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<html> <head> <title>MayaChemTools:Code:TopologicalPharmacophoreAtomPairsFingerprints.pl</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> 1 #!/usr/bin/perl -w 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: TopologicalPharmacophoreAtomPairsFingerprints.pl,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:46:23 $</span> 5 <span class="c"># $Revision: 1.36 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span> 38 <span class="k">use</span> <span class="w">MoleculeFileIO</span><span class="sc">;</span> 39 <span class="k">use</span> <span class="w">FileIO::FingerprintsSDFileIO</span><span class="sc">;</span> 40 <span class="k">use</span> <span class="w">FileIO::FingerprintsTextFileIO</span><span class="sc">;</span> 41 <span class="k">use</span> <span class="w">FileIO::FingerprintsFPFileIO</span><span class="sc">;</span> 42 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> 43 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span> 44 45 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span> 46 47 <span class="c"># Autoflush STDOUT</span> 48 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> 49 50 <span class="c"># Starting message...</span> 51 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> 52 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> 53 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 54 55 <span class="c"># Get the options and setup script...</span> 56 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 57 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 58 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span> 59 <span class="s">}</span> 60 61 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span> 62 <span class="i">@SDFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"sdf sd"</span><span class="s">)</span><span class="sc">;</span> 63 64 <span class="c"># Process options...</span> 65 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> 66 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> 67 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 68 69 <span class="c"># Setup information about input files...</span> 70 <span class="k">print</span> <span class="q">"Checking input SD file(s)...\n"</span><span class="sc">;</span> 71 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span> 72 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 73 74 <span class="c"># Process input files..</span> 75 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 76 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 77 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span> 78 <span class="s">}</span> 79 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span> 80 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> 81 <span class="k">print</span> <span class="q">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span> 82 <span class="i">GenerateTopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 83 <span class="s">}</span> 84 <span class="s">}</span> 85 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> 86 87 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 88 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span> 89 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 90 91 <span class="c">###############################################################################</span> 92 93 <span class="c"># Generate fingerprints for a SD file...</span> 94 <span class="c">#</span> <a name="GenerateTopologicalPharmacophoreAtomPairsFingerprints-"></a> 95 <span class="k">sub </span><span class="m">GenerateTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span> 96 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 97 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$MoleculeFileIO</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="cm">,</span> <span class="i">$SetupOutputFiles</span><span class="s">)</span><span class="sc">;</span> 98 99 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> 100 101 <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> 102 <span class="i">$SetupOutputFiles</span> = <span class="n">1</span><span class="sc">;</span> 103 104 <span class="i">$MoleculeFileIO</span> = <span class="w">new</span> <span class="i">MoleculeFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span> 105 <span class="i">$MoleculeFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 106 107 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span> 108 <span class="i">$IgnoredCmpdCount</span> = <span class="n">0</span><span class="sc">;</span> 109 110 <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Molecule</span> = <span class="i">$MoleculeFileIO</span><span class="i">->ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 111 <span class="i">$CmpdCount</span>++<span class="sc">;</span> 112 113 <span class="c"># Filter compound data before calculating fingerprints...</span> 114 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Filter</span>}<span class="s">)</span> <span class="s">{</span> 115 <span class="k">if</span> <span class="s">(</span><span class="i">CheckAndFilterCompound</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 116 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span> 117 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span> 118 <span class="s">}</span> 119 <span class="s">}</span> 120 121 <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span> = <span class="i">GenerateMoleculeFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 122 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">)</span> <span class="s">{</span> 123 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span> 124 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'FingerprintsGenerationFailed'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 125 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span> 126 <span class="s">}</span> 127 128 <span class="k">if</span> <span class="s">(</span><span class="i">$SetupOutputFiles</span><span class="s">)</span> <span class="s">{</span> 129 <span class="i">$SetupOutputFiles</span> = <span class="n">0</span><span class="sc">;</span> 130 <span class="i">SetupFingerprintsLabelValueIDs</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">)</span><span class="sc">;</span> 131 <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="i">SetupAndOpenOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 132 <span class="s">}</span> 133 134 <span class="i">WriteDataToOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span> 135 <span class="s">}</span> 136 <span class="i">$MoleculeFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 137 138 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span> 139 <span class="i">$NewFPSDFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 140 <span class="s">}</span> 141 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span> 142 <span class="i">$NewFPTextFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 143 <span class="s">}</span> 144 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span> 145 <span class="i">$NewFPFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 146 <span class="s">}</span> 147 148 <span class="i">WriteFingerprintsGenerationSummaryStatistics</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="s">)</span><span class="sc">;</span> 149 <span class="s">}</span> 150 151 <span class="c"># Process compound being ignored due to problems in fingerprints geneation...