span>
|
|
|
823 810 <span class="s">}</span>
|
|
|
824 811 <span class="s">}</span>
|
|
|
825 812 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataColsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
826 813 <span class="i">@DataColNumsToOutput</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span> <span class="s">}</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#DataColLabels</span><span class="s">)</span><span class="sc">;</span>
|
|
|
827 814 <span class="s">}</span>
|
|
|
828 815
|
|
|
829 816 <span class="c"># Setup data column labels to output...</span>
|
|
|
830 817 <span class="k">if</span> <span class="s">(</span><span class="k">scalar</span> <span class="i">@DataColNumsToOutput</span><span class="s">)</span> <span class="s">{</span>
|
|
|
831 818 <span class="i">@DataColLabelsToOutput</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$DataColNumToLabelMap</span>{<span class="i">$_</span>} <span class="s">}</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#DataColNumsToOutput</span><span class="s">)</span><span class="sc">;</span>
|
|
|
832 819 <span class="s">}</span>
|
|
|
833 820
|
|
|
834 821 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">OutputDataCols</span>} = <span class="k">scalar</span> <span class="i">@DataColNumsToOutput</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
835 822
|
|
|
836 823 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabels</span>}} = <span class="i">@DataColLabels</span><span class="sc">;</span>
|
|
|
837 824 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabelToNumMap</span>}} = <span class="i">%DataColLabelToNumMap</span><span class="sc">;</span>
|
|
|
838 825 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumToLabelMap</span>}} = <span class="i">%DataColNumToLabelMap</span><span class="sc">;</span>
|
|
|
839 826
|
|
|
840 827 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColNumsToOutput</span>}} = <span class="i">@DataColNumsToOutput</span><span class="sc">;</span>
|
|
|
841 828 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">DataColLabelsToOutput</span>}} = <span class="i">@DataColLabelsToOutput</span><span class="sc">;</span>
|
|
|
842 829 <span class="s">}</span>
|
|
|
843 830
|
|
|
844 831 <span class="c"># Set maximum number of similar compounds to find for individual reference of set of multiple</span>
|
|
|
845 832 <span class="c"># reference compounds...</span>
|
|
|
846 833 <span class="c">#</span>
|
|
|
847 <a name="SetMaximumSimilarMoleculesToRetrieve-"></a> 834 <span class="k">sub </span><span class="m">SetMaximumSimilarMoleculesToRetrieve</span> <span class="s">{</span>
|
|
|
848 835 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
849 836 <span class="k">my</span><span class="s">(</span><span class="i">$MaxSimilarMolecules</span><span class="cm">,</span> <span class="i">$NumOfDatabaseMolecules</span><span class="cm">,</span> <span class="i">$PercentSimilarMolecules</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
|
|
|
850 837
|
|
|
851 838 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SimilarCountMode</span>} !~ <span class="q">/^PercentSimilar$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
852 839 <span class="k">return</span><span class="sc">;</span>
|
|
|
853 840 <span class="s">}</span>
|
|
|
854 841
|
|
|
855 842 <span class="i">$PercentSimilarMolecules</span> = <span class="i">$OptionsInfo</span>{<span class="w">PercentSimilarMolecules</span>}<span class="sc">;</span>
|
|
|
856 843
|
|
|
857 844 <span class="c"># Count database entries to figure out MaxSimilarMolecules using PercentSimilarMolecules</span>
|
|
|
858 845 <span class="c"># value...</span>
|
|
|
859 846 <span class="i">$NumOfDatabaseMolecules</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
860 847 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span> && <span class="k">exists</span><span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">NumOfDatabaseMolecules</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
861 848 <span class="c"># It might already be counted for SD file...</span>
|
|
|
862 849 <span class="i">$NumOfDatabaseMolecules</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">NumOfDatabaseMolecules</span>}<span class="sc">;</span>
|
|
|
863 850 <span class="s">}</span>
|
|
|
864 851 <span class="k">else</span> <span class="s">{</span>
|
|
|
865 852 <span class="k">print</span> <span class="q">"Calculating maximum number of similar molecules to retrieve for \"PercentSimilar\" value of \"--SimilarCountMode\" option by counting number of molecules in database fingerprints file...\n"</span><span class="sc">;</span>
|
|
|
866 853 <span class="k">open</span> <span class="w">FINGERPRINTSFILE</span><span class="cm">,</span> <span class="q">"$FingerprintsFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $FingerprintsFile: $! \n"</span><span class="sc">;</span>
|
|
|
867 854 <span class="j">FILETYPE:</span> <span class="s">{</span>
|
|
|
868 855 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
869 856 <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*FINGERPRINTSFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
870 857 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
871 858 <span class="i">$NumOfDatabaseMolecules</span>++<span class="sc">;</span>
|
|
|
872 859 <span class="s">}</span>
|
|
|
873 860 <span class="s">}</span>
|
|
|
874 861 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
|
|
|
875 862 <span class="s">}</span>
|
|
|
876 863 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^Text$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
877 864 <span class="c"># Ignore column label line...</span>
|
|
|
878 865 <span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*FINGERPRINTSFILE</span><span class="s">)</span><span class="sc">;</span>
|
|
|
879 866 <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*FINGERPRINTSFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
880 867 <span class="i">$NumOfDatabaseMolecules</span>++<span class="sc">;</span>
|
|
|
881 868 <span class="s">}</span>
|
|
|
882 869 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
|
|
|
883 870 <span class="s">}</span>
|
|
|
884 871 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^FP$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
885 872 <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*FINGERPRINTSFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
886 873 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
887 874 <span class="i">$NumOfDatabaseMolecules</span>++<span class="sc">;</span>
|
|
|
888 875 <span class="s">}</span>
|
|
|
889 876 <span class="s">}</span>
|
|
|
890 877 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
|
|
|
891 878 <span class="s">}</span>
|
|
|
892 879 <span class="i">$NumOfDatabaseMolecules</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
893 880 <span class="s">}</span>
|
|
|
894 881 <span class="k">close</span> <span class="w">FINGERPRINTSFILE</span><span class="sc">;</span>
|
|
|
895 882 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">NumOfDatabaseMolecules</span>} = <span class="i">$NumOfDatabaseMolecules</span><span class="sc">;</span>
|
|
|
896 883 <span class="s">}</span>
|
|
|
897 884
|
|
|
898 885 <span class="i">$MaxSimilarMolecules</span> = <span class="k">int</span> <span class="s">(</span><span class="s">(</span><span class="i">$NumOfDatabaseMolecules</span> * <span class="i">$PercentSimilarMolecules</span><span class="s">)</span>/<span class="n">100</span><span class="s">)</span><span class="sc">;</span>
|
|
|
899 886 <span class="k">if</span> <span class="s">(</span><span class="i">$MaxSimilarMolecules</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
900 887 <span class="i">$MaxSimilarMolecules</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
901 888 <span class="s">}</span>
|
|
|
902 889
|
|
|
903 890 <span class="i">$OptionsInfo</span>{<span class="w">MaxSimilarMolecules</span>} = <span class="i">$MaxSimilarMolecules</span><span class="sc">;</span>
|
|
|
904 891 <span class="s">}</span>
|
|
|
905 892
|
|
|
906 893 <span class="c"># Retrieve information about fingerprints file...</span>
|
|
|
907 894 <span class="c">#</span>
|
|
|
908 <a name="RetrieveFingerprintsFileInfo-"></a> 895 <span class="k">sub </span><span class="m">RetrieveFingerprintsFileInfo</span> <span class="s">{</span>
|
|
|
909 896 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
910 897 <span class="k">my</span><span class="s">(</span><span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$FileName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
911 898
|
|
|
912 899 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
913 900 <span class="k">die</span> <span class="q">"Error: Input fingerprints file, $FingerprintsFile, doesn't exist.\n"</span><span class="sc">;</span>
|
|
|
914 901 <span class="s">}</span>
|
|
|
915 902
|
|
|
916 903 <span class="i">$FileType</span> = <span class="i">Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
917 904 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$FileType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
918 905 <span class="k">die</span> <span class="q">"Error: Input file, $FingerprintsFile, is not a fingerprints file.\n"</span><span class="sc">;</span>
|
|
|
919 906 <span class="s">}</span>
|
|
|
920 907
|
|
|
921 908 <span class="i">$InDelim</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
922 909 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^Text$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
923 910 <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">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
924 911 <span class="s">(</span><span class="i">$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">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
