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1 <html>
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2 <head>
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3 <title>MayaChemTools:Code:CalculatePhysicochemicalProperties.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: CalculatePhysicochemicalProperties.pl,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
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18 5 <span class="c"># $Revision: 1.20 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">MoleculeFileIO</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
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53 40 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span>
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54 41 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
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55 42 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptorsGenerator</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">1</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="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
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74 61 <span class="i">@SDFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"sdf sd"</span><span class="s">)</span><span class="sc">;</span>
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75 62
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76 63 <span class="c"># Process options...</span>
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77 64 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
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78 65 <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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79 66 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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80 67
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81 68 <span class="c"># Setup information about input files...</span>
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82 69 <span class="k">print</span> <span class="q">"Checking input SD file(s)...\n"</span><span class="sc">;</span>
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83 70 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
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84 71 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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85 72
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86 73 <span class="c"># Process input files..</span>
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87 74 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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88 75 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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89 76 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span>
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90 77 <span class="s">}</span>
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91 78 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
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92 79 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
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93 80 <span class="k">print</span> <span class="q">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
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94 81 <span class="i">CalculatePhysicochemicalProperties</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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95 82 <span class="s">}</span>
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96 83 <span class="s">}</span>
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97 84 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
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98 85
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99 86 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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100 87 <span class="i">$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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101 88 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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102 89
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103 90 <span class="c">###############################################################################</span>
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104 91
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105 92 <span class="c"># Calculate physicochemical properties for a SD file...</span>
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106 93 <span class="c">#</span>
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107 <a name="CalculatePhysicochemicalProperties-"></a> 94 <span class="k">sub </span><span class="m">CalculatePhysicochemicalProperties</span> <span class="s">{</span>
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108 95 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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109 96 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$MoleculeFileIO</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$MolecularDescriptorsGenerator</span><span class="cm">,</span> <span class="i">$PhysicochemicalPropertiesDataRef</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span>
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110 97
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111 98 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
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112 99
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113 100 <span class="c"># Setup output files...</span>
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114 101 <span class="i">$NewSDFileRef</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$NewTextFileRef</span> = <span class="q">''</span><span class="sc">;</span>
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115 102 <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="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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116 103
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117 104 <span class="c"># Setup molecular descriptor generator to calculate property values for specifed</span>
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118 105 <span class="c"># property names...</span>
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119 106 <span class="i">$MolecularDescriptorsGenerator</span> = <span class="i">SetupMolecularDescriptorsGenerator</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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120 107
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121 108 <span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">4</span><span class="sc">;</span>
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122 109
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123 110 <span class="i">$MoleculeFileIO</span> = <span class="w">new</span> <span class="i">MoleculeFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
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124 111 <span class="i">$MoleculeFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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125 112
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126 113 <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Molecule</span> = <span class="i">$MoleculeFileIO</span><span class="i">->ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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127 114 <span class="i">$CmpdCount</span>++<span class="sc">;</span>
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128 115
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129 116 <span class="c"># Filter compound data before calculating physiochemical properties...</span>
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130 117 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Filter</span>}<span class="s">)</span> <span class="s">{</span>
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131 118 <span class="k">if</span> <span class="s">(</span><span class="i">CheckAndFilterCompound</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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132 119 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
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133 120 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
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134 121 <span class="s">}</span>
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135 122 <span class="s">}</span>
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136 123
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137 124 <span class="c"># Calculate properties...</span>
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138 125 <span class="i">$PhysicochemicalPropertiesDataRef</span> = <span class="i">CalculateMoleculeProperties</span><span class="s">(</span><span class="i">$MolecularDescriptorsGenerator</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
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139 126
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140 127 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$PhysicochemicalPropertiesDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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141 128 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
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142 129 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'PropertiesCalculationFailed'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
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143 130 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
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144 131 <span class="s">}</span>
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145 132
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146 133 <span class="c"># Calculate any rule violations...</span>
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147 134 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>} && <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
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148 135 <span class="i">$RuleOf5ViolationsCount</span>++<span class="sc">;</span>
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149 136 <span class="s">}</span>
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150 137
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151 138 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>} && <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
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152 139 <span class="i">$RuleOf3ViolationsCount</span>++<span class="sc">;</span>
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153 140 <span class="s">}</span>
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154 141
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155 142 <span class="c"># Write out calculate properties...</span>
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156 143 <span class="i">WriteDataToOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$PhysicochemicalPropertiesDataRef</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span>
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157 144 <span class="s">}</span>
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158 145 <span class="i">$MoleculeFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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159 146
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160 147 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} && <span class="i">$NewSDFileRef</span><span class="s">)</span> <span class="s">{</span>
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161 148 <span class="k">close</span> <span class="i">$NewSDFileRef</span><span class="sc">;</span>
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162 149 <span class="s">}</span>
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163 150 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="i">$NewTextFileRef</span><span class="s">)</span> <span class="s">{</span>
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164 151 <span class="k">close</span> <span class="i">$NewTextFileRef</span><span class="sc">;</span>
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165 152 <span class="s">}</span>
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166 153
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167 154 <span class="i">WriteCalculationSummaryStatistics</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</span><span class="s">)</span><span class="sc">;</span>
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168 155 <span class="s">}</span>
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169 156
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170 157 <span class="c"># Process compound being ignored due to problems in physicochemical properties calculation...</span>
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171 158 <span class="c">#</span>
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172 <a name="ProcessIgnoredCompound-"></a> 159 <span class="k">sub </span><span class="m">ProcessIgnoredCompound</span> <span class="s">{</span>
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173 160 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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174 161 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
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175 162
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176 163 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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177 164 <span class="i">$CmpdID</span> = <span class="i">SetupCmpdIDForTextFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
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178 165
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179 166 <span class="j">MODE:</span> <span class="s">{</span>
|
|
|
180 167 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNonElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
181 168 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n"</span><span class="sc">;</span>
|
|
|
182 169 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
|
|
|
183 170 <span class="s">}</span>
|
|
|
184 171
|
|
|