</span> 152 <span class="c">#</span> <a name="ProcessIgnoredCompound-"></a> 153 <span class="k">sub </span><span class="m">ProcessIgnoredCompound</span> <span class="s">{</span> 154 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 155 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 156 157 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 158 <span class="i">$CmpdID</span> = <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 159 160 <span class="j">MODE:</span> <span class="s">{</span> 161 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNonElementalData$/i</span><span class="s">)</span> <span class="s">{</span> 162 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n"</span><span class="sc">;</span> 163 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span> 164 <span class="s">}</span> 165 166 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNoElementalData$/i</span><span class="s">)</span> <span class="s">{</span> 167 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n"</span><span class="sc">;</span> 168 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span> 169 <span class="s">}</span> 170 171 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^FingerprintsGenerationFailed$/i</span><span class="s">)</span> <span class="s">{</span> 172 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"</span><span class="sc">;</span> 173 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span> 174 <span class="s">}</span> 175 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"</span><span class="sc">;</span> 176 <span class="s">}</span> 177 <span class="s">}</span> 178 179 <span class="c"># Check and filter compounds....</span> 180 <span class="c">#</span> <a name="CheckAndFilterCompound-"></a> 181 <span class="k">sub </span><span class="m">CheckAndFilterCompound</span> <span class="s">{</span> 182 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 183 <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span> 184 185 <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfElementsAndNonElements</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 186 187 <span class="k">if</span> <span class="s">(</span><span class="i">$NonElementCount</span><span class="s">)</span> <span class="s">{</span> 188 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'ContainsNonElementalData'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 189 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 190 <span class="s">}</span> 191 192 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ElementCount</span><span class="s">)</span> <span class="s">{</span> 193 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'ContainsNoElementalData'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 194 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 195 <span class="s">}</span> 196 197 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 198 <span class="s">}</span> 199 200 <span class="c"># Write out compounds fingerprints generation summary statistics...</span> 201 <span class="c">#</span> <a name="WriteFingerprintsGenerationSummaryStatistics-"></a> 202 <span class="k">sub </span><span class="m">WriteFingerprintsGenerationSummaryStatistics</span> <span class="s">{</span> 203 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 204 <span class="k">my</span><span class="s">(</span><span class="i">$ProcessedCmpdCount</span><span class="s">)</span><span class="sc">;</span> 205 206 <span class="i">$ProcessedCmpdCount</span> = <span class="i">$CmpdCount</span> - <span class="i">$IgnoredCmpdCount</span><span class="sc">;</span> 207 208 <span class="k">print</span> <span class="q">"\nNumber of compounds: $CmpdCount\n"</span><span class="sc">;</span> 209 <span class="k">print</span> <span class="q">"Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n"</span><span class="sc">;</span> 210 <span class="k">print</span> <span class="q">"Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n"</span><span class="sc">;</span> 211 <span class="s">}</span> 212 213 <span class="c"># Append atom pair value IDs to fingerprint label...</span> 214 <span class="c">#</span> <a name="SetupFingerprintsLabelValueIDs-"></a> 215 <span class="k">sub </span><span class="m">SetupFingerprintsLabelValueIDs</span> <span class="s">{</span> 216 <span class="k">my</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 217 218 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomPairsSetSizeToUse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> || 219 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabelMode</span>} !~ <span class="q">/^FingerprintsLabelWithIDs$/i</span><span class="s">)</span> <span class="s">{</span> 220 <span class="k">return</span><span class="sc">;</span> 221 <span class="s">}</span> 222 223 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>} .= <span class="q">"; Value IDs: "</span> . <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="i">->GetFingerprintsVector</span><span class="i">->GetValueIDsString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 224 <span class="s">}</span> 225 226 <span class="c"># Open output files...</span> 227 <span class="c">#</span> <a name="SetupAndOpenOutputFiles-"></a> 228 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span> 229 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 230 <span class="k">my</span><span class="s">(</span><span class="i">$NewFPSDFile</span><span class="cm">,</span> <span class="i">$NewFPFile</span><span class="cm">,</span> <span class="i">$NewFPTextFile</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span> 231 232 <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> 233 234 <span class="c"># Setup common parameters for fingerprints file IO objects...</span> 235 <span class="c">#</span> 236 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Write'</span><span class="cm">,</span> <span class="q">'Overwrite'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="q">'FingerprintsVectorString'</span><span class="cm">,</span> <span class="q">'VectorStringFormat'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>}<span class="s">)</span><span class="sc">;</span> 237 238 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> 239 <span class="i">$NewFPSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 240 <span class="k">print</span> <span class="q">"Generating SD file $NewFPSDFile...\n"</span><span class="sc">;</span> 241 <span class="i">$NewFPSDFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsSDFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$NewFPSDFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">'FingerprintsFieldLabel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="s">)</span><span class="sc">;</span> 242 <span class="i">$NewFPSDFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 243 <span class="s">}</span> 244 245 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span> 246 <span class="i">$NewFPFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 247 <span class="k">print</span> <span class="q">"Generating FP file $NewFPFile...