925 912 <span class="i">$InDelim</span> = <span class="s">(</span><span class="i">$FileExt</span> =~ <span class="q">/^tsv$/i</span><span class="s">)</span> ? <span class="q">'Tab'</span> <span class="co">:</span> <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>}<span class="sc">;</span>
|
|
|
926 913 <span class="s">}</span>
|
|
|
927 914
|
|
|
928 915 <span class="k">return</span> <span class="s">(</span><span class="i">$FileType</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span>
|
|
|
929 916 <span class="s">}</span>
|
|
|
930 917
|
|
|
931 918 <span class="c"># Retrieve fingerprints file IO parameters...</span>
|
|
|
932 919 <span class="c">#</span>
|
|
|
933 <a name="RetrieveFingerprintsFileIOParameters-"></a> 920 <span class="k">sub </span><span class="m">RetrieveFingerprintsFileIOParameters</span> <span class="s">{</span>
|
|
|
934 921 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileMode</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
935 922 <span class="k">my</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
|
|
|
936 923
|
|
|
937 924 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFileMode</span> !~ <span class="q">/^(Reference|Database)$/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
938 925 <span class="k">die</span> <span class="q">"Error: Unknown fingerprints file mode: $FingerprintsFileMode. Supported values: Reference or Database\n"</span><span class="sc">;</span>
|
|
|
939 926 <span class="s">}</span>
|
|
|
940 927
|
|
|
941 928 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
942 929
|
|
|
943 930 <span class="j">FILETYPE:</span> <span class="s">{</span>
|
|
|
944 931 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
945 932 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsMode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">'FingerprintsFieldLabel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}FingerprintsField"</span>}<span class="cm">,</span> <span class="q">'CompoundIDMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}CompoundIDMode"</span>}<span class="cm">,</span> <span class="q">'CompoundIDFieldLabel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}CompoundIDField"</span>}<span class="cm">,</span> <span class="q">'CompoundIDPrefix'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}CompoundIDPrefix"</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
946 933 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
|
|
|
947 934 <span class="s">}</span>
|
|
|
948 935 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^FP$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
949 936 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsMode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
950 937 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
|
|
|
951 938 <span class="s">}</span>
|
|
|
952 939 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^Text$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
953 940 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsMode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">'FingerprintsCol'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}FingerprintsCol"</span>}<span class="cm">,</span> <span class="q">'ColMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}ColMode"</span>}<span class="cm">,</span> <span class="q">'CompoundIDCol'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}CompoundIDCol"</span>}<span class="cm">,</span> <span class="q">'CompoundIDPrefix'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="q">"${FingerprintsFileMode}CompoundIDPrefix"</span>}<span class="cm">,</span> <span class="q">'InDelim'</span> <span class="cm">=></span> <span class="i">$FingerprintsFilesInfo</span>{<span class="i">$FingerprintsFileMode</span>}{<span class="w">InDelim</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
954 941 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
|
|
|
955 942 <span class="s">}</span>
|
|
|
956 943 <span class="k">die</span> <span class="q">"Error: Fingerprints file type, $FileType, is not valid. Supported file types: SD, FP or Text\n"</span><span class="sc">;</span>
|
|
|
957 944 <span class="s">}</span>
|
|
|
958 945
|
|
|
959 946 <span class="k">return</span> <span class="i">%FingerprintsFileIOParams</span><span class="sc">;</span>
|
|
|
960 947 <span class="s">}</span>
|
|
|
961 948
|
|
|
962 949 <span class="c"># Make sure fingerprints data file contains valid dta and retrieve fingerprints string mode information...</span>
|
|
|
963 950 <span class="c">#</span>
|
|
|
964 <a name="RetrieveFingerprintsFileFingerprintsStringInfo-"></a> 951 <span class="k">sub </span><span class="m">RetrieveFingerprintsFileFingerprintsStringInfo</span> <span class="s">{</span>
|
|
|
965 952 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileMode</span><span class="cm">,</span> <span class="i">$FingerprintsFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
966 953 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span><span class="sc">;</span>
|
|
|
967 954
|
|
|
968 955 <span class="i">$FingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="i">$FingerprintsFileMode</span>}{<span class="w">FingerprintsFileIOParameters</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
969 956 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="s">)</span> <span class="s">{</span>
|
|
|
970 957 <span class="k">die</span> <span class="q">"Error: Reference fingerprints file, $FingerprintsFile, contains invalid fingerprints data.\n"</span><span class="sc">;</span>
|
|
|
971 958 <span class="s">}</span>
|
|
|
972 959 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->IsFingerprintsFileDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
973 960 <span class="k">die</span> <span class="q">"Error: Reference fingerprints file, $FingerprintsFile, contains invalid fingerprints data.\n"</span><span class="sc">;</span>
|
|
|
974 961 <span class="s">}</span>
|
|
|
975 962
|
|
|
976 963 <span class="i">$FingerprintsStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprintsStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
977 964 <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprintsBitVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
978 965 <span class="i">$FingerprintsVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprintsVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
979 966
|
|
|
980 967 <span class="i">$FirstFingerprintsStringType</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFirstFingerprintsStringType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
981 968 <span class="i">$FirstFingerprintsStringDescription</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFirstFingerprintsStringDescription</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
982 969
|
|
|
983 970 <span class="i">$FingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
984 971
|
|
|
985 972 <span class="k">return</span> <span class="s">(</span><span class="i">$FingerprintsStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="s">)</span><span class="sc">;</span>
|
|
|
986 973 <span class="s">}</span>
|
|
|
987 974
|
|
|
988 975 <span class="c"># Retrieve output files names using reference fingerprints file name...</span>
|
|
|
989 976 <span class="c">#</span>
|
|
|
990 <a name="RetrieveOutputFilesInfo-"></a> 977 <span class="k">sub </span><span class="m">RetrieveOutputFilesInfo</span> <span class="s">{</span>
|
|
|
991 978 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</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">$SDOutFileName</span><span class="cm">,</span> <span class="i">$TextOutFileName</span><span class="cm">,</span> <span class="i">$SDOutFileExt</span><span class="cm">,</span> <span class="i">$TextOutFileExt</span><span class="cm">,</span> <span class="i">$ReferenceFileName</span><span class="cm">,</span> <span class="i">$DatabaseFileName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
992 979
|
|
|
993 980 <span class="i">$OutputFilesInfo</span>{<span class="w">OutFileRoot</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
994 981 <span class="i">$OutputFilesInfo</span>{<span class="w">SDOutFileName</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
995 982 <span class="i">$OutputFilesInfo</span>{<span class="w">TextOutFileName</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
996 983
|
|
|
997 984 <span class="i">$FingerprintsFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FileName</span>}<span class="sc">;</span>
|
|
|
998 985
|
|
|
999 986 <span class="i">$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>
|
|
|
1000 987 <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">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1001 988
|
|
|
1002 989 <span class="i">$SDOutFileExt</span> = <span class="q">"sdf"</span><span class="sc">;</span>
|
|
|
1003 990 <span class="i">$TextOutFileExt</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="q">"tsv"</span> <span class="co">:</span> <span class="q">"csv"</span><span class="sc">;</span>
|
|
|
1004 991
|
|
|
1005 992 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1006 993 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1007 994 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1008 995 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
|
|
|
1009 996 <span class="s">}</span>
|
|
|
1010 997 <span class="k">else</span> <span class="s">{</span>
|
|
|
1011 998 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
|
|
|
1012 999 <span class="s">}</span>
|
|
|
1013 1000 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
|
|
|
1014 1001 <span class="s">}</span>
|
|
|
1015 1002 <span class="k">else</span> <span class="s">{</span>
|
|
|
1016 1003 <span class="i">$OutFileRoot</span> = <span class="q">"${FileName}SimilaritySearching"</span><span class="sc">;</span>
|
|
|
1017 1004 <span class="s">}</span>
|
|
|
1018 1005
|
|
|
1019 1006 <span class="i">$SDOutFileName</span> = <span class="q">"${OutFileRoot}.${SDOutFileExt}"</span><span class="sc">;</span>