185 172 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNoElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
186 173 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n"</span><span class="sc">;</span>
|
|
|
187 174 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
|
|
|
188 175 <span class="s">}</span>
|
|
|
189 176
|
|
|
190 177 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^PropertiesCalculationFailed$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
191 178 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Physicochemical properties calculation didn't succeed...\n\n"</span><span class="sc">;</span>
|
|
|
192 179 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
|
|
|
193 180 <span class="s">}</span>
|
|
|
194 181 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Physicochemical properties calculation didn't succeed...\n\n"</span><span class="sc">;</span>
|
|
|
195 182 <span class="s">}</span>
|
|
|
196 183 <span class="s">}</span>
|
|
|
197 184
|
|
|
198 185 <span class="c"># Check and filter compounds....</span>
|
|
|
199 186 <span class="c">#</span>
|
|
|
200 <a name="CheckAndFilterCompound-"></a> 187 <span class="k">sub </span><span class="m">CheckAndFilterCompound</span> <span class="s">{</span>
|
|
|
201 188 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
202 189 <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
203 190
|
|
|
204 191 <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfElementsAndNonElements</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
205 192
|
|
|
206 193 <span class="k">if</span> <span class="s">(</span><span class="i">$NonElementCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
207 194 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'ContainsNonElementalData'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
208 195 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
209 196 <span class="s">}</span>
|
|
|
210 197
|
|
|
211 198 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ElementCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
212 199 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'ContainsNoElementalData'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
213 200 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
214 201 <span class="s">}</span>
|
|
|
215 202
|
|
|
216 203 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
217 204 <span class="s">}</span>
|
|
|
218 205
|
|
|
219 206 <span class="c"># Write out compounds physicochemical properties calculation summary statistics...</span>
|
|
|
220 207 <span class="c">#</span>
|
|
|
221 <a name="WriteCalculationSummaryStatistics-"></a> 208 <span class="k">sub </span><span class="m">WriteCalculationSummaryStatistics</span> <span class="s">{</span>
|
|
|
222 209 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
223 210 <span class="k">my</span><span class="s">(</span><span class="i">$ProcessedCmpdCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
224 211
|
|
|
225 212 <span class="i">$ProcessedCmpdCount</span> = <span class="i">$CmpdCount</span> - <span class="i">$IgnoredCmpdCount</span><span class="sc">;</span>
|
|
|
226 213
|
|
|
227 214 <span class="k">print</span> <span class="q">"\nNumber of compounds: $CmpdCount\n"</span><span class="sc">;</span>
|
|
|
228 215 <span class="k">print</span> <span class="q">"Number of compounds processed successfully during physicochemical properties calculation: $ProcessedCmpdCount\n"</span><span class="sc">;</span>
|
|
|
229 216 <span class="k">print</span> <span class="q">"Number of compounds ignored during physicochemical properties calculation: $IgnoredCmpdCount\n"</span><span class="sc">;</span>
|
|
|
230 217
|
|
|
231 218 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
232 219 <span class="k">print</span> <span class="q">"Number of compounds with one or more RuleOf5 violations: $RuleOf5ViolationsCount\n"</span><span class="sc">;</span>
|
|
|
233 220 <span class="s">}</span>
|
|
|
234 221
|
|
|
235 222 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
236 223 <span class="k">print</span> <span class="q">"Number of compounds with one or more RuleOf3 violations: $RuleOf3ViolationsCount\n"</span><span class="sc">;</span>
|
|
|
237 224 <span class="s">}</span>
|
|
|
238 225
|
|
|
239 226 <span class="s">}</span>
|
|
|
240 227
|
|
|
241 228 <span class="c"># Open output files...</span>
|
|
|
242 229 <span class="c">#</span>
|
|
|
243 <a name="SetupAndOpenOutputFiles-"></a> 230 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span>
|
|
|
244 231 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
245 232 <span class="k">my</span><span class="s">(</span><span class="i">$NewSDFile</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
246 233
|
|
|
247 234 <span class="i">$NewSDFileRef</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
248 235 <span class="i">$NewTextFileRef</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
249 236
|
|
|
250 237 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
251 238 <span class="i">$NewSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
|
|
|
252 239 <span class="k">print</span> <span class="q">"Generating SD file $NewSDFile...\n"</span><span class="sc">;</span>
|
|
|
253 240 <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">">$NewSDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewSDFile: $! \n"</span><span class="sc">;</span>
|
|
|
254 241 <span class="i">$NewSDFileRef</span> = \<span class="i">*NEWSDFILE</span><span class="sc">;</span>
|
|
|
255 242 <span class="s">}</span>
|
|
|
256 243 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
257 244 <span class="i">$NewTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
|
|
|
258 245 <span class="k">print</span> <span class="q">"Generating text file $NewTextFile...\n"</span><span class="sc">;</span>
|
|
|
259 246 <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">">$NewTextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewTextFile: $! \n"</span><span class="sc">;</span>
|
|
|
260 247 <span class="i">WriteTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> \<span class="i">*NEWTEXTFILE</span><span class="s">)</span><span class="sc">;</span>
|
|
|
261 248 <span class="i">$NewTextFileRef</span> = \<span class="i">*NEWTEXTFILE</span><span class="sc">;</span>
|
|
|
262 249 <span class="s">}</span>
|
|
|
263 250 <span class="k">return</span> <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
264 251 <span class="s">}</span>
|
|
|
265 252
|
|
|
266 253 <span class="c"># Write calculated physicochemical properties and other data to appropriate output files...</span>
|
|
|
267 254 <span class="c">#</span>
|
|
|
268 <a name="WriteDataToOutputFiles-"></a> 255 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span>
|
|
|
269 256 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$PhysicochemicalPropertiesDataRef</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
270 257 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
271 258
|
|
|
272 259 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
273 260 <span class="c"># Retrieve input compound string used to create molecule and write it out</span>
|
|
|
274 261 <span class="c"># without last line containing a delimiter...</span>
|
|
|
275 262 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
276 263 <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">->GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
277 264 <span class="i">$CmpdString</span> =~ <span class="q">s/\$\$\$\$$//</span><span class="sc">;</span>
|
|
|
278 265 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"$CmpdString"</span><span class="sc">;</span>
|
|
|
279 266
|
|
|
280 267 <span class="c"># Write out calculated physicochemical properties data...</span>
|
|
|
281 268 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
282 269 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="i">$PropertyName</span>}<span class="sc">;</span>
|
|
|
283 270 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <$PropertyName>\n$PropertyValue\n\n"</span><span class="sc">;</span>
|
|
|
284 271 <span class="s">}</span>
|
|
|
285 272
|
|
|
286 273 <span class="c"># Write out RuleOf5 violations for molecule....</span>
|
|
|
287 274 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
288 275 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf5Violations</span>}<span class="sc">;</span>
|
|
|
289 276 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <RuleOf5Violations>\n$PropertyValue\n\n"</span><span class="sc">;</span>
|
|
|
290 277 <span class="s">}</span>
|
|
|
291 278
|
|
|
292 279 <span class="c"># Write out RuleOf3 violations for molecule....</span>
|
|
|
293 280 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
294 281 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf3Violations</span>}<span class="sc">;</span>
|
|
|
295 282 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <RuleOf3Violations>\n$PropertyValue\n\n"</span><span class="sc">;</span>
|
|
|
296 283 <span class="s">}</span>
|
|
|
297 284
|
|
|
298 285 <span class="c"># Write out delimiter...</span>
|
|
|
299 286 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"\$\$\$\$\n"</span><span class="sc">;</span>
|
|
|
300 287 <span class="s">}</span>
|
|
|
301 288
|
|
|
302 289 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
303 290 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="cm">,</span> <span class="i">$DataFieldLabel</span><span class="cm">,</span> <span class="i">$DataFieldValue</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span><span class="s">)</span><span class="sc">;</span>
|
|
|
304 291
|
|
|
305 292 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
306 293 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
307 294 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
308 295 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">SetupCmpdIDForTextFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
309 296 <span class="s">}</span>
|
|
|
310 297 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
311 298 <span class="i">@LineWords</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
|
|
|
312 299 <span class="s">}</span>
|
|
|
313 300 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
314 301 <span class="i">@LineWords</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
|
|
|
315 302 <span class="s">}</span>
|
|
|
316 303 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
317 304 <span class="i">@LineWords</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
|
|
|
318 305 <span class="s">}</span>
|
|
|
319 306
|
|
|
320 307 <span class="c"># Append calculated physicochemical properties data...</span>
|
|
|
321 308 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
322 309 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="i">$PropertyName</span>}<span class="sc">;</span>
|
|
|
323 310 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span>
|
|
|
324 311 <span class="s">}</span>
|
|
|
325 312
|
|
|
326 313 <span class="c"># Write out RuleOf5 violations for molecule....</span>
|
|
|
327 314 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
328 315 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf5Violations</span>}<span class="sc">;</span>
|
|
|
329 316 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span>
|
|
|
330 317 <span class="s">}</span>
|
|
|
331 318
|
|
|
332 319 <span class="c"># Write out RuleOf3 violations for molecule....</span>
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|
|
333 320 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
334 321 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf3Violations</span>}<span class="sc">;</span>
|
|
|
335 322 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span>
|
|
|
336 323 <span class="s">}</span>
|
|
|
337 324
|
|
|
338 325 <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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
339 326 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
|
|
|
340 327 <span class="s">}</span>
|
|
|
341 328 <span class="s">}</span>
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342 329
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|
|
343 330 <span class="c"># Write out approriate column labels to text file...</span>
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|
344 <a name="WriteTextFileCoulmnLabels-"></a> 331 <span class="k">sub </span><span class="m">WriteTextFileCoulmnLabels</span> <span class="s">{</span>
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|
|
345 332 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
|
346 333 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
|
|
|
347 334
|
|
|
348 335 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
349 336 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
350 337 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
|
|
|
351 338 <span class="s">}</span>
|
|
|
352 339 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
353 340 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
|
|
|
354 341 <span class="s">}</span>
|
|
|
355 342 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
356 343 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
|
|
|
357 344 <span class="s">}</span>
|
|
|
358 345 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
359 346 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span>
|
|
|
360 347 <span class="s">}</span>
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|
|
361 348 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
362 349
|
|
|
363 350 <span class="c"># Append physicochemical properties column labels...</span>
|
|
|
364 351 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="sc">;</span>
|
|
|
365 352
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|
|
366 353 <span class="c"># Write out RuleOf5 violations label...</span>
|
|
|
367 354 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
368 355 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">'RuleOf5Violations'</span><span class="sc">;</span>
|
|
|
369 356 <span class="s">}</span>
|
|
|
370 357
|
|
|
371 358 <span class="c"># Write out RuleOf3 violations label...</span>
|
|
|
372 359 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
373 360 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">'RuleOf3Violations'</span><span class="sc">;</span>
|
|
|
374 361 <span class="s">}</span>
|
|
|
375 362
|
|
|
376 363 <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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
377 364 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