\n"</span><span class="sc">;</span> 248 <span class="i">$NewFPFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsFPFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$NewFPFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span> 249 <span class="i">$NewFPFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 250 <span class="s">}</span> 251 252 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span> 253 <span class="k">my</span><span class="s">(</span><span class="i">$ColLabelsRef</span><span class="s">)</span><span class="sc">;</span> 254 255 <span class="i">$NewFPTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 256 <span class="i">$ColLabelsRef</span> = <span class="i">SetupFPTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 257 258 <span class="k">print</span> <span class="q">"Generating text file $NewFPTextFile...\n"</span><span class="sc">;</span> 259 <span class="i">$NewFPTextFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsTextFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$NewFPTextFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">'DataColLabels'</span> <span class="cm">=></span> <span class="i">$ColLabelsRef</span><span class="cm">,</span> <span class="q">'OutDelim'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="q">'OutQuote'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> 260 <span class="i">$NewFPTextFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 261 <span class="s">}</span> 262 263 <span class="k">return</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span> 264 <span class="s">}</span> 265 266 <span class="c"># Write fingerpritns and other data to appropriate output files...</span> 267 <span class="c">#</span> <a name="WriteDataToOutputFiles-"></a> 268 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span> 269 <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">$Molecule</span><span class="cm">,</span> <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 270 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 271 272 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="k">undef</span><span class="sc">;</span> 273 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span> || <span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span> 274 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 275 <span class="s">}</span> 276 277 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span> 278 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span> 279 280 <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">->GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 281 <span class="i">$NewFPSDFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span> 282 <span class="s">}</span> 283 284 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span> 285 <span class="k">my</span><span class="s">(</span><span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span> 286 287 <span class="i">$ColValuesRef</span> = <span class="i">SetupFPTextFileCoulmnValues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 288 <span class="i">$NewFPTextFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="cm">,</span> <span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span> 289 <span class="s">}</span> 290 291 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span> 292 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span> 293 294 <span class="i">$CompoundID</span> = <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 295 <span class="i">$NewFPFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="cm">,</span> <span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span> 296 <span class="s">}</span> 297 <span class="s">}</span> 298 299 <span class="c"># Generate approriate column labels for FPText output file...</span> 300 <span class="c">#</span> <a name="SetupFPTextFileCoulmnLabels-"></a> 301 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnLabels</span> <span class="s">{</span> 302 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 303 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span> 304 305 <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 306 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> 307 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span> 308 <span class="s">}</span> 309 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span> 310 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span> 311 <span class="s">}</span> 312 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> 313 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span> 314 <span class="s">}</span> 315 <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> 316 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span> 317 <span class="s">}</span> 318 <span class="c"># Add fingerprints label...</span> 319 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="sc">;</span> 320 321 <span class="k">return</span> \<span class="i">@ColLabels</span><span class="sc">;</span> 322 <span class="s">}</span> 323 324 <span class="c"># Generate column values FPText output file..</span> 325 <span class="c">#</span> <a name="SetupFPTextFileCoulmnValues-"></a> 326 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnValues</span> <span class="s">{</span> 327 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 328 <span class="k">my</span><span class="s">(</span><span class="i">@ColValues</span><span class="s">)</span><span class="sc">;</span> 329 330 <span class="i">@ColValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 331 <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> 332 <span class="k">push</span> <span class="i">@ColValues</span><span class="cm">,</span> <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 333 <span class="s">}</span> 334 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> 335 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span> 336 <span class="s">}</span> 337 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span> 338 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span> 339 <span class="s">}</span> 340 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> 341 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span> 342 <span class="s">}</span> 343 344 <span class="k">return</span> \<span class="i">@ColValues</span><span class="sc">;</span> 345 <span class="s">}</span> 346 347 <span class="c"># Generate compound ID for FP and FPText output files..</span> 348 <span class="c">#</span> <a name="SetupCmpdIDForOutputFiles-"></a> 349 <span class="k">sub </span><span class="m">SetupCmpdIDForOutputFiles</span> <span class="s">{</span> 350 <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 351 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span> 352 353 <span class="i">$CmpdID</span> = <span class="q">''</span><span class="sc">;</span> 354 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolNameOrLabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span> 355 <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span> 356 <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> 357 <span class="i">$CmpdID</span> = <span class="i">$MolName</span> ? <span class="i">$MolName</span> <span class="co">:</span> <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span> 358 <span class="s">}</span> 359 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^LabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span> 360 <span class="i">$CmpdID</span> = <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span> 361 <span class="s">}</span> 362 <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> 363 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span> 364 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span> 365 <span class="i">$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> 366 <span class="s">}</span> 367 <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> 368 <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> 369 <span class="s">}</span> 370 <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span> 371 <span class="s">}</span> 372 373 <span class="c"># Generate fingerprints for molecule...