|
|
|
1020 1007 <span class="i">$TextOutFileName</span> = <span class="q">"${OutFileRoot}.${TextOutFileExt}"</span><span class="sc">;</span>
|
|
|
1021 1008
|
|
|
1022 1009 <span class="i">$ReferenceFileName</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Reference</span>}{<span class="w">FileName</span>}<span class="sc">;</span>
|
|
|
1023 1010 <span class="i">$DatabaseFileName</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">Database</span>}{<span class="w">FileName</span>}<span class="sc">;</span>
|
|
|
1024 1011
|
|
|
1025 1012 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1026 1013 <span class="k">if</span> <span class="s">(</span><span class="i">$SDOutFileName</span> =~ <span class="q">/^$ReferenceFileName$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1027 1014 <span class="k">die</span> <span class="q">"Error: Same output, $SDOutFileName, and reference input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span>
|
|
|
1028 1015 <span class="s">}</span>
|
|
|
1029 1016 <span class="k">if</span> <span class="s">(</span><span class="i">$SDOutFileName</span> =~ <span class="q">/^$DatabaseFileName$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1030 1017 <span class="k">die</span> <span class="q">"Error: Same output, $SDOutFileName, and database input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span>
|
|
|
1031 1018 <span class="s">}</span>
|
|
|
1032 1019 <span class="s">}</span>
|
|
|
1033 1020
|
|
|
1034 1021 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1035 1022 <span class="k">if</span> <span class="s">(</span><span class="i">$TextOutFileName</span> =~ <span class="q">/^$ReferenceFileName$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1036 1023 <span class="k">die</span> <span class="q">"Error: Same output, $TextOutFileName, and reference input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span>
|
|
|
1037 1024 <span class="s">}</span>
|
|
|
1038 1025 <span class="k">if</span> <span class="s">(</span><span class="i">$TextOutFileName</span> =~ <span class="q">/^$DatabaseFileName$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1039 1026 <span class="k">die</span> <span class="q">"Error: Same output, $TextOutFileName, and database input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span>
|
|
|
1040 1027 <span class="s">}</span>
|
|
|
1041 1028 <span class="s">}</span>
|
|
|
1042 1029
|
|
|
1043 1030 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1044 1031 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1045 1032 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$SDOutFileName</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1046 1033 <span class="k">die</span> <span class="q">"Error: The output file $SDOutFileName already exists.\n"</span><span class="sc">;</span>
|
|
|
1047 1034 <span class="s">}</span>
|
|
|
1048 1035 <span class="s">}</span>
|
|
|
1049 1036 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1050 1037 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$TextOutFileName</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1051 1038 <span class="k">die</span> <span class="q">"Error: The output file $TextOutFileName already exists.\n"</span><span class="sc">;</span>
|
|
|
1052 1039 <span class="s">}</span>
|
|
|
1053 1040 <span class="s">}</span>
|
|
|
1054 1041 <span class="s">}</span>
|
|
|
1055 1042
|
|
|
1056 1043 <span class="i">$OutputFilesInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$OutFileRoot</span><span class="sc">;</span>
|
|
|
1057 1044 <span class="i">$OutputFilesInfo</span>{<span class="w">SDOutFileName</span>} = <span class="i">$SDOutFileName</span><span class="sc">;</span>
|
|
|
1058 1045 <span class="i">$OutputFilesInfo</span>{<span class="w">TextOutFileName</span>} = <span class="i">$TextOutFileName</span><span class="sc">;</span>
|
|
|
1059 1046
|
|
|
1060 1047 <span class="s">}</span>
|
|
|
1061 1048
|
|
|
1062 1049 <span class="c"># Process input fingerprints file names...</span>
|
|
|
1063 1050 <span class="c">#</span>
|
|
|
1064 <a name="ProcessFingerprintsFileNames-"></a>1051 <span class="k">sub </span><span class="m">ProcessFingerprintsFileNames</span> <span class="s">{</span>
|
|
|
1065 1052 <span class="i">@FingerprintsFilesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1066 1053
|
|
|
1067 1054 <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1068 1055 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1069 1056 <span class="s">}</span>
|
|
|
1070 1057
|
|
|
1071 1058 <span class="c"># Reference fingerprints file name...</span>
|
|
|
1072 1059 <span class="k">push</span> <span class="i">@FingerprintsFilesList</span><span class="cm">,</span> <span class="i">$ARGV</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
1073 1060
|
|
|
1074 1061 <span class="c"># Database fingerprints file name...</span>
|
|
|
1075 1062 <span class="k">push</span> <span class="i">@FingerprintsFilesList</span><span class="cm">,</span> <span class="i">$ARGV</span>[<span class="n">1</span>]<span class="sc">;</span>
|
|
|
1076 1063
|
|
|
1077 1064 <span class="s">}</span>
|
|
|
1078 1065
|
|
|
1079 1066 <span class="c"># Process option values...</span>
|
|
|
1080 <a name="ProcessOptions-"></a>1067 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
|
|
|
1081 1068 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1082 1069
|
|
|
1083 1070 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
|
|
|
1084 1071 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsMode</span>} = <span class="i">$Options</span>{<span class="w">fingerprintsmode</span>}<span class="sc">;</span>
|
|
|
1085 1072
|
|
|
1086 1073 <span class="i">$OptionsInfo</span>{<span class="w">SearchMode</span>} = <span class="i">$Options</span>{<span class="w">searchmode</span>}<span class="sc">;</span>
|
|
|
1087 1074
|
|
|
1088 1075 <span class="i">ProcessBitVectorComparisonOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1089 1076 <span class="i">ProcessVectorComparisonOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1090 1077
|
|
|
1091 1078 <span class="i">$OptionsInfo</span>{<span class="w">GroupFusionRule</span>} = <span class="i">$Options</span>{<span class="w">groupfusionrule</span>}<span class="sc">;</span>
|
|
|
1092 1079 <span class="i">$OptionsInfo</span>{<span class="w">GroupFusionApplyCutoff</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">groupfusionapplycutoff</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span><span class="sc">;</span>
|
|
|
1093 1080
|
|
|
1094 1081 <span class="i">$OptionsInfo</span>{<span class="w">SimilarCountMode</span>} = <span class="i">$Options</span>{<span class="w">similarcountmode</span>}<span class="sc">;</span>
|
|
|
1095 1082 <span class="i">$OptionsInfo</span>{<span class="w">NumOfSimilarMolecules</span>} = <span class="i">$Options</span>{<span class="w">numofsimilarmolecules</span>}<span class="sc">;</span>
|
|
|
1096 1083 <span class="i">$OptionsInfo</span>{<span class="w">PercentSimilarMolecules</span>} = <span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>}<span class="sc">;</span>
|
|
|
1097 1084
|
|
|
1098 1085 <span class="c"># Set MaxSimilarMolecules to NumOfSimilarMolecules. For PercentSimilar value of SimilarCountMode,</span>
|
|
|
1099 1086 <span class="c"># it'll be overwritten using number of entries in database fingerprints file and value of PercentSimilarMolecules...</span>
|
|
|
1100 1087 <span class="c">#</span>
|
|
|
1101 1088 <span class="i">$OptionsInfo</span>{<span class="w">MaxSimilarMolecules</span>} = <span class="i">$OptionsInfo</span>{<span class="w">NumOfSimilarMolecules</span>}<span class="sc">;</span>
|
|
|
1102 1089
|
|
|
1103 1090 <span class="i">$OptionsInfo</span>{<span class="w">SimilarityCutoff</span>} = <span class="i">$Options</span>{<span class="w">similaritycutoff</span>}<span class="sc">;</span>
|
|
|
1104 1091 <span class="i">$OptionsInfo</span>{<span class="w">DistanceCutoff</span>} = <span class="i">$Options</span>{<span class="w">distancecutoff</span>}<span class="sc">;</span>
|
|
|
1105 1092
|
|
|
1106 1093 <span class="i">$OptionsInfo</span>{<span class="w">kNN</span>} = <span class="i">$Options</span>{<span class="w">knn</span>}<span class="sc">;</span>
|
|
|
1107 1094 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">knn</span>} !~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1108 1095 <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">knn</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1109 1096 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{knn}, for option \"-k, --KNN\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
|
|
|
1110 1097 <span class="s">}</span>
|
|
|
1111 1098 <span class="s">}</span>
|
|
|
1112 1099
|
|
|
1113 1100 <span class="i">ProcessReferenceFingerprintsDataOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1114 1101 <span class="i">ProcessDatabaseFingerprintsDataOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1115 1102
|
|
|
1116 1103 <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span>
|
|
|
1117 1104
|
|
|
1118 1105 <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>} = <span class="i">$Options</span>{<span class="w">indelim</span>}<span class="sc">;</span>
|
|
|
1119 1106 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/tab/i</span> <span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span><span class="s">)</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1120 1107 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1121 1108
|
|
|
1122 1109 <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
|
|
|
1123 1110 <span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(SD|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1124 1111 <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|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1125 1112
|
|
|