|
|
|
378 365 <span class="s">}</span>
|
|
|
379 366
|
|
|
380 367 <span class="c"># Generate compound ID for text files..</span>
|
|
|
381 368 <span class="c">#</span>
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|
382 <a name="SetupCmpdIDForTextFiles-"></a> 369 <span class="k">sub </span><span class="m">SetupCmpdIDForTextFiles</span> <span class="s">{</span>
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|
|
383 370 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
384 371 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
385 372
|
|
|
386 373 <span class="i">$CmpdID</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
387 374 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolNameOrLabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
388 375 <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
389 376 <span class="i">$MolName</span> = <span class="i">$Molecule</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
390 377 <span class="i">$CmpdID</span> = <span class="i">$MolName</span> ? <span class="i">$MolName</span> <span class="co">:</span> <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span>
|
|
|
391 378 <span class="s">}</span>
|
|
|
392 379 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^LabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
393 380 <span class="i">$CmpdID</span> = <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span>
|
|
|
394 381 <span class="s">}</span>
|
|
|
395 382 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
396 383 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span>
|
|
|
397 384 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
|
|
|
398 385 <span class="i">$CmpdID</span> = <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$SpecifiedDataField</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$SpecifiedDataField</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
399 386 <span class="s">}</span>
|
|
|
400 387 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolName$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
401 388 <span class="i">$CmpdID</span> = <span class="i">$Molecule</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
402 389 <span class="s">}</span>
|
|
|
403 390 <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span>
|
|
|
404 391 <span class="s">}</span>
|
|
|
405 392
|
|
|
406 393 <span class="c"># Calculate physicochemical properties for molecule...</span>
|
|
|
407 394 <span class="c">#</span>
|
|
|
408 <a name="CalculateMoleculeProperties-"></a> 395 <span class="k">sub </span><span class="m">CalculateMoleculeProperties</span> <span class="s">{</span>
|
|
|
409 396 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularDescriptorsGenerator</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
410 397 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="cm">,</span> <span class="i">$MolecularDescriptorsObject</span><span class="cm">,</span> <span class="i">%CalculatedPhysicochemicalProperties</span><span class="s">)</span><span class="sc">;</span>
|
|
|
411 398
|
|
|
412 399 <span class="i">%CalculatedPhysicochemicalProperties</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
413 400
|
|
|
414 401 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
415 402 <span class="i">$Molecule</span><span class="i">->KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
416 403 <span class="s">}</span>
|
|
|
417 404
|
|
|
418 405 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">->DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
419 406 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
420 407 <span class="s">}</span>
|
|
|
421 408 <span class="i">$Molecule</span><span class="i">->SetAromaticityModel</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
422 409 <span class="i">$Molecule</span><span class="i">->DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
423 410
|
|
|
424 411 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AddHydrogens</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
425 412 <span class="i">$Molecule</span><span class="i">->AddHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
426 413 <span class="s">}</span>
|
|
|
427 414
|
|
|
428 415 <span class="c"># Calculate physicochemical properties...</span>
|
|
|
429 416 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetMolecule</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
430 417 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
431 418
|
|
|
432 419 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MolecularDescriptorsGenerator</span><span class="i">->IsDescriptorsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
433 420 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
434 421 <span class="s">}</span>
|
|
|
435 422
|
|
|
436 423 <span class="i">%CalculatedPhysicochemicalProperties</span> = <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
437 424
|
|
|
438 425 <span class="c"># Count RuleOf3 violations...</span>
|
|
|
439 426 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
440 427 <span class="i">CalculateRuleViolationsCount</span><span class="s">(</span><span class="q">'RuleOf3Violations'</span><span class="cm">,</span> \<span class="i">%CalculatedPhysicochemicalProperties</span><span class="s">)</span><span class="sc">;</span>
|
|
|
441 428 <span class="s">}</span>
|
|
|
442 429
|
|
|
443 430 <span class="c"># Count RuleOf5 violations...</span>
|
|
|
444 431 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
445 432 <span class="i">CalculateRuleViolationsCount</span><span class="s">(</span><span class="q">'RuleOf5Violations'</span><span class="cm">,</span> \<span class="i">%CalculatedPhysicochemicalProperties</span><span class="s">)</span><span class="sc">;</span>
|
|
|
446 433 <span class="s">}</span>
|
|
|
447 434
|
|
|
448 435 <span class="k">return</span> \<span class="i">%CalculatedPhysicochemicalProperties</span><span class="sc">;</span>
|
|
|
449 436 <span class="s">}</span>
|
|
|
450 437
|
|
|
451 438 <span class="c"># Setup molecular descriptor generator to calculate property values for specifed</span>
|
|
|
452 439 <span class="c"># property names...</span>
|
|
|
453 440 <span class="c">#</span>
|
|
|
454 <a name="SetupMolecularDescriptorsGenerator-"></a> 441 <span class="k">sub </span><span class="m">SetupMolecularDescriptorsGenerator</span> <span class="s">{</span>
|
|
|
455 442 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$MolecularDescriptorsGenerator</span><span class="s">)</span><span class="sc">;</span>
|
|
|
456 443
|
|
|
457 444 <span class="i">$MolecularDescriptorsGenerator</span> = <span class="w">new</span> <span class="i">MolecularDescriptors::MolecularDescriptorsGenerator</span><span class="s">(</span><span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Specify'</span><span class="cm">,</span> <span class="q">'DescriptorNames'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
458 445
|
|
|
459 446 <span class="c"># Setup molecular desciptor calculation parameters...</span>
|
|
|
460 447 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'MolecularWeight'</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'ExactMass'</span><span class="s">)</span>}<span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
461 448 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetDescriptorClassParameters</span><span class="s">(</span><span class="q">'DescriptorClassName'</span> <span class="cm">=></span> <span class="q">'WeightAndMassDescriptors'</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">PrecisionParametersMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
462 449 <span class="s">}</span>
|
|
|
463 450
|
|
|
464 451 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'RotatableBonds'</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
465 452 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetDescriptorClassParameters</span><span class="s">(</span><span class="q">'DescriptorClassName'</span> <span class="cm">=></span> <span class="q">'RotatableBondsDescriptors'</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RotatableBondsParametersMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
466 453 <span class="s">}</span>
|
|
|
467 454
|
|
|
468 455 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'HydrogenBondDonors'</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'HydrogenBondAcceptors'</span><span class="s">)</span>}<span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
469 456 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetDescriptorClassParameters</span><span class="s">(</span><span class="q">'DescriptorClassName'</span> <span class="cm">=></span> <span class="q">'HydrogenBondsDescriptors'</span><span class="cm">,</span> <span class="q">'HydrogenBondsType'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">HydrogenBonds</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
470 457 <span class="s">}</span>
|
|
|
471 458
|
|
|
472 459 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'TPSA'</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
473 460 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetDescriptorClassParameters</span><span class="s">(</span><span class="q">'DescriptorClassName'</span> <span class="cm">=></span> <span class="q">'TPSADescriptors'</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">TPSAParametersMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
474 461 <span class="s">}</span>
|
|
|
475 462
|
|
|
476 463 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'MolecularComplexity'</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
477 464 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetDescriptorClassParameters</span><span class="s">(</span><span class="q">'DescriptorClassName'</span> <span class="cm">=></span> <span class="q">'MolecularComplexityDescriptors'</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
478 465 <span class="s">}</span>
|
|
|
479 466
|
|
|
480 467 <span class="k">return</span> <span class="i">$MolecularDescriptorsGenerator</span><span class="sc">;</span>
|
|
|
481 468 <span class="s">}</span>
|
|
|
482 469
|
|
|
483 470 <span class="c"># Calculate RuleOf3 or RuleOf5 violations count...</span>
|
|
|
484 471 <span class="c">#</span>
|
|
|
485 <a name="CalculateRuleViolationsCount-"></a> 472 <span class="k">sub </span><span class="m">CalculateRuleViolationsCount</span> <span class="s">{</span>
|
|
|
486 473 <span class="k">my</span><span class="s">(</span><span class="i">$RuleViolationsType</span><span class="cm">,</span> <span class="i">$CalculatedPropertiesMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
487 474 <span class="k">my</span><span class="s">(</span><span class="i">$RuleViolationsCount</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
488 475
|
|
|
489 476 <span class="i">$RuleViolationsCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
490 477
|
|
|
491 478 <span class="j">RULEVIOLATIONSTYPE:</span> <span class="s">{</span>
|
|
|
492 479 <span class="k">if</span> <span class="s">(</span><span class="i">$RuleViolationsType</span> =~ <span class="q">/^RuleOf3Violations$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
493 480 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
494 481 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculatedPropertiesMapRef</span>->{<span class="i">$PropertyName</span>} > <span class="i">$OptionsInfo</span>{<span class="w">RuleOf3MaxPropertyValuesMap</span>}{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
495 482 <span class="i">$RuleViolationsCount</span>++<span class="sc">;</span>
|
|
|
496 483 <span class="s">}</span>
|
|
|
497 484 <span class="s">}</span>
|
|
|
498 485 <span class="k">last</span> <span class="j">RULEVIOLATIONSTYPE</span><span class="sc">;</span>
|
|
|
499 486 <span class="s">}</span>
|
|
|
500 487
|
|
|
501 488 <span class="k">if</span> <span class="s">(</span><span class="i">$RuleViolationsType</span> =~ <span class="q">/^RuleOf5Violations$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
502 489 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
503 490 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculatedPropertiesMapRef</span>->{<span class="i">$PropertyName</span>} > <span class="i">$OptionsInfo</span>{<span class="w">RuleOf5MaxPropertyValuesMap</span>}{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
504 491 <span class="i">$RuleViolationsCount</span>++<span class="sc">;</span>
|
|
|
505 492 <span class="s">}</span>
|
|
|
506 493 <span class="s">}</span>
|
|
|
507 494 <span class="k">last</span> <span class="j">RULEVIOLATIONSTYPE</span><span class="sc">;</span>
|
|
|
508 495 <span class="s">}</span>
|
|
|
509 496
|
|
|
510 497 <span class="k">die</span> <span class="q">"Warning: Unknown rule violation type: $RuleViolationsType..."</span><span class="sc">;</span>
|
|
|
511 498 <span class="s">}</span>
|
|
|
512 499
|
|
|
513 500 <span class="c"># Set rule violation count...</span>
|
|
|
514 501 <span class="i">$CalculatedPropertiesMapRef</span>->{<span class="i">$RuleViolationsType</span>} = <span class="i">$RuleViolationsCount</span><span class="sc">;</span>
|
|
|
515 502
|
|
|
516 503 <span class="s">}</span>
|
|
|
517 504
|
|
|
518 505 <span class="c"># Retrieve information about SD files...</span>
|
|
|
519 506 <span class="c">#</span>
|
|
|
520 <a name="RetrieveSDFilesInfo-"></a> 507 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
|
|
|
521 508 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$TextOutFileExt</span><span class="cm">,</span> <span class="i">$SDOutFileExt</span><span class="cm">,</span> <span class="i">$NewSDFileName</span><span class="cm">,</span> <span class="i">$NewTextFileName</span><span class="cm">,</span> <span class="i">$CheckDataField</span><span class="cm">,</span> <span class="i">$CollectDataFields</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
522 509
|
|
|
523 510 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
524 511 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
525 512 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
526 513 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
527 514 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
528 515 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
529 516 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
530 517
|
|
|
531 518 <span class="i">$CheckDataField</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
532 519 <span class="i">$CollectDataFields</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^(All|Common)$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