</span> 374 <span class="c">#</span> <a name="GenerateMoleculeFingerprints-"></a> 375 <span class="k">sub </span><span class="m">GenerateMoleculeFingerprints</span> <span class="s">{</span> 376 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 377 <span class="k">my</span><span class="s">(</span><span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">)</span><span class="sc">;</span> 378 379 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span> 380 <span class="i">$Molecule</span><span class="i">->KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 381 <span class="s">}</span> 382 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">->DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 383 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 384 <span class="s">}</span> 385 <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> 386 <span class="i">$Molecule</span><span class="i">->DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 387 388 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FuzzifyAtomPairsCount</span>}<span class="s">)</span> <span class="s">{</span> 389 <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">'AtomPairsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">AtomPairsSetSizeToUse</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="cm">,</span> <span class="q">'NormalizationMethodology'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">NormalizationMethodology</span>}<span class="cm">,</span> <span class="cm">,</span> <span class="q">'ValuesPrecision'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValuesPrecision</span>}<span class="cm">,</span> <span class="q">'FuzzifyAtomPairsCount'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FuzzifyAtomPairsCount</span>}<span class="cm">,</span> <span class="q">'FuzzificationMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FuzzificationMode</span>}<span class="cm">,</span> <span class="q">'FuzzificationMethodology'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FuzzificationMethodology</span>}<span class="cm">,</span> <span class="q">'FuzzFactor'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FuzzFactor</span>}<span class="s">)</span><span class="sc">;</span> 390 <span class="s">}</span> 391 <span class="k">else</span> <span class="s">{</span> 392 <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">'AtomPairsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">AtomPairsSetSizeToUse</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="q">'NormalizationMethodology'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">NormalizationMethodology</span>}<span class="cm">,</span> <span class="q">'ValuesPrecision'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValuesPrecision</span>}<span class="s">)</span><span class="sc">;</span> 393 <span class="s">}</span> 394 395 <span class="c"># Set atom types weights...</span> 396 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">UseAtomTypesWeight</span>}<span class="s">)</span> <span class="s">{</span> 397 <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="i">->SetAtomTypesWeight</span><span class="s">(</span><span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesWeight</span>}}<span class="s">)</span><span class="sc">;</span> 398 <span class="s">}</span> 399 400 <span class="c"># Generate fingerprints...</span> 401 <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="i">->GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 402 403 <span class="c"># Make sure fingerprints generation is successful...</span> 404 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="i">->IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 405 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 406 <span class="s">}</span> 407 408 <span class="k">return</span> <span class="i">$TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span> 409 <span class="s">}</span> 410 411 <span class="c"># Retrieve information about SD files...</span> 412 <span class="c">#</span> <a name="RetrieveSDFilesInfo-"></a> 413 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span> 414 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$TextOutFileExt</span><span class="cm">,</span> <span class="i">$SDOutFileExt</span><span class="cm">,</span> <span class="i">$FPOutFileExt</span><span class="cm">,</span> <span class="i">$NewSDFileName</span><span class="cm">,</span> <span class="i">$NewFPFileName</span><span class="cm">,</span> <span class="i">$NewTextFileName</span><span class="cm">,</span> <span class="i">$CheckDataField</span><span class="cm">,</span> <span class="i">$CollectDataFields</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span><span class="sc">;</span> 415 416 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 417 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 418 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 419 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 420 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 421 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 422 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 423 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 424 425 <span class="i">$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$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 426 <span class="i">$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)$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 427 428 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span> 429 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 430 431 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> 432 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 433 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 434 <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 435 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 436 437 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 438 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 439 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span> 440 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 441 <span class="s">}</span> 442 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 443 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span> 444 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 445 <span class="s">}</span> 446 447 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span> 448 <span class="c"># Make sure data field exists in SD file..