1126 1113 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1127 1114 <span class="i">$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>
|
|
|
1128 1115
|
|
|
1129 1116 <span class="i">$OptionsInfo</span>{<span class="w">Fast</span>} = <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1130 1117 <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>} = <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
1131 1118
|
|
|
1132 1119 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
|
|
|
1133 1120 <span class="s">}</span>
|
|
|
1134 1121
|
|
|
1135 1122 <span class="c"># Process options related to comparion of bit vector strings...</span>
|
|
|
1136 1123 <span class="c">#</span>
|
|
|
1137 <a name="ProcessBitVectorComparisonOptions-"></a>1124 <span class="k">sub </span><span class="m">ProcessBitVectorComparisonOptions</span> <span class="s">{</span>
|
|
|
1138 1125 <span class="c"># Setup supported bit vector similarity coefficients for bit vector strings...</span>
|
|
|
1139 1126 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="cm">,</span> <span class="i">$SupportedComparisonMeasure</span><span class="cm">,</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresNameMap</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresMethodMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1140 1127
|
|
|
1141 1128 <span class="i">@SupportedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1142 1129 <span class="i">%SupportedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1143 1130 <span class="i">%SupportedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1144 1131
|
|
|
1145 1132 <span class="k">for</span> <span class="i">$SupportedComparisonMeasure</span> <span class="s">(</span><span class="i">Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1146 1133 <span class="c"># Similarity coefficient function/method names contain "Coefficient" in their names.</span>
|
|
|
1147 1134 <span class="c"># So take 'em out and setup a map to original function/method name...</span>
|
|
|
1148 1135 <span class="i">$ComparisonMeasure</span> = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span>
|
|
|
1149 1136 <span class="i">$ComparisonMeasure</span> =~ <span class="q">s/Coefficient$//</span><span class="sc">;</span>
|
|
|
1150 1137
|
|
|
1151 1138 <span class="k">push</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="sc">;</span>
|
|
|
1152 1139 <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$ComparisonMeasure</span><span class="sc">;</span>
|
|
|
1153 1140 <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span>
|
|
|
1154 1141 <span class="s">}</span>
|
|
|
1155 1142
|
|
|
1156 1143 <span class="c"># Setup similarity coefficient to use for calculating similarity matrices for bit vector strings...</span>
|
|
|
1157 1144 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="cm">,</span> <span class="i">$SpecifiedComparisonMeasureName</span><span class="cm">,</span> <span class="i">$SpecifiedComparisonMeasureMethod</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1158 1145
|
|
|
1159 1146 <span class="i">$SpecifiedComparisonMeasureName</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
1160 1147 <span class="i">$SpecifiedComparisonMeasureMethod</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
1161 1148
|
|
|
1162 1149 <span class="i">$SpecifiedMeasure</span> = <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>}<span class="sc">;</span>
|
|
|
1163 1150
|
|
|
1164 1151 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>} <span class="s">)</span> <span class="s">{</span>
|
|
|
1165 1152 <span class="k">die</span> <span class="q">"Error: The value specified, $SpecifiedMeasure, for option \"-b --BitVectorComparisonMode\" is not valid.\nAllowed values:"</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
1166 1153 <span class="s">}</span>
|
|
|
1167 1154
|
|
|
1168 1155 <span class="i">$SpecifiedComparisonMeasureMethod</span> = <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
1169 1156 <span class="i">$SpecifiedComparisonMeasureName</span> = <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
1170 1157
|
|
|
1171 1158 <span class="i">$OptionsInfo</span>{<span class="w">BitVectorComparisonMode</span>} = <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>}<span class="sc">;</span>
|
|
|
1172 1159
|
|
|
1173 1160 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonMeasure</span>} = <span class="i">$SpecifiedMeasure</span><span class="sc">;</span>
|
|
|
1174 1161 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonMeasureName</span>} = <span class="i">$SpecifiedComparisonMeasureName</span><span class="sc">;</span>
|
|
|
1175 1162 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonMeasureMethod</span>} = <span class="i">$SpecifiedComparisonMeasureMethod</span><span class="sc">;</span>
|
|
|
1176 1163
|
|
|
1177 1164 <span class="c"># Make sure valid alpha parameter is specified for Tversky calculation...</span>
|
|
|
1178 1165 <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
1179 1166 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedMeasure</span> =~ <span class="q">/^(TverskySimilarity|WeightedTverskySimilarity)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1180 1167 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">alpha</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1181 1168 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"-a, --alpha\" option in \"TverskySimilarity or WeightedTverskySimilarity\" \"-m --mode\". \n"</span><span class="sc">;</span>
|
|
|
1182 1169 <span class="s">}</span>
|
|
|
1183 1170 <span class="k">my</span><span class="s">(</span><span class="i">$Alpha</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1184 1171 <span class="i">$Alpha</span> = <span class="i">$Options</span>{<span class="w">alpha</span>}<span class="sc">;</span>
|
|
|
1185 1172 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$Alpha</span><span class="s">)</span> && <span class="i">$Alpha</span> >=<span class="n">0</span> && <span class="i">$Alpha</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1186 1173 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{alpha}, for option \"-a, --alpha\" is not valid. Allowed values: >= 0 and <= 1\n"</span><span class="sc">;</span>
|
|
|
1187 1174 <span class="s">}</span>
|
|
|
1188 1175 <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>} = <span class="i">$Alpha</span><span class="sc">;</span>
|
|
|
1189 1176 <span class="s">}</span>
|
|
|
1190 1177
|
|
|
1191 1178 <span class="c"># Make sure valid beta parameter is specified for WeightedTanimoto and WeightedTversky</span>
|
|
|
1192 1179 <span class="c"># calculations...</span>
|
|
|
1193 1180 <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
1194 1181 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedMeasure</span> =~ <span class="q">/^(WeightedTverskySimilarity|WeightedTanimotoSimilarity)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1195 1182 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">beta</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1196 1183 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"-b, --beta\" option in \"WeightedTverskySimilarity or WeightedTanimotoSimilarity\" \"-m --mode\". \n"</span><span class="sc">;</span>
|
|
|
1197 1184 <span class="s">}</span>
|
|
|
1198 1185 <span class="k">my</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1199 1186 <span class="i">$Beta</span> = <span class="i">$Options</span>{<span class="w">beta</span>}<span class="sc">;</span>
|
|
|
1200 1187 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span> && <span class="i">$Beta</span> >=<span class="n">0</span> && <span class="i">$Beta</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1201 1188 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{beta}, for option \"-b, --beta\" is not valid. Allowed values: >= 0 and <= 1\n"</span><span class="sc">;</span>
|
|
|
1202 1189 <span class="s">}</span>
|
|
|
1203 1190 <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>} = <span class="i">$Beta</span><span class="sc">;</span>
|
|
|
1204 1191 <span class="s">}</span>
|
|
|
1205 1192 <span class="s">}</span>
|
|
|
1206 1193
|
|
|
1207 1194 <span class="c"># Process options related to comparion of vector strings...</span>
|
|
|
1208 1195 <span class="c">#</span>
|
|
|
1209 <a name="ProcessVectorComparisonOptions-"></a>1196 <span class="k">sub </span><span class="m">ProcessVectorComparisonOptions</span> <span class="s">{</span>
|
|
|
1210 1197 <span class="c"># Setup specified similarity coefficients for vector strings..</span>
|
|
|
1211 1198 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="cm">,</span> <span class="i">$SupportedComparisonMeasure</span><span class="cm">,</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresNameMap</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresMethodMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1212 1199
|
|
|
1213 1200 <span class="i">@SupportedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1214 1201 <span class="i">%SupportedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1215 1202 <span class="i">%SupportedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1216 1203 <span class="k">for</span> <span class="i">$SupportedComparisonMeasure</span> <span class="s">(</span><span class="i">Fingerprints::FingerprintsVector::GetSupportedDistanceAndSimilarityCoefficients</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1217 1204 <span class="c"># Similarity and distance coefficient function/method names contain "Coefficient" in their names.</span>
|
|
|
1218 1205 <span class="c"># So take 'em out and setup a map to original function/method name...</span>
|
|
|
1219 1206 <span class="i">$ComparisonMeasure</span> = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span>
|
|
|