533 520
|
|
|
534 521 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
|
|
|
535 522 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
536 523
|
|
|
537 524 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
538 525 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
|
|
|
539 526 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
|
|
|
540 527 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
|
|
|
541 528
|
|
|
542 529 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
543 530 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
544 531 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span>
|
|
|
545 532 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
546 533 <span class="s">}</span>
|
|
|
547 534 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
548 535 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span>
|
|
|
549 536 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
550 537 <span class="s">}</span>
|
|
|
551 538
|
|
|
552 539 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span>
|
|
|
553 540 <span class="c"># Make sure data field exists in SD file..</span>
|
|
|
554 541 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$SpecifiedDataField</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
555 542
|
|
|
556 543 <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
557 544 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $SDFile: $! \n"</span><span class="sc">;</span>
|
|
|
558 545 <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
|
|
|
559 546 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
|
|
|
560 547 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
|
|
|
561 548 <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
|
|
|
562 549 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
|
|
|
563 550 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
564 551 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n"</span><span class="sc">;</span>
|
|
|
565 552 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
566 553 <span class="s">}</span>
|
|
|
567 554 <span class="s">}</span>
|
|
|
568 555
|
|
|
569 556 <span class="i">$AllDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
570 557 <span class="i">$CommonDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
571 558 <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span>
|
|
|
572 559 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
573 560 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $SDFile: $! \n"</span><span class="sc">;</span>
|
|
|
574 561 <span class="s">(</span><span class="i">$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>
|
|
|
575 562 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
|
|
|
576 563 <span class="s">}</span>
|
|
|
577 564
|
|
|
578 565 <span class="c"># Setup output file names...</span>
|
|
|
579 566 <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">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
580 567 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
581 568
|
|
|
582 569 <span class="i">$TextOutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span>
|
|
|
583 570 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
584 571 <span class="i">$TextOutFileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span>
|
|
|
585 572 <span class="s">}</span>
|
|
|
586 573 <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span>
|
|
|
587 574
|
|
|
588 575 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
589 576 <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>
|
|
|
590 577 <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>
|
|
|
591 578 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
|
|
|
592 579 <span class="s">}</span>
|
|
|
593 580 <span class="k">else</span> <span class="s">{</span>
|
|
|
594 581 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
|
|
|
595 582 <span class="s">}</span>
|
|
|
596 583 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
|
|
|
597 584 <span class="s">}</span>
|
|
|
598 585 <span class="k">else</span> <span class="s">{</span>
|
|
|
599 586 <span class="i">$OutFileRoot</span> = <span class="q">"${FileName}PhysicochemicalProperties"</span><span class="sc">;</span>
|
|
|
600 587 <span class="s">}</span>
|
|
|
601 588
|
|
|
602 589 <span class="i">$NewSDFileName</span> = <span class="q">"${OutFileRoot}.${SDOutFileExt}"</span><span class="sc">;</span>
|
|
|
603 590 <span class="i">$NewTextFileName</span> = <span class="q">"${OutFileRoot}.${TextOutFileExt}"</span><span class="sc">;</span>
|
|
|
604 591
|
|
|
605 592 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
606 593 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
607 594 <span class="k">warn</span> <span class="q">"Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n"</span><span class="sc">;</span>
|
|
|
608 595 <span class="k">print</span> <span class="q">"Specify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span>
|
|
|
609 596 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
610 597 <span class="s">}</span>
|
|
|
611 598 <span class="s">}</span>
|
|
|
612 599
|
|
|
613 600 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
614 601 <span class="c"># Check SD and text outout files...</span>
|
|
|
615 602 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
616 603 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span>
|
|
|
617 604 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n"</span><span class="sc">;</span>
|
|
|
618 605 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
619 606 <span class="s">}</span>
|
|
|
620 607 <span class="s">}</span>
|
|
|
621 608 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
622 609 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewTextFileName</span><span class="s">)</span> <span class="s">{</span>
|
|
|
623 610 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n"</span><span class="sc">;</span>
|
|
|
624 611 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
625 612 <span class="s">}</span>
|
|
|
626 613 <span class="s">}</span>
|
|
|
627 614 <span class="s">}</span>
|
|
|
628 615
|
|
|
629 616 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
|
|
|
630 617
|
|
|
631 618 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
|
|
|
632 619 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span>
|
|
|
633 620 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span>
|
|
|
634 621
|
|
|
635 622 <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span>
|
|
|
636 623 <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span>
|
|
|
637 624 <span class="s">}</span>
|
|
|
638 625 <span class="s">}</span>
|
|
|
639 626
|
|
|
640 627 <span class="c"># Process option values...</span>
|
|
|
641 <a name="ProcessOptions-"></a> 628 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
|
|
|
642 629 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
643 630
|
|
|
644 631 <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span>
|
|
|
645 632
|
|
|
646 633 <span class="c"># Process property name related options...</span>
|
|
|
647 634 <span class="i">ProcessPropertyNamesOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
648 635
|
|
|
649 636 <span class="c"># Setup RuleOf3 and RuleOf5 violation calculations...</span>
|
|
|
650 637 <span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
651 638 <span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
652 639
|
|
|
653 640 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span>
|
|
|
654 641 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span>
|
|
|
655 642 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span>
|
|
|
656 643
|
|
|
657 644 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span>
|
|
|
658 645 <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
659 646
|
|
|
660 647 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
661 648 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
662 649
|
|
|
663 650 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
664 651 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
665 652 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
666 653 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n"</span><span class="sc">;</span>
|
|
|
667 654 <span class="s">}</span>
|
|
|
668 655 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span>
|
|
|
669 656 <span class="s">}</span>
|
|
|
670 657 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^(LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
671 658 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>} ? <span class="i">$Options</span>{<span class="w">compoundid</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span>
|
|
|
672 659 <span class="s">}</span>
|
|
|
673 660 <span class="s">}</span>
|
|
|
674 661 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
675 662 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
676 663 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n"</span><span class="sc">;</span>
|
|
|
677 664 <span class="s">}</span>
|
|
|
678 665 <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span>
|
|
|
679 666 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span>
|
|
|
680 667 <span class="s">}</span>
|
|
|
681 668
|
|
|
682 669 <span class="c"># Types of hydrogen bonds...</span>
|
|
|
683 670 <span class="i">$OptionsInfo</span>{<span class="w">HydrogenBonds</span>} = <span class="i">$Options</span>{<span class="w">hydrogenbonds</span>}<span class="sc">;</span>
|
|
|
684 671
|
|
|
685 672 <span class="c"># Process precision value parameters...</span>
|
|
|
686 673 <span class="i">ProcessPrecisionOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
687 674
|
|
|
688 675 <span class="c"># Process rotatable bonds parameters...</span>
|
|
|
689 676 <span class="i">ProcessRotatableBondsOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
690 677
|
|
|
691 678 <span class="c"># Process TPSA parameters...</span>
|
|
|
692 679 <span class="i">ProcessTPSAOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
693 680
|
|
|
694 681 <span class="c"># Process molecular complexity parameters...</span>
|
|
|
695 682 <span class="i">ProcessMolecularComplexityOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
696 683
|
|
|
697 684 <span class="i">$OptionsInfo</span>{<span class="w">Filter</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
698 685
|
|
|
699 686 <span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
700 687
|
|
|
701 688 <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
|
|
|
702 689 <span class="i">$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>
|
|
|
703 690 <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
704 691
|
|
|
705 692 <span class="i">$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>
|
|
|
706 693 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
707 694
|
|
|
708 695 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
709 696 <span class="i">$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>
|
|
|
710 697 <span class="s">}</span>
|
|
|
711 698
|
|
|
712 699 <span class="c"># Process property name related options...</span>
|
|
|
713 700 <span class="c">#</span>
|
|
|
714 <a name="ProcessPropertyNamesOption-"></a> 701 <span class="k">sub </span><span class="m">ProcessPropertyNamesOption</span> <span class="s">{</span>
|
|
|
715 702
|
|
|
716 703 <span class="c"># Setup supported physicochemical properties...</span>
|
|
|
717 704 <span class="k">my</span><span class="s">(</span><span class="i">$SupportedProperty</span><span class="s">)</span><span class="sc">;</span>
|
|
|
718 705
|
|
|
719 706 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
720 707 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
721 708
|
|
|
722 709 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
723 710 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
724 711
|
|
|
725 712 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
726 713 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
727 714
|
|
|
728 715 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">DefaultPropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
729 716
|
|
|
730 717 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}} = <span class="q">qw(MolecularWeight ExactMass HeavyAtoms Rings AromaticRings MolecularVolume RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP SMR TPSA Fsp3Carbons Sp3Carbons MolecularComplexity)</span><span class="sc">;</span>
|
|
|
731 718
|
|
|
732 719 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}} = <span class="q">qw(MolecularWeight HydrogenBondDonors HydrogenBondAcceptors SLogP)</span><span class="sc">;</span>
|
|
|
733 720 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="q">'MolecularWeight'</span> <span class="cm">=></span> <span class="n">500</span><span class="cm">,</span> <span class="q">'HydrogenBondDonors'</span> <span class="cm">=></span> <span class="n">5</span><span class="cm">,</span> <span class="q">'HydrogenBondAcceptors'</span> <span class="cm">=></span> <span class="n">10</span><span class="cm">,</span> <span class="q">'SLogP'</span> <span class="cm">=></span> <span class="n">5</span><span class="s">)</span><span class="sc">;</span>
|
|
|
734 721
|
|
|
735 722 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}} = <span class="q">qw(MolecularWeight RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA)</span><span class="sc">;</span>
|
|
|
736 723 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="q">'MolecularWeight'</span> <span class="cm">=></span> <span class="n">300</span><span class="cm">,</span> <span class="q">'RotatableBonds'</span> <span class="cm">=></span> <span class="n">3</span><span class="cm">,</span> <span class="q">'HydrogenBondDonors'</span> <span class="cm">=></span> <span class="n">3</span><span class="cm">,</span> <span class="q">'HydrogenBondAcceptors'</span> <span class="cm">=></span> <span class="n">3</span><span class="cm">,</span> <span class="q">'SLogP'</span> <span class="cm">=></span> <span class="n">3</span><span class="cm">,</span> <span class="q">'TPSA'</span> <span class="cm">=></span> <span class="n">60</span><span class="s">)</span><span class="sc">;</span>
|
|
|
737 724
|
|
|
738 725 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">DefaultPropertyNames</span>}} = <span class="q">qw(MolecularWeight HeavyAtoms MolecularVolume RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA)</span><span class="sc">;</span>
|
|
|
739 726
|
|
|
740 727 <span class="k">for</span> <span class="i">$SupportedProperty</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