</span> 449 <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> 450 451 <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 452 <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: $! \n"</span><span class="sc">;</span> 453 <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span> 454 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> 455 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span> 456 <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span> 457 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span> 458 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span> 459 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n"</span><span class="sc">;</span> 460 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 461 <span class="s">}</span> 462 <span class="s">}</span> 463 464 <span class="i">$AllDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span> 465 <span class="i">$CommonDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span> 466 <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span> 467 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span> 468 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $SDFile: $! \n"</span><span class="sc">;</span> 469 <span class="s">(</span><span class="i">$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> 470 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> 471 <span class="s">}</span> 472 473 <span class="c"># Setup output file names...</span> 474 <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">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> 475 <span class="s">(</span><span class="i">$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">$SDFile</span><span class="s">)</span><span class="sc">;</span> 476 477 <span class="i">$TextOutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span> 478 <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> 479 <span class="i">$TextOutFileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span> 480 <span class="s">}</span> 481 <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span> 482 <span class="i">$FPOutFileExt</span> = <span class="q">"fpf"</span><span class="sc">;</span> 483 484 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 485 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> 486 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> 487 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> 488 <span class="s">}</span> 489 <span class="k">else</span> <span class="s">{</span> 490 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> 491 <span class="s">}</span> 492 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> 493 <span class="s">}</span> 494 <span class="k">else</span> <span class="s">{</span> 495 <span class="i">$OutFileRoot</span> = <span class="q">"${FileName}TopologicalPharmacophoreAtomPairsFP"</span><span class="sc">;</span> 496 <span class="s">}</span> 497 498 <span class="i">$NewSDFileName</span> = <span class="q">"${OutFileRoot}.${SDOutFileExt}"</span><span class="sc">;</span> 499 <span class="i">$NewFPFileName</span> = <span class="q">"${OutFileRoot}.${FPOutFileExt}"</span><span class="sc">;</span> 500 <span class="i">$NewTextFileName</span> = <span class="q">"${OutFileRoot}.${TextOutFileExt}"</span><span class="sc">;</span> 501 502 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> 503 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span> 504 <span class="k">warn</span> <span class="q">"Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n"</span><span class="sc">;</span> 505 <span class="k">print</span> <span class="q">"Specify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span> 506 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 507 <span class="s">}</span> 508 <span class="s">}</span> 509 510 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span> 511 <span class="c"># Check SD and text outout files...</span> 512 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> 513 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span> 514 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n"</span><span class="sc">;</span> 515 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 516 <span class="s">}</span> 517 <span class="s">}</span> 518 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span> 519 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewFPFileName</span><span class="s">)</span> <span class="s">{</span> 520 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n"</span><span class="sc">;</span> 521 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 522 <span class="s">}</span> 523 <span class="s">}</span> 524 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span> 525 <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> 526 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n"</span><span class="sc">;</span> 527 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 528 <span class="s">}</span> 529 <span class="s">}</span> 530 <span class="s">}</span> 531 532 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> 533 534 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> 535 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span> 536 <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewFPFileName</span><span class="sc">;</span> 537 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span> 538 539 <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span> 540 <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span> 541 <span class="s">}</span> 542 <span class="s">}</span> 543 544 <span class="c"># Process option values...</span> <a name="ProcessOptions-"></a> 545 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> 546 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 547 548 <span class="i">ProcessAtomTypesToUseOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 549 <span class="i">ProcessAtomTypesWeightOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 550 551 <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span> 552 553 <span class="i">$OptionsInfo</span>{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="i">$Options</span>{<span class="w">atompairssetsizetouse</span>}<span class="sc">;</span> 554 555 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span> 556 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span> 557 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span> 558 559 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span> 560 <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 561 562 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 563 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">''</span><span class="sc">;</span> 564 565 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span> 566 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span> 567 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span> 568 <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> 569 <span class="s">}</span> 570 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span> 571 <span class="s">}</span> 572 <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> 573 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>} ? <span class="i">$Options</span>{<span class="w">compoundid</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span> 574 <span class="s">}</span> 575 <span class="s">}</span> 576 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> 577 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span> 578 <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> 579 <span class="s">}</span> 580 <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span> 581 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span> 582 <span class="s">}</span> 583 584 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 585 586 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabelMode</span>} = <span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>}<span