1220 1207 <span class="k">if</span> <span class="s">(</span><span class="i">$ComparisonMeasure</span> =~ <span class="q">/Coefficient$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1221 1208 <span class="i">$ComparisonMeasure</span> =~ <span class="q">s/Coefficient$//i</span><span class="sc">;</span>
|
|
|
1222 1209 <span class="s">}</span>
|
|
|
1223 1210 <span class="k">push</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="sc">;</span>
|
|
|
1224 1211 <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$ComparisonMeasure</span><span class="sc">;</span>
|
|
|
1225 1212 <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span>
|
|
|
1226 1213 <span class="s">}</span>
|
|
|
1227 1214
|
|
|
1228 1215 <span class="c"># Setup a list of similarity coefficients to use for calculating similarity matrices for bit vector strings...</span>
|
|
|
1229 1216 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="cm">,</span> <span class="i">$SpecifiedComparisonMeasureName</span><span class="cm">,</span> <span class="i">$SpecifiedComparisonMeasureMethod</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1230 1217
|
|
|
1231 1218 <span class="i">$SpecifiedComparisonMeasureName</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
1232 1219 <span class="i">$SpecifiedComparisonMeasureMethod</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
1233 1220
|
|
|
1234 1221 <span class="i">$SpecifiedMeasure</span> = <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>}<span class="sc">;</span>
|
|
|
1235 1222 <span class="i">$SpecifiedMeasure</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
1236 1223
|
|
|
1237 1224 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span><span class="s">(</span><span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1238 1225 <span class="k">die</span> <span class="q">"Error: The value specified, $SpecifiedMeasure, for option \"-v --VectorComparisonMode\" is not valid.\nAllowed values:"</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
1239 1226 <span class="s">}</span>
|
|
|
1240 1227
|
|
|
1241 1228 <span class="i">$SpecifiedComparisonMeasureMethod</span> = <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
1242 1229 <span class="i">$SpecifiedComparisonMeasureName</span> = <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
1243 1230
|
|
|
1244 1231 <span class="i">$OptionsInfo</span>{<span class="w">VectorComparisonMode</span>} = <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>}<span class="sc">;</span>
|
|
|
1245 1232
|
|
|
1246 1233 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMeasure</span>} = <span class="i">$SpecifiedMeasure</span><span class="sc">;</span>
|
|
|
1247 1234 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMeasuresName</span>} = <span class="i">$SpecifiedComparisonMeasureName</span><span class="sc">;</span>
|
|
|
1248 1235 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMeasuresMethod</span>} = <span class="i">$SpecifiedComparisonMeasureMethod</span><span class="sc">;</span>
|
|
|
1249 1236
|
|
|
1250 1237 <span class="c"># Setup specified vector comparison calculation modes...</span>
|
|
|
1251 1238 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedFormulism</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1252 1239
|
|
|
1253 1240 <span class="i">$SpecifiedFormulism</span> = <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>}<span class="sc">;</span>
|
|
|
1254 1241 <span class="i">$SpecifiedFormulism</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
1255 1242 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedFormulism</span> !~ <span class="q">/^(AlgebraicForm|BinaryForm|SetTheoreticForm)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1256 1243 <span class="k">die</span> <span class="q">"Error: The value specified, $SpecifiedFormulism, for option \"--VectorComparisonFormulism\" is not valid. Allowed values: AlgebraicForm, BinaryForm or SetTheoreticForm\n"</span><span class="sc">;</span>
|
|
|
1257 1244 <span class="s">}</span>
|
|
|
1258 1245
|
|
|
1259 1246 <span class="i">$OptionsInfo</span>{<span class="w">VectorComparisonFormulism</span>} = <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>}<span class="sc">;</span>
|
|
|
1260 1247 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonMode</span>} = <span class="i">$SpecifiedFormulism</span><span class="sc">;</span>
|
|
|
1261 1248
|
|
|
1262 1249 <span class="s">}</span>
|
|
|
1263 1250
|
|
|
1264 1251 <span class="c"># Process options related to data retrieval from reference fingerprints SD and CSV/TSV</span>
|
|
|
1265 1252 <span class="c"># text files...</span>
|
|
|
1266 1253 <span class="c">#</span>
|
|
|
1267 <a name="ProcessReferenceFingerprintsDataOptions-"></a>1254 <span class="k">sub </span><span class="m">ProcessReferenceFingerprintsDataOptions</span> <span class="s">{</span>
|
|
|
1268 1255
|
|
|
1269 1256 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDPrefix</span>} = <span class="i">$Options</span>{<span class="w">referencecompoundidprefix</span>} ? <span class="i">$Options</span>{<span class="w">referencecompoundidprefix</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span>
|
|
|
1270 1257
|
|
|
1271 1258 <span class="c"># Compound ID and fingerprints column options for text files...</span>
|
|
|
1272 1259
|
|
|
1273 1260 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceColMode</span>} = <span class="i">$Options</span>{<span class="w">referencecolmode</span>}<span class="sc">;</span>
|
|
|
1274 1261
|
|
|
1275 1262 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1276 1263 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecolmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1277 1264 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1278 1265 <span class="k">die</span> <span class="q">"Error: Column value, $Options{referencecompoundidcol}, specified using \"--ReferenceCompoundIDCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span>
|
|
|
1279 1266 <span class="s">}</span>
|
|
|
1280 1267 <span class="s">}</span>
|
|
|
1281 1268 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDCol</span>} = <span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="sc">;</span>
|
|
|
1282 1269 <span class="s">}</span>
|
|
|
1283 1270 <span class="k">else</span> <span class="s">{</span>
|
|
|
1284 1271 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
|
|
|
1285 1272 <span class="s">}</span>
|
|
|
1286 1273
|
|
|
1287 1274 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1288 1275 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecolmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1289 1276 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1290 1277 <span class="k">die</span> <span class="q">"Error: Column value, $Options{referencefingerprintscol}, specified using \"--ReferenceFingerprintsCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span>
|
|
|
1291 1278 <span class="s">}</span>
|
|
|
1292 1279 <span class="s">}</span>
|
|
|
1293 1280 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceFingerprintsCol</span>} = <span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="sc">;</span>
|
|
|
1294 1281 <span class="s">}</span>
|
|
|
1295 1282 <span class="k">else</span> <span class="s">{</span>
|
|
|
1296 1283 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceFingerprintsCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
|
|
|
1297 1284 <span class="s">}</span>
|
|
|
1298 1285
|
|
|
1299 1286 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="s">)</span> && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1300 1287 <span class="k">if</span> <span class="s">(</span><span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>}<span class="s">)</span> && <span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1301 1288 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>} == <span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1302 1289 <span class="k">die</span> <span class="q">"Error: Values specified using \"--ReferenceCompoundIDCol\" and \"--ReferenceFingerprintsCol\", $Options{referencecompoundidcol}, must be different.\n"</span><span class="sc">;</span>
|
|
|
1303 1290 <span class="s">}</span>
|
|
|
1304 1291 <span class="s">}</span>
|
|
|
1305 1292 <span class="k">else</span> <span class="s">{</span>
|
|
|
1306 1293 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidcol</span>} <span class="k">eq</span> <span class="i">$Options</span>{<span class="w">referencefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1307 1294 <span class="k">die</span> <span class="q">"Error: Values specified using \"--ReferenceCompoundIDCol\" and \"--ReferenceFingerprintsCol\", $Options{referencecompoundidcol}, must be different.\n"</span><span class="sc">;</span>
|
|
|
1308 1295 <span class="s">}</span>
|
|
|
1309 1296 <span class="s">}</span>
|
|
|
1310 1297 <span class="s">}</span>
|
|
|
1311 1298
|
|
|
1312 1299 <span class="c"># Compound ID and fingerprints field options for SD files...</span>
|
|
|
1313 1300
|
|
|
1314 1301 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">referencecompoundidmode</span>}<span class="sc">;</span>
|
|
|
1315 1302 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDField</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
1316 1303
|
|
|
1317 1304 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidmode</span>} =~ <span class="q">/^DataField$/i</span> && !<span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1318 1305 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--ReferenceCompoundIDField\" option in \"DataField\" \"--ReferenceCompoundIDMode\". \n"</span><span class="sc">;</span>
|
|
|
1319 1306 <span class="s">}</span>
|
|
|
1320 1307 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1321 1308 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceCompoundIDField</span>} = <span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>}<span class="sc">;</span>
|
|
|
1322 1309 <span class="s">}</span>