741 728 <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$SupportedProperty</span><span class="s">)</span>} = <span class="i">$SupportedProperty</span><span class="sc">;</span>
|
|
|
742 729 <span class="s">}</span>
|
|
|
743 730
|
|
|
744 731 <span class="c"># Process specified properties....</span>
|
|
|
745 732 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="cm">,</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">%SpecifiedPropertyNamesMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
746 733
|
|
|
747 734 <span class="i">@SpecifiedPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
748 735 <span class="i">%SpecifiedPropertyNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
749 736
|
|
|
750 737 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
751 738 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
752 739
|
|
|
753 740 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
754 741 <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}}<span class="sc">;</span>
|
|
|
755 742 <span class="s">}</span>
|
|
|
756 743 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf5$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
757 744 <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}}<span class="sc">;</span>
|
|
|
758 745 <span class="s">}</span>
|
|
|
759 746 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf3$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
760 747 <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}}<span class="sc">;</span>
|
|
|
761 748 <span class="s">}</span>
|
|
|
762 749 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
763 750 <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">DefaultPropertyNames</span>}}<span class="sc">;</span>
|
|
|
764 751 <span class="s">}</span>
|
|
|
765 752 <span class="k">else</span> <span class="s">{</span>
|
|
|
766 753 <span class="c"># Comma delimited lisr of specified property names...</span>
|
|
|
767 754 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">@UnsupportedPropertyNames</span><span class="s">)</span><span class="sc">;</span>
|
|
|
768 755
|
|
|
769 756 <span class="i">$Mode</span> = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
|
|
|
770 757 <span class="i">$Mode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
771 758
|
|
|
772 759 <span class="i">@PropertyNames</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$Mode</span><span class="sc">;</span>
|
|
|
773 760 <span class="i">@UnsupportedPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
774 761
|
|
|
775 762 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@PropertyNames</span><span class="s">)</span> <span class="s">{</span>
|
|
|
776 763 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
777 764 <span class="k">push</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span>
|
|
|
778 765 <span class="s">}</span>
|
|
|
779 766 <span class="k">else</span> <span class="s">{</span>
|
|
|
780 767 <span class="k">push</span> <span class="i">@UnsupportedPropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span>
|
|
|
781 768 <span class="s">}</span>
|
|
|
782 769 <span class="s">}</span>
|
|
|
783 770 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedPropertyNames</span><span class="s">)</span> <span class="s">{</span>
|
|
|
784 771 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedPropertyNames</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
785 772 <span class="k">warn</span> <span class="q">"Error: The physicochemical property names specified - "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@UnsupportedPropertyNames</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">" - for option \"-m --mode\" are not valid.\n"</span><span class="sc">;</span>
|
|
|
786 773 <span class="s">}</span>
|
|
|
787 774 <span class="k">else</span> <span class="s">{</span>
|
|
|
788 775 <span class="k">warn</span> <span class="q">"Error: The physicochemical property name specified, @UnsupportedPropertyNames , for option \"-m --mode\" is not valid.\n"</span><span class="sc">;</span>
|
|
|
789 776 <span class="s">}</span>
|
|
|
790 777 <span class="k">die</span> <span class="q">"Allowed values:"</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
791 778 <span class="s">}</span>
|
|
|
792 779 <span class="k">if</span> <span class="s">(</span>!<span class="i">@SpecifiedPropertyNames</span><span class="s">)</span> <span class="s">{</span>
|
|
|
793 780 <span class="k">die</span> <span class="q">"Error: No valid physicochemical property names specified for option \"-m --mode\".\n"</span><span class="sc">;</span>
|
|
|
794 781 <span class="s">}</span>
|
|
|
795 782 <span class="s">}</span>
|
|
|
796 783
|
|
|
797 784 <span class="c"># Set up specified property names map...</span>
|
|
|
798 785 <span class="j">PROPERTY:</span> <span class="k">for</span> <span class="i">$SpecifiedPropertyName</span> <span class="s">(</span><span class="i">@SpecifiedPropertyNames</span><span class="s">)</span> <span class="s">{</span>
|
|
|
799 786 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
800 787 <span class="k">warn</span> <span class="q">"Warning: The physicochemical property name, $SpecifiedPropertyName, is specified multiple times as value of option \"-m --mode\" .\n"</span><span class="sc">;</span>
|
|
|
801 788 <span class="k">next</span> <span class="j">PROPERTY</span><span class="sc">;</span>
|
|
|
802 789 <span class="s">}</span>
|
|
|
803 790 <span class="c"># Canonical specified property name...</span>
|
|
|
804 791 <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>} = <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
805 792 <span class="s">}</span>
|
|
|
806 793
|
|
|
807 794 <span class="c"># Make sure for calculation of RuleOf3Violations, all appropriate property names are specified...</span>
|
|
|
808 795 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} =~ <span class="q">/^Yes$/i</span> && <span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf5$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
809 796 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ruleof3violations}, for \"--RuleOf3Violations\" option in \"RuleOf5\" \"-m --Mode\" is not valid. You must specify RuleOf3 value for \"-m --Mode\" to calculate RuleOf3 violations.\n"</span><span class="sc">;</span>
|
|
|
810 797 <span class="s">}</span>
|
|
|
811 798
|
|
|
812 799 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
813 800 <span class="k">my</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="cm">,</span> <span class="i">@MissingRuleOf3Names</span><span class="s">)</span><span class="sc">;</span>
|
|
|
814 801
|
|
|
815 802 <span class="i">@MissingRuleOf3Names</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
816 803 <span class="j">PROPERTY:</span> <span class="k">for</span> <span class="i">$RuleOf3PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
817 804 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
818 805 <span class="k">next</span> <span class="j">PROPERTY</span><span class="sc">;</span>
|
|
|
819 806 <span class="s">}</span>
|
|
|
820 807 <span class="k">push</span> <span class="i">@MissingRuleOf3Names</span><span class="cm">,</span> <span class="i">$RuleOf3PropertyName</span><span class="sc">;</span>
|
|
|
821 808
|
|
|
822 809 <span class="c"># Add property name to specified properties names list and map...</span>
|
|
|
823 810 <span class="k">push</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">$RuleOf3PropertyName</span><span class="sc">;</span>
|
|
|
824 811 <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="s">)</span>} = <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
825 812 <span class="s">}</span>
|
|
|
826 813 <span class="k">if</span> <span class="s">(</span><span class="i">@MissingRuleOf3Names</span><span class="s">)</span> <span class="s">{</span>
|
|
|
827 814 <span class="k">warn</span> <span class="q">"Warning: The following physicochemical property names not specified in \"-m --Mode\" option are required for calculating RuleOf3Violations and have been added to the list of property names: @MissingRuleOf3Names\n"</span><span class="sc">;</span>
|
|
|
828 815 <span class="s">}</span>
|
|
|
829 816 <span class="s">}</span>
|
|
|
830 817
|
|
|
831 818 <span class="c"># Make sure for calculation of RuleOf5Violations, all appropriate property names are specified...</span>
|
|
|
832 819 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} =~ <span class="q">/^Yes$/i</span> && <span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf3$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
833 820 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ruleof5violations}, for \"--RuleOf5Violations\" option in \"RuleOf3\" \"-m --Mode\" is not valid. You must specify RuleOf5 value for \"-m --Mode\" to calculate RuleOf5 violations.\n"</span><span class="sc">;</span>
|
|
|
834 821 <span class="s">}</span>
|
|
|
835 822
|
|
|
836 823 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
837 824 <span class="k">my</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="cm">,</span> <span class="i">@MissingRuleOf5Names</span><span class="s">)</span><span class="sc">;</span>
|
|
|
838 825
|
|
|
839 826 <span class="i">@MissingRuleOf5Names</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
840 827 <span class="j">PROPERTY:</span> <span class="k">for</span> <span class="i">$RuleOf5PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
841 828 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
842 829 <span class="k">next</span> <span class="j">PROPERTY</span><span class="sc">;</span>
|
|
|
843 830 <span class="s">}</span>
|
|
|
844 831 <span class="k">push</span> <span class="i">@MissingRuleOf5Names</span><span class="cm">,</span> <span class="i">$RuleOf5PropertyName</span><span class="sc">;</span>
|
|
|
845 832
|
|
|
846 833 <span class="c"># Add property name to specified properties names list and map...</span>
|
|
|
847 834 <span class="k">push</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">$RuleOf5PropertyName</span><span class="sc">;</span>
|
|
|
848 835 <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="s">)</span>} = <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
849 836 <span class="s">}</span>
|
|
|
850 837 <span class="k">if</span> <span class="s">(</span><span class="i">@MissingRuleOf5Names</span><span class="s">)</span> <span class="s">{</span>
|
|
|
851 838 <span class="k">warn</span> <span class="q">"Warning: The following physicochemical property names not specified in \"-m --Mode\" option are required for calculating RuleOf5Violations and have been added to the list of property names: @MissingRuleOf5Names\n"</span><span class="sc">;</span>
|
|
|
852 839 <span class="s">}</span>
|
|
|
853 840 <span class="s">}</span>
|
|
|
854 841 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
|
|
|
855 842
|
|
|
856 843 <span class="c"># Setup canonical specified property names corresponding to supported names in mixed case...</span>
|
|
|
857 844 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedCanonicalPropertyNames</span><span class="s">)</span><span class="sc">;</span>
|
|
|
858 845
|
|
|
859 846 <span class="i">@SpecifiedCanonicalPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
860 847 <span class="k">for</span> <span class="i">$SpecifiedPropertyName</span> <span class="s">(</span><span class="i">@SpecifiedPropertyNames</span><span class="s">)</span> <span class="s">{</span>
|
|
|
861 848 <span class="k">push</span> <span class="i">@SpecifiedCanonicalPropertyNames</span><span class="cm">,</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
862 849 <span class="s">}</span>
|
|
|
863 850 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}} = <span class="i">@SpecifiedCanonicalPropertyNames</span><span class="sc">;</span>
|
|
|
864 851 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}} = <span class="i">%SpecifiedPropertyNamesMap</span><span class="sc">;</span>
|
|
|
865 852
|
|
|
866 853 <span class="c"># Based on specified property names, figure out whether hydrogens need to be added before</span>
|
|
|
867 854 <span class="c"># calculation of properties...</span>
|
|
|
868 855 <span class="c">#</span>
|
|
|
869 856 <span class="i">$OptionsInfo</span>{<span class="w">AddHydrogens</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
870 857 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="q">'MolecularVolume'</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="q">'SLogP'</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="q">'SMR'</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
871 858 <span class="i">$OptionsInfo</span>{<span class="w">AddHydrogens</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
872 859 <span class="s">}</span>
|
|
|
873 860 <span class="s">}</span>
|
|
|
874 861
|
|
|
875 862 <span class="c"># Process precision option...</span>
|
|
|
876 863 <span class="c">#</span>
|
|
|
877 <a name="ProcessPrecisionOption-"></a> 864 <span class="k">sub </span><span class="m">ProcessPrecisionOption</span> <span class="s">{</span>
|
|
|
878 865 <span class="k">my</span><span class="s">(</span><span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">%PrecisionParametersMap</span><span class="cm">,</span> <span class="i">%PrecisionParameterNamesMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
879 866
|
|
|
880 867 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">PrecisionParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
881 868
|
|
|
882 869 <span class="i">%PrecisionParametersMap</span> = <span class="s">(</span><span class="q">'WeightPrecision'</span> <span class="cm">=></span> <span class="n">2</span><span class="cm">,</span> <span class="q">'MassPrecision'</span> <span class="cm">=></span> <span class="n">4</span><span class="s">)</span><span class="sc">;</span>
|
|
|
883 870 <span class="i">%PrecisionParameterNamesMap</span> = <span class="s">(</span><span class="q">'molecularweight'</span> <span class="cm">=></span> <span class="q">'WeightPrecision'</span><span class="cm">,</span> <span class="q">'exactmass'</span> <span class="cm">=></span> <span class="q">'MassPrecision'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
884 871
|
|
|
885 872 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
886 873 <span class="c"># Process specified values...</span>
|
|
|
887 874 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedPrecision</span><span class="cm">,</span> <span class="i">@SpecifiedPrecisionValuePairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