class="sc">;</span> 587 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>} = <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} ? <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} <span class="co">:</span> <span class="q">'TopologicalPharmacophoreAtomPairsFingerprints'</span><span class="sc">;</span> 588 589 <span class="i">$OptionsInfo</span>{<span class="w">FuzzifyAtomPairsCount</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzifyatompairscount</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 590 <span class="i">$OptionsInfo</span>{<span class="w">FuzzificationMode</span>} = <span class="i">$Options</span>{<span class="w">fuzzificationmode</span>}<span class="sc">;</span> 591 <span class="i">$OptionsInfo</span>{<span class="w">FuzzificationMethodology</span>} = <span class="i">$Options</span>{<span class="w">fuzzificationmethodology</span>}<span class="sc">;</span> 592 <span class="i">$OptionsInfo</span>{<span class="w">FuzzFactor</span>} = <span class="i">$Options</span>{<span class="w">fuzzfactor</span>}<span class="sc">;</span> 593 594 <span class="i">$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> 595 596 <span class="i">$OptionsInfo</span>{<span class="w">MinDistance</span>} = <span class="i">$Options</span>{<span class="w">mindistance</span>}<span class="sc">;</span> 597 <span class="i">$OptionsInfo</span>{<span class="w">MaxDistance</span>} = <span class="i">$Options</span>{<span class="w">maxdistance</span>}<span class="sc">;</span> 598 599 <span class="i">$OptionsInfo</span>{<span class="w">NormalizationMethodology</span>} = <span class="i">$Options</span>{<span class="w">normalizationmethodology</span>}<span class="sc">;</span> 600 601 <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span> 602 <span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(SD|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 603 <span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(FP|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 604 <span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(Text|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 605 606 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="i">$Options</span>{<span class="w">outdelim</span>}<span class="sc">;</span> 607 <span class="i">$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> 608 609 <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> 610 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 611 612 <span class="i">$OptionsInfo</span>{<span class="w">ValuesPrecision</span>} = <span class="i">$Options</span>{<span class="w">valuesprecision</span>}<span class="sc">;</span> 613 614 <span class="c"># Setup default vector string format...</span> 615 <span class="k">my</span><span class="s">(</span><span class="i">$VectorStringFormat</span><span class="s">)</span><span class="sc">;</span> 616 <span class="i">$VectorStringFormat</span> = <span class="q">''</span><span class="sc">;</span> 617 618 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="s">)</span> <span class="s">{</span> 619 <span class="i">$VectorStringFormat</span> = <span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="sc">;</span> 620 621 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atompairssetsizetouse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> && <span class="i">$VectorStringFormat</span> =~ <span class="q">/^ValuesString$/i</span><span class="s">)</span> <span class="s">{</span> 622 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid for $Options{atompairssetsizetouse} value of \"--AtomPairsSetSizeToUse\" option. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"</span><span class="sc">;</span> 623 <span class="s">}</span> 624 <span class="s">}</span> 625 <span class="k">else</span> <span class="s">{</span> 626 <span class="i">$VectorStringFormat</span> = <span class="s">(</span><span class="i">$Options</span>{<span class="w">atompairssetsizetouse</span>} =~ <span class="q">/^FixedSize$/</span><span class="s">)</span> ? <span class="q">"ValuesString"</span> <span class="co">:</span> <span class="q">"IDsAndValuesString"</span><span class="sc">;</span> 627 <span class="s">}</span> 628 <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>} = <span class="i">$VectorStringFormat</span><span class="sc">;</span> 629 <span class="s">}</span> 630 631 <span class="c"># Process atom type to use option...</span> 632 <span class="c">#</span> <a name="ProcessAtomTypesToUseOption-"></a> 633 <span class="k">sub </span><span class="m">ProcessAtomTypesToUseOption</span> <span class="s">{</span> 634 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypesToUse</span><span class="cm">,</span> <span class="i">@AtomTypesWords</span><span class="s">)</span><span class="sc">;</span> 635 636 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 637 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomtypestouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 638 <span class="k">die</span> <span class="q">"Error: Atom types value specified using \"-a, --AtomTypesToUse\" option is empty\n"</span><span class="sc">;</span> 639 <span class="s">}</span> 640 641 <span class="i">$SpecifiedAtomTypesToUse</span> = <span class="i">$Options</span>{<span class="w">atomtypestouse</span>}<span class="sc">;</span> 642 <span class="i">$SpecifiedAtomTypesToUse</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 643 <span class="i">@AtomTypesWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypesToUse</span><span class="sc">;</span> 644 645 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypesWords</span><span class="s">)</span> <span class="s">{</span> 646 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$AtomType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 647 <span class="k">die</span> <span class="q">"Error: Atomic type specified, $AtomType, using \"-a, --AtomTypesToUse\" option is not valid...\n "</span><span class="sc">;</span> 648 <span class="s">}</span> 649 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span> 650 <span class="s">}</span> 651 <span class="s">}</span> 652 653 <span class="c"># Process atom types weight option...</span> 654 <span class="c">#</span> <a name="ProcessAtomTypesWeightOption-"></a> 655 <span class="k">sub </span><span class="m">ProcessAtomTypesWeightOption</span> <span class="s">{</span> 656 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$AtomTypeWeight</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypesWeight</span><span class="cm">,</span> <span class="i">@AtomTypesWeightsPairs</span><span class="s">)</span><span class="sc">;</span> 657 658 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomTypesWeight</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 659 660 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomtypesweight</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 661 <span class="k">die</span> <span class="q">"Error: Atom types weight value specified using \"--AtomTypesWeight\" option is empty\n"</span><span class="sc">;</span> 662 <span class="s">}</span> 663 <span class="i">$OptionsInfo</span>{<span class="w">UseAtomTypesWeight</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomtypesweight</span>} =~ <span class="q">/^None$/i</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 664 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">UseAtomTypesWeight</span>}<span class="s">)</span> <span class="s">{</span> 665 <span class="k">return</span><span class="sc">;</span> 666 <span class="s">}</span> 667 668 <span class="c"># Process specified atom type/weight pairs...