|
|
|
1323 1310
|
|
|
1324 1311 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1325 1312 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceFingerprintsField</span>} = <span class="i">$Options</span>{<span class="w">referencefingerprintsfield</span>}<span class="sc">;</span>
|
|
|
1326 1313 <span class="s">}</span>
|
|
|
1327 1314 <span class="k">else</span> <span class="s">{</span>
|
|
|
1328 1315 <span class="i">$OptionsInfo</span>{<span class="w">ReferenceFingerprintsField</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
|
|
|
1329 1316 <span class="s">}</span>
|
|
|
1330 1317
|
|
|
1331 1318 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>} && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1332 1319 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidfield</span>} <span class="k">eq</span> <span class="i">$Options</span>{<span class="w">referencefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1333 1320 <span class="k">die</span> <span class="q">"Error: Values specified using \"--ReferenceCompoundIDField\" and \"--ReferenceFingerprintsfield\", $Options{referencecompoundidfield}, must be different.\n"</span><span class="sc">;</span>
|
|
|
1334 1321 <span class="s">}</span>
|
|
|
1335 1322 <span class="s">}</span>
|
|
|
1336 1323
|
|
|
1337 1324 <span class="s">}</span>
|
|
|
1338 1325
|
|
|
1339 1326 <span class="c"># Process options related to data retrieval from database fingerprints SD and CSV/TSV</span>
|
|
|
1340 1327 <span class="c"># text files...</span>
|
|
|
1341 1328 <span class="c">#</span>
|
|
|
1342 <a name="ProcessDatabaseFingerprintsDataOptions-"></a>1329 <span class="k">sub </span><span class="m">ProcessDatabaseFingerprintsDataOptions</span> <span class="s">{</span>
|
|
|
1343 1330
|
|
|
1344 1331 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDPrefix</span>} = <span class="i">$Options</span>{<span class="w">databasecompoundidprefix</span>} ? <span class="i">$Options</span>{<span class="w">databasecompoundidprefix</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span>
|
|
|
1345 1332
|
|
|
1346 1333 <span class="c"># Compound ID and fingerprints column options for text files...</span>
|
|
|
1347 1334
|
|
|
1348 1335 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseColMode</span>} = <span class="i">$Options</span>{<span class="w">databasecolmode</span>}<span class="sc">;</span>
|
|
|
1349 1336
|
|
|
1350 1337 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1351 1338 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecolmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1352 1339 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1353 1340 <span class="k">die</span> <span class="q">"Error: Column value, $Options{databasecompoundidcol}, specified using \"--DatabaseCompoundIDCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span>
|
|
|
1354 1341 <span class="s">}</span>
|
|
|
1355 1342 <span class="s">}</span>
|
|
|
1356 1343 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDCol</span>} = <span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="sc">;</span>
|
|
|
1357 1344 <span class="s">}</span>
|
|
|
1358 1345 <span class="k">else</span> <span class="s">{</span>
|
|
|
1359 1346 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
|
|
|
1360 1347 <span class="s">}</span>
|
|
|
1361 1348
|
|
|
1362 1349 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1363 1350 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecolmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1364 1351 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1365 1352 <span class="k">die</span> <span class="q">"Error: Column value, $Options{databasefingerprintscol}, specified using \"--DatabaseFingerprintsCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span>
|
|
|
1366 1353 <span class="s">}</span>
|
|
|
1367 1354 <span class="s">}</span>
|
|
|
1368 1355 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseFingerprintsCol</span>} = <span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="sc">;</span>
|
|
|
1369 1356 <span class="s">}</span>
|
|
|
1370 1357 <span class="k">else</span> <span class="s">{</span>
|
|
|
1371 1358 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseFingerprintsCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
|
|
|
1372 1359 <span class="s">}</span>
|
|
|
1373 1360
|
|
|
1374 1361 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="s">)</span> && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1375 1362 <span class="k">if</span> <span class="s">(</span><span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>}<span class="s">)</span> && <span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1376 1363 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>} == <span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1377 1364 <span class="k">die</span> <span class="q">"Error: Values specified using \"--DatabaseCompoundIDCol\" and \"--DatabaseFingerprintsCol\", $Options{databasecompoundidcol}, must be different.\n"</span><span class="sc">;</span>
|
|
|
1378 1365 <span class="s">}</span>
|
|
|
1379 1366 <span class="s">}</span>
|
|
|
1380 1367 <span class="k">else</span> <span class="s">{</span>
|
|
|
1381 1368 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidcol</span>} <span class="k">eq</span> <span class="i">$Options</span>{<span class="w">databasefingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1382 1369 <span class="k">die</span> <span class="q">"Error: Values specified using \"--DatabaseCompoundIDCol\" and \"--DatabaseFingerprintsCol\", $Options{databasecompoundidcol}, must be different.\n"</span><span class="sc">;</span>
|
|
|
1383 1370 <span class="s">}</span>
|
|
|
1384 1371 <span class="s">}</span>
|
|
|
1385 1372 <span class="s">}</span>
|
|
|
1386 1373
|
|
|
1387 1374 <span class="c"># Database data column options for text files...</span>
|
|
|
1388 1375
|
|
|
1389 1376 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataColsMode</span>} = <span class="i">$Options</span>{<span class="w">databasedatacolsmode</span>}<span class="sc">;</span>
|
|
|
1390 1377 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataCols</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
1391 1378 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataCols</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1392 1379
|
|
|
1393 1380 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatacolsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1394 1381 <span class="k">my</span><span class="s">(</span><span class="i">$DatabaseDataCols</span><span class="cm">,</span> <span class="i">$DatabaseColNum</span><span class="cm">,</span> <span class="i">@SpecifiedDataCols</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1395 1382
|
|
|
1396 1383 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">databasedatacols</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1397 1384 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DatabaseDataCols\" option in \"Specify\" \"--DatabaseDataColsMode\". \n"</span><span class="sc">;</span>
|
|
|
1398 1385 <span class="s">}</span>
|
|
|
1399 1386 <span class="i">$DatabaseDataCols</span> = <span class="i">$Options</span>{<span class="w">databasedatacols</span>}<span class="sc">;</span>
|
|
|
1400 1387
|
|
|
1401 1388 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecolmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1402 1389 <span class="i">$DatabaseDataCols</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
1403 1390 <span class="i">@SpecifiedDataCols</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$DatabaseDataCols</span><span class="sc">;</span>
|
|
|
1404 1391 <span class="k">for</span> <span class="i">$DatabaseColNum</span> <span class="s">(</span><span class="i">@SpecifiedDataCols</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1405 1392 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$DatabaseColNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1406 1393 <span class="k">die</span> <span class="q">"Error: Column value, $DatabaseColNum, specified using \"--DatabaseDataCols\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span>
|
|
|
1407 1394 <span class="s">}</span>
|
|
|
1408 1395 <span class="s">}</span>
|
|
|
1409 1396 <span class="s">}</span>
|
|
|
1410 1397 <span class="k">else</span> <span class="s">{</span>
|
|
|
1411 1398 <span class="i">@SpecifiedDataCols</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$DatabaseDataCols</span><span class="sc">;</span>
|
|
|
1412 1399 <span class="s">}</span>
|
|
|
1413 1400 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataCols</span>} = <span class="i">$DatabaseDataCols</span><span class="sc">;</span>
|
|
|
1414 1401 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataCols</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataCols</span><span class="sc">;</span>
|
|
|
1415 1402 <span class="s">}</span>
|
|
|
1416 1403 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatacolsmode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1417 1404 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataCols</span>} = <span class="q">'All'</span><span class="sc">;</span>
|
|
|
1418 1405 <span class="s">}</span>
|
|
|
1419 1406
|
|
|
1420 1407 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataColsMode</span>} =~ <span class="q">/^Specify$/i</span> && !<span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataCols</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1421 1408 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DatabaseDataCols\" option in \"Specify\" \"--DatabaseDataColsMode\". \n"</span><span class="sc">;</span>
|
|
|
1422 1409 <span class="s">}</span>
|
|
|
1423 1410
|
|
|
1424 1411 <span class="c"># Compound ID and fingerprints field options for SD files...</span>
|
|
|
1425 1412
|
|
|
1426 1413 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">databasecompoundidmode</span>}<span class="sc">;</span>