888 875
|
|
|
889 876 <span class="i">$SpecifiedPrecision</span> = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
|
|
|
890 877 <span class="i">$SpecifiedPrecision</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
891 878 <span class="i">@SpecifiedPrecisionValuePairs</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$SpecifiedPrecision</span><span class="sc">;</span>
|
|
|
892 879 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedPrecisionValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
893 880 <span class="k">die</span> <span class="q">"Error: Invalid number of values specified using \"--Precision\" option: It must contain even number of values.\n"</span><span class="sc">;</span>
|
|
|
894 881 <span class="s">}</span>
|
|
|
895 882 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> < <span class="i">@SpecifiedPrecisionValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
896 883 <span class="i">$ParameterName</span> = <span class="i">$SpecifiedPrecisionValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
897 884 <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedPrecisionValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
898 885 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$PrecisionParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
899 886 <span class="k">die</span> <span class="q">"Error: The precision parameter name specified, $ParameterName, for option \"--Precision\" is not valid.\n"</span><span class="sc">;</span>
|
|
|
900 887 <span class="s">}</span>
|
|
|
901 888 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
902 889 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--Precision\" is not valid. Allowed values: positive integer. \n"</span><span class="sc">;</span>
|
|
|
903 890 <span class="s">}</span>
|
|
|
904 891 <span class="i">$ParameterName</span> = <span class="i">$PrecisionParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
905 892 <span class="i">$PrecisionParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span>
|
|
|
906 893 <span class="s">}</span>
|
|
|
907 894 <span class="s">}</span>
|
|
|
908 895 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
|
|
|
909 896 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">PrecisionParametersMap</span>}} = <span class="i">%PrecisionParametersMap</span><span class="sc">;</span>
|
|
|
910 897 <span class="s">}</span>
|
|
|
911 898
|
|
|
912 899 <span class="c"># Process rotatable bonds option...</span>
|
|
|
913 <a name="ProcessRotatableBondsOption-"></a> 900 <span class="k">sub </span><span class="m">ProcessRotatableBondsOption</span> <span class="s">{</span>
|
|
|
914 901 <span class="k">my</span><span class="s">(</span><span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">%RotatableBondsParametersMap</span><span class="cm">,</span> <span class="i">%RotatableBondsParameterNamesMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
915 902
|
|
|
916 903 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RotatableBondsParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
917 904 <span class="i">%RotatableBondsParametersMap</span> = <span class="s">(</span><span class="q">'IgnoreTerminalBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'IgnoreBondsToTripleBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'IgnoreAmideBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'IgnoreThioamideBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'IgnoreSulfonamideBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
918 905
|
|
|
919 906 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%RotatableBondsParametersMap</span><span class="s">)</span> <span class="s">{</span>
|
|
|
920 907 <span class="i">$RotatableBondsParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>} = <span class="i">$ParameterName</span><span class="sc">;</span>
|
|
|
921 908 <span class="s">}</span>
|
|
|
922 909
|
|
|
923 910 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">rotatablebonds</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
924 911 <span class="c"># Process specified values...</span>
|
|
|
925 912 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedRotatableBonds</span><span class="cm">,</span> <span class="i">@SpecifiedRotatableBondsValuePairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
926 913
|
|
|
927 914 <span class="i">$SpecifiedRotatableBonds</span> = <span class="i">$Options</span>{<span class="w">rotatablebonds</span>}<span class="sc">;</span>
|
|
|
928 915 <span class="i">$SpecifiedRotatableBonds</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
929 916 <span class="i">@SpecifiedRotatableBondsValuePairs</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$SpecifiedRotatableBonds</span><span class="sc">;</span>
|
|
|
930 917 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedRotatableBondsValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
931 918 <span class="k">die</span> <span class="q">"Error: Invalid number of values specified using \"--RotatableBonds\" option: It must contain even number of values.\n"</span><span class="sc">;</span>
|
|
|
932 919 <span class="s">}</span>
|
|
|
933 920 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> < <span class="i">@SpecifiedRotatableBondsValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
934 921 <span class="i">$ParameterName</span> = <span class="i">$SpecifiedRotatableBondsValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
935 922 <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedRotatableBondsValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
936 923 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$RotatableBondsParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
937 924 <span class="k">die</span> <span class="q">"Error: The rotatable bonds parameter name specified, $ParameterName, for option \"--RotatableBonds\" is not valid.\n"</span><span class="sc">;</span>
|
|
|
938 925 <span class="s">}</span>
|
|
|
939 926 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
940 927 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--RotatableBonds\" is not valid. Allowed values: Yes or No. \n"</span><span class="sc">;</span>
|
|
|
941 928 <span class="s">}</span>
|
|
|
942 929 <span class="i">$ParameterName</span> = <span class="i">$RotatableBondsParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
943 930 <span class="i">$ParameterValue</span> = <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
944 931 <span class="i">$RotatableBondsParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span>
|
|
|
945 932 <span class="s">}</span>
|
|
|
946 933 <span class="s">}</span>
|
|
|
947 934 <span class="i">$OptionsInfo</span>{<span class="w">RotatableBonds</span>} = <span class="i">$Options</span>{<span class="w">rotatablebonds</span>}<span class="sc">;</span>
|
|
|
948 935 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RotatableBondsParametersMap</span>}} = <span class="i">%RotatableBondsParametersMap</span><span class="sc">;</span>
|
|
|
949 936 <span class="s">}</span>
|
|
|
950 937
|
|
|
951 938 <span class="c"># Process TPSA option...</span>
|
|
|
952 939 <span class="c">#</span>
|
|
|
953 <a name="ProcessTPSAOption-"></a> 940 <span class="k">sub </span><span class="m">ProcessTPSAOption</span> <span class="s">{</span>
|
|
|
954 941 <span class="k">my</span><span class="s">(</span><span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">%TPSAParametersMap</span><span class="cm">,</span> <span class="i">%TPSAParameterNamesMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
955 942
|
|
|
956 943 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">TPSAParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
957 944
|
|
|
958 945 <span class="i">%TPSAParametersMap</span> = <span class="s">(</span><span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
959 946 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%TPSAParametersMap</span><span class="s">)</span> <span class="s">{</span>
|
|
|
960 947 <span class="i">$TPSAParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>} = <span class="i">$ParameterName</span><span class="sc">;</span>
|
|
|
961 948 <span class="s">}</span>
|
|
|
962 949
|
|
|
963 950 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">tpsa</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
964 951 <span class="c"># Process specified values...</span>
|
|
|
965 952 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedTPSA</span><span class="cm">,</span> <span class="i">@SpecifiedTPSAValuePairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
966 953
|
|
|
967 954 <span class="i">$SpecifiedTPSA</span> = <span class="i">$Options</span>{<span class="w">tpsa</span>}<span class="sc">;</span>
|
|
|
968 955 <span class="i">$SpecifiedTPSA</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
969 956 <span class="i">@SpecifiedTPSAValuePairs</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$SpecifiedTPSA</span><span class="sc">;</span>
|
|
|
970 957 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedTPSAValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
971 958 <span class="k">die</span> <span class="q">"Error: Invalid number of values specified using \"--TPSA\" option: It must contain even number of values.\n"</span><span class="sc">;</span>
|
|
|
972 959 <span class="s">}</span>
|
|
|
973 960 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> < <span class="i">@SpecifiedTPSAValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
974 961 <span class="i">$ParameterName</span> = <span class="i">$SpecifiedTPSAValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
975 962 <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedTPSAValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
976 963 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$TPSAParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
977 964 <span class="k">die</span> <span class="q">"Error: The TPSA parameter name specified, $ParameterName, for option \"--TPSA\" is not valid.\n"</span><span class="sc">;</span>
|
|
|
978 965 <span class="s">}</span>
|
|
|
979 966 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
980 967 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--TPSA\" is not valid. Allowed values: Yes or No. \n"</span><span class="sc">;</span>
|
|
|
981 968 <span class="s">}</span>
|
|
|
982 969 <span class="i">$ParameterName</span> = <span class="i">$TPSAParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
983 970 <span class="i">$ParameterValue</span> = <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
984 971 <span class="i">$TPSAParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span>
|
|
|
985 972 <span class="s">}</span>
|
|
|
986 973 <span class="s">}</span>
|
|
|
987 974 <span class="i">$OptionsInfo</span>{<span class="w">TPSA</span>} = <span class="i">$Options</span>{<span class="w">tpsa</span>}<span class="sc">;</span>
|
|
|
988 975 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">TPSAParametersMap</span>}} = <span class="i">%TPSAParametersMap</span><span class="sc">;</span>
|
|
|
989 976 <span class="s">}</span>
|
|
|
990 977
|
|
|
991 978 <span class="c"># Process molecular complexity parameters...</span>
|
|
|
992 979 <span class="c">#</span>
|
|
|
993 <a name="ProcessMolecularComplexityOption-"></a> 980 <span class="k">sub </span><span class="m">ProcessMolecularComplexityOption</span> <span class="s">{</span>
|
|
|
994 981 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularComplexityType</span><span class="cm">,</span> <span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@ParameterValues</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="i">%ComplexityParametersMap</span><span class="cm">,</span> <span class="i">%ComplexityParameterNamesMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
995 982
|
|
|
996 983 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
997 984
|
|
|
998 985 <span class="i">%ComplexityParametersMap</span> = <span class="s">(</span><span class="q">'MolecularComplexityType'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span>
|
|
|
999 986 <span class="q">'AtomicInvariantsToUse'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span>
|
|
|
1000 987 <span class="q">'MACCSKeysSize'</span> <span class="cm">=></span> <span class="q">'166'</span><span class="cm">,</span> <span class="q">'NeighborhoodRadius'</span> <span class="cm">=></span> <span class="q">'2'</span><span class="cm">,</span>
|
|
|
1001 988 <span class="q">'MinPathLength'</span> <span class="cm">=></span> <span class="q">'1'</span><span class="cm">,</span> <span class="q">'MaxPathLength'</span> <span class="cm">=></span> <span class="q">'8'</span><span class="cm">,</span> <span class="q">'UseBondSymbols'</span> <span class="cm">=></span> <span class="q">'1'</span><span class="cm">,</span>
|
|
|
1002 989 <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="q">'1'</span><span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="q">'10'</span><span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span>
|
|
|
1003 990 <span class="q">'DistanceBinSize'</span> <span class="cm">=></span> <span class="q">'2'</span><span class="cm">,</span> <span class="q">'NormalizationMethodology'</span> <span class="cm">=></span> <span class="q">'None'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1004 991
|
|
|
1005 992 <span class="i">%ComplexityParameterNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1006 993 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%ComplexityParametersMap</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1007 994 <span class="i">$ComplexityParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>} = <span class="i">$ParameterName</span><span class="sc">;</span>
|
|
|
1008 995 <span class="s">}</span>
|
|
|
1009 996
|
|
|
1010 997 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">molecularcomplexity</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1011 998 <span class="c"># Process specified values...</span>
|
|
|
1012 999 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedComplexity</span><span class="cm">,</span> <span class="i">@SpecifiedComplexityValuePairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1013 1000
|
|
|
1014 1001 <span class="i">$SpecifiedComplexity</span> = <span class="i">$Options</span>{<span class="w">molecularcomplexity</span>}<span class="sc">;</span>
|
|
|
1015 1002
|
|
|
1016 1003 <span class="i">@SpecifiedComplexityValuePairs</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$SpecifiedComplexity</span><span class="sc">;</span>