</span> 669 <span class="i">$SpecifiedAtomTypesWeight</span> = <span class="i">$Options</span>{<span class="w">atomtypesweight</span>}<span class="sc">;</span> 670 <span class="i">$SpecifiedAtomTypesWeight</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 671 <span class="i">@AtomTypesWeightsPairs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypesWeight</span><span class="sc">;</span> 672 673 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomTypesWeightsPairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 674 <span class="k">die</span> <span class="q">"Error: Invalid number of values specified using \"--AtomTypesWeight\" option: It must contain even number of values.\n"</span><span class="sc">;</span> 675 <span class="s">}</span> 676 677 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">@AtomTypesWeightsPairs</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 678 <span class="i">$AtomType</span> = <span class="i">$AtomTypesWeightsPairs</span>[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$AtomTypeWeight</span> = <span class="i">$AtomTypesWeightsPairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> 679 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$AtomType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 680 <span class="k">die</span> <span class="q">"Error: Atom type specified, $AtomType, using \"--AtomTypesWeight\" option is not valid\n "</span><span class="sc">;</span> 681 <span class="s">}</span> 682 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$AtomTypeWeight</span><span class="s">)</span> && <span class="i">$AtomTypeWeight</span> >= <span class="n">0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 683 <span class="k">die</span> <span class="q">"Error: Atom type weight specified, $AtomTypeWeight, using option \"--AtomTypesWeight\" is not valid. Allowed values: real numbers >= 0 \n"</span><span class="sc">;</span> 684 <span class="s">}</span> 685 <span class="i">$OptionsInfo</span>{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>} = <span class="i">$AtomTypeWeight</span><span class="sc">;</span> 686 <span class="s">}</span> 687 <span class="s">}</span> 688 689 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> <a name="SetupScriptUsage-"></a> 690 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> 691 692 <span class="c"># Retrieve all the options...</span> 693 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 694 695 <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span> 696 697 <span class="i">$Options</span>{<span class="w">atompairssetsizetouse</span>} = <span class="q">'ArbitrarySize'</span><span class="sc">;</span> 698 699 <span class="i">$Options</span>{<span class="w">atomtypestouse</span>} = <span class="q">'HBD,HBA,PI,NI,H'</span><span class="sc">;</span> 700 <span class="i">$Options</span>{<span class="w">atomtypesweight</span>} = <span class="q">'None'</span><span class="sc">;</span> 701 702 <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span> 703 <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span> 704 <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span> 705 706 <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">'Yes'</span><span class="sc">;</span> 707 708 <span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>} = <span class="q">'FingerprintsLabelOnly'</span><span class="sc">;</span> 709 710 <span class="i">$Options</span>{<span class="w">fuzzifyatompairscount</span>} = <span class="q">'No'</span><span class="sc">;</span> 711 <span class="i">$Options</span>{<span class="w">fuzzificationmode</span>} = <span class="q">'AfterNormalization'</span><span class="sc">;</span> 712 <span class="i">$Options</span>{<span class="w">fuzzificationmethodology</span>} = <span class="q">'FuzzyBinning'</span><span class="sc">;</span> 713 <span class="i">$Options</span>{<span class="w">fuzzfactor</span>} = <span class="n">0.15</span><span class="sc">;</span> 714 715 <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">'Yes'</span><span class="sc">;</span> 716 717 <span class="i">$Options</span>{<span class="w">mindistance</span>} = <span class="n">1</span><span class="sc">;</span> 718 <span class="i">$Options</span>{<span class="w">maxdistance</span>} = <span class="n">10</span><span class="sc">;</span> 719 720 <span class="i">$Options</span>{<span class="w">normalizationmethodology</span>} = <span class="q">'None'</span><span class="sc">;</span> 721 722 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">'text'</span><span class="sc">;</span> 723 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> 724 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span> 725 726 <span class="i">$Options</span>{<span class="w">valuesprecision</span>} = <span class="n">2</span><span class="sc">;</span> 727 728 <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} = <span class="q">''</span><span class="sc">;</span> 729 730 <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">"atompairssetsizetouse=s"</span><span class="cm">,</span> <span class="q">"atomtypestouse|a=s"</span><span class="cm">,</span> <span class="q">"atomtypesweight=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">"fingerprintslabelmode=s"</span><span class="cm">,</span> <span class="q">"fingerprintslabel=s"</span><span class="cm">,</span> <span class="q">"fuzzifyatompairscount=s"</span><span class="cm">,</span> <span class="q">"fuzzificationmode=s"</span><span class="cm">,</span> <span class="q">"fuzzificationmethodology=s"</span><span class="cm">,</span> <span class="q">"fuzzfactor=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"keeplargestcomponent|k=s"</span><span class="cm">,</span> <span class="q">"mindistance=s"</span><span class="cm">,</span> <span class="q">"maxdistance=s"</span><span class="cm">,</span> <span class="q">"normalizationmethodology|n=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"output=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"valuesprecision=s"</span><span class="cm">,</span> <span class="q">"vectorstringformat|v=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 731 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> 732 <span class="s">}</span> 733 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 734 <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> 735 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> 736 <span class="s">}</span> 737 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span> 738 <span class="s">}</span> 739 <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 740 <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> 741 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"</span><span class="sc">;</span> 742 <span class="s">}</span> 743 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atompairssetsizetouse</span>} !