|
|
|
1427 1414 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDField</span>} = <span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>} ? <span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
1428 1415
|
|
|
1429 1416 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1430 1417 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1431 1418 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DatabaseCompoundIDField\" option in \"DataField\" \"--DatabaseCompoundIDMode\". \n"</span><span class="sc">;</span>
|
|
|
1432 1419 <span class="s">}</span>
|
|
|
1433 1420 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseCompoundIDField</span>} = <span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>}<span class="sc">;</span>
|
|
|
1434 1421 <span class="s">}</span>
|
|
|
1435 1422
|
|
|
1436 1423
|
|
|
1437 1424 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1438 1425 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseFingerprintsField</span>} = <span class="i">$Options</span>{<span class="w">databasefingerprintsfield</span>}<span class="sc">;</span>
|
|
|
1439 1426 <span class="s">}</span>
|
|
|
1440 1427 <span class="k">else</span> <span class="s">{</span>
|
|
|
1441 1428 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseFingerprintsField</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
|
|
|
1442 1429 <span class="s">}</span>
|
|
|
1443 1430
|
|
|
1444 1431 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>} && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1445 1432 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidfield</span>} <span class="k">eq</span> <span class="i">$Options</span>{<span class="w">databasefingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1446 1433 <span class="k">die</span> <span class="q">"Error: Values specified using \"--DatabaseCompoundIDField\" and \"--DatabaseFingerprintsfield\", $Options{databasecompoundidfield}, must be different.\n"</span><span class="sc">;</span>
|
|
|
1447 1434 <span class="s">}</span>
|
|
|
1448 1435 <span class="s">}</span>
|
|
|
1449 1436
|
|
|
1450 1437 <span class="c"># Database data field options for SD files...</span>
|
|
|
1451 1438
|
|
|
1452 1439 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">databasedatafieldsmode</span>}<span class="sc">;</span>
|
|
|
1453 1440 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFields</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
1454 1441 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1455 1442
|
|
|
1456 1443 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatafieldsmode</span>} =~ <span class="q">/^Specify$/i</span> && !<span class="i">$Options</span>{<span class="w">databasedatafields</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1457 1444 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DatabaseDataFields\" option in \"Specify\" \"--DatabaseDataFieldsMode\". \n"</span><span class="sc">;</span>
|
|
|
1458 1445 <span class="s">}</span>
|
|
|
1459 1446 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatafields</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1460 1447 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1461 1448 <span class="i">$OptionsInfo</span>{<span class="w">DatabaseDataFields</span>} = <span class="i">$Options</span>{<span class="w">databasedatafields</span>}<span class="sc">;</span>
|
|
|
1462 1449
|
|
|
1463 1450 <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">databasedatafields</span>}<span class="sc">;</span>
|
|
|
1464 1451 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDatabaseDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span>
|
|
|
1465 1452 <span class="s">}</span>
|
|
|
1466 1453 <span class="s">}</span>
|
|
|
1467 1454
|
|
|
1468 1455 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
|
|
|
1469 <a name="SetupScriptUsage-"></a>1456 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
|
|
|
1470 1457
|
|
|
1471 1458 <span class="c"># Retrieve all the options...</span>
|
|
|
1472 1459 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1473 1460
|
|
|
1474 1461 <span class="i">$Options</span>{<span class="w">alpha</span>} = <span class="n">0.5</span><span class="sc">;</span>
|
|
|
1475 1462 <span class="i">$Options</span>{<span class="w">beta</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1476 1463
|
|
|
1477 1464 <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>} = <span class="q">"TanimotoSimilarity"</span><span class="sc">;</span>
|
|
|
1478 1465
|
|
|
1479 1466 <span class="i">$Options</span>{<span class="w">databasecolmode</span>} = <span class="q">'colnum'</span><span class="sc">;</span>
|
|
|
1480 1467
|
|
|
1481 1468 <span class="i">$Options</span>{<span class="w">databasecompoundidprefix</span>} = <span class="q">'Cmpd'</span><span class="sc">;</span>
|
|
|
1482 1469 <span class="i">$Options</span>{<span class="w">databasecompoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span>
|
|
|
1483 1470
|
|
|
1484 1471 <span class="i">$Options</span>{<span class="w">databasedatacolsmode</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span>
|
|
|
1485 1472 <span class="i">$Options</span>{<span class="w">databasedatafieldsmode</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span>
|
|
|
1486 1473
|
|
|
1487 1474 <span class="i">$Options</span>{<span class="w">distancecutoff</span>} = <span class="n">10</span><span class="sc">;</span>
|
|
|
1488 1475
|
|
|
1489 1476 <span class="i">$Options</span>{<span class="w">referencecolmode</span>} = <span class="q">'colnum'</span><span class="sc">;</span>
|
|
|
1490 1477
|
|
|
1491 1478 <span class="i">$Options</span>{<span class="w">referencecompoundidprefix</span>} = <span class="q">'Cmpd'</span><span class="sc">;</span>
|
|
|
1492 1479 <span class="i">$Options</span>{<span class="w">referencecompoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span>
|
|
|
1493 1480
|
|
|
1494 1481 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1495 1482
|
|
|
1496 1483 <span class="i">$Options</span>{<span class="w">fingerprintsmode</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
|
|
|
1497 1484 <span class="i">$Options</span>{<span class="w">groupfusionrule</span>} = <span class="q">'Max'</span><span class="sc">;</span>
|
|
|
1498 1485 <span class="i">$Options</span>{<span class="w">groupfusionapplycutoff</span>} = <span class="q">'Yes'</span><span class="sc">;</span>
|
|
|
1499 1486
|
|
|
1500 1487 <span class="i">$Options</span>{<span class="w">knn</span>} = <span class="q">'All'</span><span class="sc">;</span>
|
|
|
1501 1488
|
|
|
1502 1489 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'MultipleReferences'</span><span class="sc">;</span>
|
|
|
1503 1490
|
|
|
1504 1491 <span class="i">$Options</span>{<span class="w">numofsimilarmolecules</span>} = <span class="n">10</span><span class="sc">;</span>
|
|
|
1505 1492 <span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1506 1493
|
|
|
1507 1494 <span class="i">$Options</span>{<span class="w">indelim</span>} = <span class="q">'comma'</span><span class="sc">;</span>
|
|
|
1508 1495 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span>
|
|
|
1509 1496 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span>
|
|
|
1510 1497
|
|
|
1511 1498 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">'text'</span><span class="sc">;</span>
|
|
|
1512 1499
|
|
|
1513 1500 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span>
|
|
|
1514 1501
|
|
|
1515 1502 <span class="i">$Options</span>{<span class="w">searchmode</span>} = <span class="q">'SimilaritySearch'</span><span class="sc">;</span>
|
|
|
1516 1503
|
|
|
1517 1504 <span class="i">$Options</span>{<span class="w">similarcountmode</span>} = <span class="q">'NumOfSimilar'</span><span class="sc">;</span>
|
|
|
1518 1505
|
|
|
1519 1506 <span class="i">$Options</span>{<span class="w">similaritycutoff</span>} = <span class="n">0.75</span><span class="sc">;</span>
|
|
|
1520 1507
|
|
|
1521 1508 <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>} = <span class="q">'TanimotoSimilarity'</span><span class="sc">;</span>
|
|
|
1522 1509 <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>} = <span class="q">'AlgebraicForm'</span><span class="sc">;</span>
|
|
|
1523 1510
|
|
|
1524 1511 <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">"alpha=f"</span><span class="cm">,</span> <span class="q">"beta=f"</span><span class="cm">,</span> <span class="q">"bitvectorcomparisonmode|b=s"</span><span class="cm">,</span> <span class="q">"databasecolmode=s"</span><span class="cm">,</span> <span class="q">"databasecompoundidcol=s"</span><span class="cm">,</span> <span class="q">"databasecompoundidprefix=s"</span><span class="cm">,</span> <span class="q">"databasecompoundidfield=s"</span><span class="cm">,</span> <span class="q">"databasecompoundidmode=s"</span><span class="cm">,</span> <span class="q">"databasedatacols=s"</span><span class="cm">,</span> <span class="q">"databasedatacolsmode=s"</span><span class="cm">,</span> <span class="q">"databasedatafields=s"</span><span class="cm">,</span> <span class="q">"databasedatafieldsmode=s"</span><span class="cm">,</span> <span class="q">"databasefingerprintscol=s"</span><span class="cm">,</span> <span class="q">"databasefingerprintsfield=s"</span><span class="cm">,</span> <span class="q">"distancecutoff=f"</span><span class="cm">,</span> <span class="q">"detail|d=i"</span><span class="cm">,</span> <span class="q">"fast|f"</span><span class="cm">,</span> <span class="q">"fingerprintsmode=s"</span><span class="cm">,</span> <span class="q">"groupfusionrule|g=s"</span><span class="cm">,</span> <span class="cm">,</span> <span class="q">"groupfusionapplycutoff=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"indelim=s"</span><span class="cm">,</span> <span class="q">"knn|k=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"numofsimilarmolecules|n=i"</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">"percentsimilarmolecules|p=f"</span><span class="cm">,</span> <span class="q">"precision=s"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"referencecolmode=s"</span><span class="cm">,</span> <span class="q">"referencecompoundidcol=s"</span><span class="cm">,</span> <span class="q">"referencecompoundidprefix=s"</span><span class="cm">,</span> <span class="q">"referencecompoundidfield=s"</span><span class="cm">,</span> <span class="q">"referencecompoundidmode=s"</span><span class="cm">,</span> <span class="q">"referencefingerprintscol=s"</span><span class="cm">,</span> <span class="q">"referencefingerprintsfield=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"searchmode|s=s"</span><span class="cm">,</span> <span class="q">"similarcountmode=s"</span><span class="cm">,</span> <span class="q">"similaritycutoff=f"</span><span class="cm">,</span> <span class="q">"vectorcomparisonmode|v=s"</span><span class="cm">,</span> <span class="q">"vectorcomparisonformulism=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>