|
|
|
1017 1004 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedComplexityValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1018 1005 <span class="k">die</span> <span class="q">"Error: Invalid number of values specified using \"--MolecularComplexity\" option: It must contain even number of values.\n"</span><span class="sc">;</span>
|
|
|
1019 1006 <span class="s">}</span>
|
|
|
1020 1007
|
|
|
1021 1008 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> < <span class="i">@SpecifiedComplexityValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
1022 1009 <span class="i">$ParameterName</span> = <span class="i">$SpecifiedComplexityValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1023 1010 <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedComplexityValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
1024 1011
|
|
|
1025 1012 <span class="i">$ParameterName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1026 1013 <span class="i">$ParameterValue</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1027 1014
|
|
|
1028 1015 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ComplexityParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1029 1016 <span class="k">die</span> <span class="q">"Error: The molecular complexity parameter name specified, $ParameterName, for option \"--MolecularComplexity\" is not valid.\n"</span><span class="sc">;</span>
|
|
|
1030 1017 <span class="s">}</span>
|
|
|
1031 1018 <span class="i">$ParameterName</span> = <span class="i">$ComplexityParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
1032 1019
|
|
|
1033 1020 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^AtomicInvariantsToUse$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1034 1021 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbolFound</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1035 1022
|
|
|
1036 1023 <span class="i">$AtomSymbolFound</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1037 1024 <span class="i">@ParameterValues</span> = <span class="k">split</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1038 1025 <span class="k">for</span> <span class="i">$ParameterValue</span> <span class="s">(</span><span class="i">@ParameterValues</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1039 1026 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1040 1027 <span class="k">die</span> <span class="q">"Error: The atomic invariant specified, $ParameterValue, for AtomicInvariantsToUse in option \"--MolecularComplexity\" is not valid.\n"</span><span class="sc">;</span>
|
|
|
1041 1028 <span class="s">}</span>
|
|
|
1042 1029 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^(AS|AtomSymbol)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1043 1030 <span class="i">$AtomSymbolFound</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
1044 1031 <span class="s">}</span>
|
|
|
1045 1032 <span class="s">}</span>
|
|
|
1046 1033 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSymbolFound</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1047 1034 <span class="k">die</span> <span class="q">"Error: The atomic invariants specified using AtomicInvariantsToUse in option \"--MolecularComplexity\" is not valid: AtomicInvariant atom symbol, AS or AtomSymbol, must be specified.\n"</span><span class="sc">;</span>
|
|
|
1048 1035 <span class="s">}</span>
|
|
|
1049 1036 <span class="i">$ParameterValue</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ParameterValues</span><span class="cm">,</span> <span class="q">","</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1050 1037 <span class="s">}</span>
|
|
|
1051 1038 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^FunctionalClassesToUse$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1052 1039 <span class="i">@ParameterValues</span> = <span class="k">split</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1053 1040 <span class="k">for</span> <span class="i">$ParameterValue</span> <span class="s">(</span><span class="i">@ParameterValues</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1054 1041 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1055 1042 <span class="k">die</span> <span class="q">"Error: The functional class specified, $ParameterValue, for FunctionalClassesToUse in option \"--MolecularComplexity\" is not valid.\n"</span><span class="sc">;</span>
|
|
|
1056 1043 <span class="s">}</span>
|
|
|
1057 1044 <span class="s">}</span>
|
|
|
1058 1045 <span class="i">$ParameterValue</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ParameterValues</span><span class="cm">,</span> <span class="q">","</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1059 1046 <span class="s">}</span>
|
|
|
1060 1047 <span class="k">else</span> <span class="s">{</span>
|
|
|
1061 1048 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/ /</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1062 1049 <span class="i">$ParameterValue</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
1063 1050 <span class="s">}</span>
|
|
|
1064 1051 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1065 1052 <span class="i">$ParameterValue</span> = <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1066 1053 <span class="s">}</span>
|
|
|
1067 1054 <span class="s">}</span>
|
|
|
1068 1055
|
|
|
1069 1056 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^MolecularComplexityType$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1070 1057 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|MACCSKeys|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1071 1058 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: AtomTypesFingerprints, ExtendedConnectivityFingerprints, MACCSKeys, PathLengthFingerprints, TopologicalAtomPairsFingerprints, TopologicalAtomTripletsFingerprints, TopologicalAtomTorsionsFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints..\n"</span><span class="sc">;</span>
|
|
|
1072 1059 <span class="s">}</span>
|
|
|
1073 1060 <span class="s">}</span>
|
|
|
1074 1061 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^AtomIdentifierType$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1075 1062 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1076 1063 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes.\n"</span><span class="sc">;</span>
|
|
|
1077 1064 <span class="s">}</span>
|
|
|
1078 1065 <span class="s">}</span>
|
|
|
1079 1066 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^(MACCSKeysSize|MinPathLength|MaxPathLength|MinDistance|MaxDistance|DistanceBinSize)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1080 1067 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1081 1068 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: positive integer. \n"</span><span class="sc">;</span>
|
|
|
1082 1069 <span class="s">}</span>
|
|
|
1083 1070 <span class="s">}</span>
|
|
|
1084 1071 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^NeighborhoodRadius$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1085 1072 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsInteger</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span> && <span class="i">$ParameterValue</span> >=<span class="n">0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1086 1073 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: 0 or positive integer. \n"</span><span class="sc">;</span>
|
|
|
1087 1074 <span class="s">}</span>
|
|
|
1088 1075 <span class="s">}</span>
|
|
|
1089 1076 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^NormalizationMethodology$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1090 1077 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(None|ByHeavyAtomsCount|ByPossibleKeysCount)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1091 1078 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: None, ByHeavyAtomsCount, or ByPossibleKeysCount\n"</span><span class="sc">;</span>
|
|
|
1092 1079 <span class="s">}</span>
|
|
|
1093 1080 <span class="s">}</span>
|
|
|
1094 1081 <span class="i">$ComplexityParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span>
|
|
|
1095 1082 <span class="s">}</span>
|
|
|
1096 1083
|
|
|
1097 1084 <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MACCSKeysSize</span>} !~ <span class="q">/^(166|322)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1098 1085 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ComplexityParametersMap{MACCSKeysSize}, for parameter name, MACCSKeysSize in option \"--MolecularComplexity\" is not valid. Allowed values: 166 or 322\n"</span><span class="sc">;</span>
|
|
|
1099 1086 <span class="s">}</span>
|
|
|
1100 1087 <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MinPathLength</span>} > <span class="i">$ComplexityParametersMap</span>{<span class="w">MaxPathLength</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1101 1088 <span class="k">die</span> <span class="q">"Error: The parameter value specified for MinPathLength, $ComplexityParametersMap{MinPathLength}, must be <= MaxPathLength, $ComplexityParametersMap{MaxPathLength} ...\n"</span><span class="sc">;</span>
|
|
|
1102 1089 <span class="s">}</span>
|
|
|
1103 1090 <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MinDistance</span>} > <span class="i">$ComplexityParametersMap</span>{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1104 1091 <span class="k">die</span> <span class="q">"Error: The parameter value specified for MinDistance, $ComplexityParametersMap{MinDistance}, must be <= MaxDistance, $ComplexityParametersMap{MaxDistance} ...\n"</span><span class="sc">;</span>
|
|
|
1105 1092 <span class="s">}</span>
|
|
|
1106 1093 <span class="s">}</span>
|
|
|
1107 1094
|
|
|
1108 1095 <span class="c"># Set default parameter values...</span>
|
|
|
1109 1096
|
|
|
1110 1097 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MolecularComplexityType</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1111 1098 <span class="i">$ComplexityParametersMap</span>{<span class="w">MolecularComplexityType</span>} = <span class="q">'MACCSKeys'</span><span class="sc">;</span>
|
|
|
1112 1099 <span class="s">}</span>
|
|
|
1113 1100 <span class="i">$MolecularComplexityType</span> = <span class="i">$ComplexityParametersMap</span>{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span>
|
|
|
1114 1101
|
|
|
1115 1102
|
|
|
1116 1103 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1117 1104 <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} = <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> ? <span class="q">"FunctionalClassAtomTypes"</span> <span class="co">:</span> <span class="q">"AtomicInvariantsAtomTypes"</span><span class="sc">;</span>
|
|
|
1118 1105 <span class="s">}</span>
|
|
|
1119 1106
|
|
|
1120 1107 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1121 1108 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1122 1109
|
|
|
1123 1110 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^(AtomTypesFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1124 1111 <span class="i">$AtomicInvariantsToUse</span> = <span class="q">"AS,X,BO,H,FC"</span><span class="sc">;</span>
|
|
|
1125 1112 <span class="s">}</span>
|
|
|
1126 1113 <span class="k">elsif</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1127 1114 <span class="i">$AtomicInvariantsToUse</span> = <span class="q">"AS,X,BO,H,FC,MN"</span><span class="sc">;</span>
|
|
|
1128 1115 <span class="s">}</span>
|
|
|
1129 1116 <span class="k">else</span> <span class="s">{</span>
|
|
|
1130 1117 <span class="i">$AtomicInvariantsToUse</span> = <span class="q">"AS"</span><span class="sc">;</span>
|
|
|
1131 1118 <span class="s">}</span>
|
|
|
1132 1119 <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>} = <span class="i">$AtomicInvariantsToUse</span><span class="sc">;</span>
|
|
|
1133 1120 <span class="s">}</span>
|
|
|
1134 1121
|
|
|
1135 1122 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1136 1123 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1137 1124
|
|
|
1138 1125 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1139 1126 <span class="i">$FunctionalClassesToUse</span> = <span class="q">"HBD,HBA,PI,NI,H"</span><span class="sc">;</span>
|
|
|
1140 1127 <span class="s">}</span>
|
|
|
1141 1128 <span class="k">elsif</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1142 1129 <span class="i">$FunctionalClassesToUse</span> = <span class="q">"HBD,HBA,PI,NI,H,Ar"</span><span class="sc">;</span>
|
|
|
1143 1130 <span class="s">}</span>
|
|
|
1144 1131 <span class="k">else</span> <span class="s">{</span>
|
|
|
1145 1132 <span class="i">$FunctionalClassesToUse</span> = <span class="q">"HBD,HBA,PI,NI,H,Ar,Hal"</span><span class="sc">;</span>
|
|
|
1146 1133 <span class="s">}</span>
|
|
|
1147 1134 <span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>} = <span class="i">$FunctionalClassesToUse</span><span class="sc">;</span>
|
|
|
1148 1135 <span class="s">}</span>
|
|
|
1149 1136
|
|
|
1150 1137 <span class="k">my</span><span class="s">(</span><span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1151 1138 <span class="i">@AtomicInvariantsToUse</span> = <span class="k">split</span> <span class="q">','</span><span class="cm">,</span> <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>}<span class="sc">;</span>
|
|
|
1152 1139 <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>} = \<span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span>
|
|
|
1153 1140
|
|
|
1154 1141 <span class="k">my</span><span class="s">(</span><span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1155 1142 <span class="i">@FunctionalClassesToUse</span> = <span class="k">split</span> <span class="q">','</span><span class="cm">,</span> <span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>}<span class="sc">;</span>
|
|
|
1156 1143 <span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>} = \<span class="i">@FunctionalClassesToUse</span><span class="sc">;</span>
|
|
|
1157 1144
|
|
|
1158 1145 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">UseTriangleInequality</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1159 1146 <span class="i">$ComplexityParametersMap</span>{<span class="w">UseTriangleInequality</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
1160 1147 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1161 1148 <span class="i">$ComplexityParametersMap</span>{<span class="w">UseTriangleInequality</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1162 1149 <span class="s">}</span>
|
|
|
1163 1150 <span class="s">}</span>