~ <span class="q">/^(ArbitrarySize|FixedSize)$/i</span><span class="s">)</span> <span class="s">{</span> 744 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{atompairssetsizetouse}, for option \"--AtomPairsSetSizeToUse\" is not valid. Allowed values: ArbitrarySize or FixedSize\n"</span><span class="sc">;</span> 745 <span class="s">}</span> 746 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span> 747 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span> 748 <span class="s">}</span> 749 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span> 750 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"</span><span class="sc">;</span> 751 <span class="s">}</span> 752 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 753 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 754 <span class="s">}</span> 755 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintslabelmode</span>} !~ <span class="q">/^(FingerprintsLabelOnly|FingerprintsLabelWithIDs)$/i</span><span class="s">)</span> <span class="s">{</span> 756 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{fingerprintslabelmode}, for option \"--FingerprintsLabelMode\" is not valid. Allowed values: FingerprintsLabelOnly or FingerprintsLabelWithIDs\n"</span><span class="sc">;</span> 757 <span class="s">}</span> 758 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzifyatompairscount</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 759 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{fuzzifyatompairscount}, for option \"--FuzzifyAtomPairsCount\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 760 <span class="s">}</span> 761 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzificationmode</span>} !~ <span class="q">/^(BeforeNormalization|AfterNormalization)$/i</span><span class="s">)</span> <span class="s">{</span> 762 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{fuzzificationmode}, for option \"--FuzzificationMode\" is not valid. Allowed values: BeforeNormalization or AfterNormalization\n"</span><span class="sc">;</span> 763 <span class="s">}</span> 764 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzificationmethodology</span>} !~ <span class="q">/^(FuzzyBinning|FuzzyBinSmoothing)$/i</span><span class="s">)</span> <span class="s">{</span> 765 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{fuzzificationmethodology}, for option \"--FuzzificationMethodology\" is not valid. Allowed values: FuzzyBinning or FuzzyBinSmoothing\n"</span><span class="sc">;</span> 766 <span class="s">}</span> 767 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsFloat</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzfactor</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 768 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{fuzzfactor}, for option \"--FuzzFactor\" is not valid. Allowed values: real numbers >= 0 \n"</span><span class="sc">;</span> 769 <span class="s">}</span> 770 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzificationmethodology</span>} !~ <span class="q">/^FuzzyBinning$/i</span><span class="s">)</span> <span class="s">{</span> 771 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzfactor</span>} >=<span class="n">0</span> && <span class="i">$Options</span>{<span class="w">fuzzfactor</span>} <= <span class="n">1.0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 772 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{fuzzfactor}, for option \"--FuzzFactor\" during FuzzyBinning \"--FuzzificationMethodology\" is not valid. Allowed values: >= 0 and <= 1 \n"</span><span class="sc">;</span> 773 <span class="s">}</span> 774 <span class="s">}</span> 775 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzificationmethodology</span>} !~ <span class="q">/^FuzzyBinSmoothing$/i</span><span class="s">)</span> <span class="s">{</span> 776 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Options</span>{<span class="w">fuzzfactor</span>} >=<span class="n">0</span> && <span class="i">$Options</span>{<span class="w">fuzzfactor</span>} <= <span class="n">0.5</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 777 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{fuzzfactor}, for option \"--FuzzFactor\" during FuzzyBinSmoothing \"--FuzzificationMethodology\" is not valid. Allowed values: >= 0 and <= 0.5 \n"</span><span class="sc">;</span> 778 <span class="s">}</span> 779 <span class="s">}</span> 780 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 781 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 782 <span class="s">}</span> 783 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">mindistance</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 784 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mindistance}, for option \"--MinDistance\" is not valid. Allowed values: >= 0 \n"</span><span class="sc">;</span> 785 <span class="s">}</span> 786 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">maxdistance</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 787 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{maxdistance}, for option \"--MaxDistance\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> 788 <span class="s">}</span> 789 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mindistance</span>} > <span class="i">$Options</span>{<span class="w">maxdistance</span>}<span class="s">)</span> <span class="s">{</span> 790 <span class="k">die</span> <span class="q">"Error: The value specified, specified, $Options{mindistance}, for option \"--MinDistance\" must be less than the value specified, $Options{maxdistance}, for option \"--MaxDistance\" \n"</span><span class="sc">;</span> 791 <span class="s">}</span> 792 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">normalizationmethodology</span>} !~ <span class="q">/^(None|ByHeavyAtomsCount|ByAtomTypesCount)$/i</span><span class="s">)</span> <span class="s">{</span> 793 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{normalizationmethodology}, for option \"--NormalizationMethodology\" is not valid. Allowed values: None, ByHeavyAtomsCount, or ByAtomTypesCount\n"</span><span class="sc">;</span> 794 <span class="s">}</span> 795 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|FP|text|all)$/i</span><span class="s">)</span> <span class="s">{</span> 796 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n"</span><span class="sc">;</span> 797 <span class="s">}</span> 798 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span> 799 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span> 800 <span class="s">}</span> 801 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 802 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 803 <span class="s">}</span> 804 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span> && <span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^No$/i</span><span class="s">)</span> <span class="s">{</span> 805 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"</span><span class="sc">;</span> 806 <span class="s">}</span> 807 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">valuesprecision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 808 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{valuesprecision}, for option \"--ValuesPrecision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> 809 <span class="s">}</span> 810 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>} && <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} !~ <span class="q">/^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i</span><span class="s">)</span> <span class="s">{</span> 811 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"</span><span class="sc">;</span> 812 <span class="s">}</span> 813 <span class="s">}</span> 814 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>