|
|
|
1525 1512 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
|
|
|
1526 1513 <span class="s">}</span>
|
|
|
1527 1514 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1528 1515 <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>
|
|
|
1529 1516 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
|
|
|
1530 1517 <span class="s">}</span>
|
|
|
1531 1518 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span>
|
|
|
1532 1519 <span class="s">}</span>
|
|
|
1533 1520 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecolmode</span>} !~ <span class="q">/^(ColNum|ColLabel)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1534 1521 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{databasecolmode}, for option \"--DatabaseColMode\" is not valid. Allowed values: ColNum, or ColLabel\n"</span><span class="sc">;</span>
|
|
|
1535 1522 <span class="s">}</span>
|
|
|
1536 1523 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasecompoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1537 1524 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{databasecompoundidmode}, for option \"--DatabaseCompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span>
|
|
|
1538 1525 <span class="s">}</span>
|
|
|
1539 1526 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatacolsmode</span>} !~ <span class="q">/^(All|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1540 1527 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{databasedatacolsmode}, for option \"--DatabaseDataColsMode\" is not valid. Allowed values: All, Specify, or CompoundID\n"</span><span class="sc">;</span>
|
|
|
1541 1528 <span class="s">}</span>
|
|
|
1542 1529 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">databasedatafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1543 1530 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{databasedatafieldsmode}, for option \"--DatabaseDataFieldsMode\" is not valid. Allowed values: All, Common, Specify, or CompoundID\n"</span><span class="sc">;</span>
|
|
|
1544 1531 <span class="s">}</span>
|
|
|
1545 1532 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1546 1533 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{detail}, for option \"-d, --detail\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
|
|
|
1547 1534 <span class="s">}</span>
|
|
|
1548 1535 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintsmode</span>} !~ <span class="q">/^(AutoDetect|FingerprintsBitVectorString|FingerprintsVectorString)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1549 1536 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{fingerprintsmode}, for option \"--FingerprintsMode\" is not valid. Allowed values: AutoDetect, FingerprintsBitVectorString or FingerprintsVectorString \n"</span><span class="sc">;</span>
|
|
|
1550 1537 <span class="s">}</span>
|
|
|
1551 1538 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">groupfusionrule</span>} !~ <span class="q">/^(Max|Min|Mean|Median|Sum|Euclidean)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1552 1539 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{groupfusionrule}, for option \"-g, --GroupFusionRule\" is not valid. Allowed values: Max, Min, Mean, Median, Sum, Euclidean\n"</span><span class="sc">;</span>
|
|
|
1553 1540 <span class="s">}</span>
|
|
|
1554 1541 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">groupfusionapplycutoff</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1555 1542 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"--GroupFusionApplyCutoff\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
|
|
|
1556 1543 <span class="s">}</span>
|
|
|
1557 1544 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} !~ <span class="q">/^(comma|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1558 1545 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{indelim}, for option \"--InDelim\" is not valid. Allowed values: comma, or semicolon\n"</span><span class="sc">;</span>
|
|
|
1559 1546 <span class="s">}</span>
|
|
|
1560 1547 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(IndividualReference|MultipleReferences)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1561 1548 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: IndividualReference, MultipleReferences\n"</span><span class="sc">;</span>
|
|
|
1562 1549 <span class="s">}</span>
|
|
|
1563 1550 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">numofsimilarmolecules</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1564 1551 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{numofsimilarmolecules}, for option \"-n, --NumOfSimilarMolecules\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
|
|
|
1565 1552 <span class="s">}</span>
|
|
|
1566 1553 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1567 1554 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--OutDelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span>
|
|
|
1568 1555 <span class="s">}</span>
|
|
|
1569 1556 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|text|both)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1570 1557 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, text, or both\n"</span><span class="sc">;</span>
|
|
|
1571 1558 <span class="s">}</span>
|
|
|
1572 1559 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>}<span class="s">)</span> && <span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>} > <span class="n">0</span> && <span class="i">$Options</span>{<span class="w">percentsimilarmolecules</span>} <= <span class="n">100</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
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1573 1560 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{percentsimilarmolecules}, for option \"-p, --PercentSimilarMolecules\" is not valid. Allowed values: > 0 and <= 100 \n"</span><span class="sc">;</span>
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|
1574 1561 <span class="s">}</span>
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1575 1562 <span class="k">if</span> <span class="s">(</span><span class="i">$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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|
1576 1563 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
|
|
|
1577 1564 <span class="s">}</span>
|
|
|
1578 1565 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1579 1566 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{precision}, for option \"--precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
|
|
|
1580 1567 <span class="s">}</span>
|
|
|
1581 1568 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecolmode</span>} !~ <span class="q">/^(ColNum|ColLabel)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1582 1569 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{referencecolmode}, for option \"--ReferenceColMode\" is not valid. Allowed values: ColNum, or ColLabel\n"</span><span class="sc">;</span>
|
|
|
1583 1570 <span class="s">}</span>
|
|
|
1584 1571 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">referencecompoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1585 1572 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{referencecompoundidmode}, for option \"--ReferenceCompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span>
|
|
|
1586 1573 <span class="s">}</span>
|
|
|
1587 1574 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">searchmode</span>} !~ <span class="q">/^(SimilaritySearch|DissimilaritySearch)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1588 1575 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{searchmode}, for option \"-s, --SearchMode\" is not valid. Allowed values: SimilaritySearch, DissimilaritySearch \n"</span><span class="sc">;</span>
|
|
|
1589 1576 <span class="s">}</span>
|
|
|
1590 1577 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">similarcountmode</span>} !~ <span class="q">/^(NumOfSimilar|PercentSimilar)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1591 1578 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{similarcountmode}, for option \"--SimilarCountMode\" is not valid. Allowed values: NumOfSimilar, PercentSimilar \n"</span><span class="sc">;</span>
|
|
|
1592 1579 <span class="s">}</span>
|
|
|
1593 1580 <span class="s">}</span>
|
|
|
1594 1581
|
|
|
1595 <a name="EOF-"></a></pre>
|
|
|
1596 <p> </p>
|
|
|
1597 <br />
|
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|
1598 <center>
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1599 <img src="../../../images/h2o2.png">
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1600 </center>
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1601 </body>
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1602 </html>
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