|
|
|
1164 1151
|
|
|
1165 1152 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1166 1153 <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1167 1154 <span class="k">die</span> <span class="q">"Error: The parameter value specified for AtomIdentifierType, $ComplexityParametersMap{AtomIdentifierType}, in option \"--MolecularComplexity\" is not valid for MolecularComplexityType, $MolecularComplexityType: Allowed value: FunctionalClassAtomTypes...\n"</span><span class="sc">;</span>
|
|
|
1168 1155 <span class="s">}</span>
|
|
|
1169 1156 <span class="s">}</span>
|
|
|
1170 1157
|
|
|
1171 1158 <span class="c"># Set up approprate paremeter names for specified molecular complexity...</span>
|
|
|
1172 1159
|
|
|
1173 1160 <span class="i">@ParameterNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1174 1161 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="q">'MolecularComplexityType'</span><span class="sc">;</span>
|
|
|
1175 1162
|
|
|
1176 1163 <span class="i">@AtomIdentifierTypeParameters</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1177 1164 <span class="k">push</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span><span class="sc">;</span>
|
|
|
1178 1165 <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1179 1166 <span class="k">push</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="q">'AtomicInvariantsToUse'</span><span class="sc">;</span>
|
|
|
1180 1167 <span class="s">}</span>
|
|
|
1181 1168 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1182 1169 <span class="k">push</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span><span class="sc">;</span>
|
|
|
1183 1170 <span class="s">}</span>
|
|
|
1184 1171
|
|
|
1185 1172 <span class="j">COMPLEXITYTYPE:</span> <span class="s">{</span>
|
|
|
1186 1173 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^AtomTypesFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1187 1174 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
|
|
|
1188 1175 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
|
|
|
1189 1176 <span class="s">}</span>
|
|
|
1190 1177 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1191 1178 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
|
|
|
1192 1179 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'NeighborhoodRadius'</span><span class="cm">,</span> <span class="q">'NormalizationMethodology'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1193 1180 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
|
|
|
1194 1181 <span class="s">}</span>
|
|
|
1195 1182 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1196 1183 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="q">'MACCSKeysSize'</span><span class="sc">;</span>
|
|
|
1197 1184 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
|
|
|
1198 1185 <span class="s">}</span>
|
|
|
1199 1186 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1200 1187 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
|
|
|
1201 1188 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'MinPathLength'</span><span class="cm">,</span> <span class="q">'MaxPathLength'</span><span class="cm">,</span> <span class="q">'UseBondSymbols'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1202 1189 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
|
|
|
1203 1190 <span class="s">}</span>
|
|
|
1204 1191 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1205 1192 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
|
|
|
1206 1193 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'MinDistance'</span><span class="cm">,</span> <span class="q">'MaxDistance'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1207 1194 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
|
|
|
1208 1195 <span class="s">}</span>
|
|
|
1209 1196 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1210 1197 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
|
|
|
1211 1198 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'MinDistance'</span><span class="cm">,</span> <span class="q">'MaxDistance'</span><span class="cm">,</span> <span class="q">'UseTriangleInequality'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1212 1199 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
|
|
|
1213 1200 <span class="s">}</span>
|
|
|
1214 1201 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalAtomTorsionsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1215 1202 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span>
|
|
|
1216 1203 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
|
|
|
1217 1204 <span class="s">}</span>
|
|
|
1218 1205 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1219 1206 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'AtomIdentifierType'</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span><span class="cm">,</span> <span class="q">'MinDistance'</span><span class="cm">,</span> <span class="q">'MaxDistance'</span><span class="cm">,</span> <span class="q">'NormalizationMethodology'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1220 1207 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
|
|
|
1221 1208 <span class="s">}</span>
|
|
|
1222 1209 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1223 1210 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'AtomIdentifierType'</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span><span class="cm">,</span> <span class="q">'MinDistance'</span><span class="cm">,</span> <span class="q">'MaxDistance'</span><span class="cm">,</span> <span class="q">'UseTriangleInequality'</span><span class="cm">,</span> <span class="q">'NormalizationMethodology'</span><span class="cm">,</span> <span class="q">'DistanceBinSize'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1224 1211 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span>
|
|
|
1225 1212 <span class="s">}</span>
|
|
|
1226 1213 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name MolecularComplexityType using \"--MolecularComplexity\" is not valid.\n"</span><span class="sc">;</span>
|
|
|
1227 1214 <span class="s">}</span>
|
|
|
1228 1215
|
|
|
1229 1216 <span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexity</span>} = <span class="i">$Options</span>{<span class="w">molecularcomplexity</span>}<span class="sc">;</span>
|
|
|
1230 1217
|
|
|
1231 1218 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1232 1219 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="i">@ParameterNames</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1233 1220 <span class="i">$ParameterValue</span> = <span class="i">$ComplexityParametersMap</span>{<span class="i">$ParameterName</span>}<span class="sc">;</span>
|
|
|
1234 1221 <span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span>
|
|
|
1235 1222 <span class="s">}</span>
|
|
|
1236 1223 <span class="s">}</span>
|
|
|
1237 1224
|
|
|
1238 1225 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
|
|
|
1239 <a name="SetupScriptUsage-"></a>1226 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
|
|
|
1240 1227
|
|
|
1241 1228 <span class="c"># Retrieve all the options...</span>
|
|
|
1242 1229 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1243 1230
|
|
|
1244 1231 <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span>
|
|
|
1245 1232
|
|
|
1246 1233 <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span>
|
|
|
1247 1234 <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span>
|
|
|
1248 1235 <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span>
|
|
|
1249 1236
|
|
|
1250 1237 <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">'Yes'</span><span class="sc">;</span>
|
|
|
1251 1238
|
|
|
1252 1239 <span class="i">$Options</span>{<span class="w">hydrogenbonds</span>} = <span class="q">'HBondsType2'</span><span class="sc">;</span>
|
|
|
1253 1240
|
|
|
1254 1241 <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">'Yes'</span><span class="sc">;</span>
|
|
|
1255 1242
|
|
|
1256 1243 <span class="c"># Default mode values are set later...</span>
|
|
|
1257 1244 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
1258 1245
|
|
|
1259 1246 <span class="c"># Default moelcular complexity values are set later...</span>
|
|
|
1260 1247 <span class="i">$Options</span>{<span class="w">molecularcomplexity</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
1261 1248
|
|
|
1262 1249 <span class="c"># Default precision values are set later...</span>
|
|
|
1263 1250 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
1264 1251
|
|
|
1265 1252 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">'text'</span><span class="sc">;</span>
|
|
|
1266 1253 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span>
|
|
|
1267 1254 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span>
|
|
|
1268 1255
|
|
|
1269 1256 <span class="c"># Default rotatable bond parameter values are set later...</span>
|
|
|
1270 1257 <span class="i">$Options</span>{<span class="w">rotatablebonds</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
1271 1258
|
|
|
1272 1259 <span class="i">$Options</span>{<span class="w">ruleof3violations</span>} = <span class="q">'No'</span><span class="sc">;</span>
|
|
|
1273 1260 <span class="i">$Options</span>{<span class="w">ruleof5violations</span>} = <span class="q">'No'</span><span class="sc">;</span>
|
|
|
1274 1261
|
|
|
1275 1262 <span class="c"># Default TPSA paramater values are set later...</span>
|
|
|
1276 1263 <span class="i">$Options</span>{<span class="w">tpsa</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
1277 1264
|
|
|
1278 1265 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"aromaticitymodel=s"</span><span class="cm">,</span> <span class="q">"compoundid=s"</span><span class="cm">,</span> <span class="q">"compoundidlabel=s"</span><span class="cm">,</span> <span class="q">"compoundidmode=s"</span><span class="cm">,</span> <span class="q">"datafields=s"</span><span class="cm">,</span> <span class="q">"datafieldsmode|d=s"</span><span class="cm">,</span> <span class="q">"filter|f=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"hydrogenbonds=s"</span><span class="cm">,</span> <span class="q">"keeplargestcomponent|k=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"molecularcomplexity=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"output=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"precision=s"</span><span class="cm">,</span> <span class="q">"rotatablebonds=s"</span><span class="cm">,</span> <span class="q">"ruleof3violations=s"</span><span class="cm">,</span> <span class="q">"ruleof5violations=s"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"tpsa=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>
|
|
|
1279 1266 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
|
|
|
1280 1267 <span class="s">}</span>
|
|
|
1281 1268 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1282 1269 <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>
|
|
|
1283 1270 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
|
|
|
1284 1271 <span class="s">}</span>
|
|
|
1285 1272 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span>
|
|
|
1286 1273 <span class="s">}</span>
|
|
|
1287 1274 <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1288 1275 <span class="k">my</span><span class="s">(</span><span class="i">@SupportedModels</span><span class="s">)</span> = <span class="i">Molecule::GetSupportedAromaticityModels</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1289 1276 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"</span><span class="sc">;</span>
|
|
|
1290 1277 <span class="s">}</span>
|
|
|
1291 1278 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1292 1279 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span>
|
|
|
1293 1280 <span class="s">}</span>
|
|
|
1294 1281 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1295 1282 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"</span><span class="sc">;</span>
|
|
|
1296 1283 <span class="s">}</span>
|
|
|
1297 1284 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1298 1285 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
|
|
|
1299 1286 <span class="s">}</span>
|
|
|
1300 1287 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">hydrogenbonds</span>} !~ <span class="q">/^(HBondsType1|HydrogenBondsType1|HBondsType2|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1301 1288 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{hydrogenbonds}, for option \"--HydrogenBonds\" is not valid. Allowed values: HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2\n"</span><span class="sc">;</span>
|
|
|
1302 1289 <span class="s">}</span>
|
|
|
1303 1290 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1304 1291 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
|
|
|
1305 1292 <span class="s">}</span>
|
|
|
1306 1293 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|text|both)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1307 1294 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, text, or both\n"</span><span class="sc">;</span>
|
|
|
1308 1295 <span class="s">}</span>
|
|
|
1309 1296 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1310 1297 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span>
|
|
|
1311 1298 <span class="s">}</span>
|
|
|
1312 1299 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1313 1300 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
|
|
|
1314 1301 <span class="s">}</span>
|
|
|
1315 1302 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1316 1303 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ruleof3violations}, for option \"--RuleOf3Violations\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
|
|
|
1317 1304 <span class="s">}</span>
|
|
|
1318 1305 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1319 1306 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ruleof5violations}, for option \"--RuleOf5Violations\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
|
|
|
1320 1307 <span class="s">}</span>
|
|
|
1321 1308 <span class="s">}</span>
|
|
|
1322 1309
|
|
|
1323 <a name="EOF-"></a></pre>
|
|
|
1324 <p> </p>
|
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1325 <br />
|
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|
1326 <center>
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|
1327 <img src="../../../images/h2o2.png">
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1328 </center>
|
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|
1329 </body>
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1330 </html>
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