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<html> <head> <title>MayaChemTools:Code:ExtendedConnectivityFingerprints.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: ExtendedConnectivityFingerprints.pl,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span> 5 <span class="c"># $Revision: 1.37 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$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::AtomicInvariantsAtomTypes</span><span class="sc">;</span> 43 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> 44 <span class="k">use</span> <span class="w">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span> 45 46 <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> 47 48 <span class="c"># Autoflush STDOUT</span> 49 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> 50 51 <span class="c"># Starting message...</span> 52 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> 53 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> 54 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 55 56 <span class="c"># Get the options and setup script...</span> 57 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 58 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 59 <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> 60 <span class="s">}</span> 61 62 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span> 63 <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> 64 65 <span class="c"># Process options...</span> 66 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> 67 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> 68 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 69 70 <span class="c"># Setup information about input files...</span> 71 <span class="k">print</span> <span class="q">"Checking input SD file(s)...\n"</span><span class="sc">;</span> 72 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span> 73 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 74 75 <span class="c"># Process input files..</span> 76 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 77 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 78 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span> 79 <span class="s">}</span> 80 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span> 81 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> 82 <span class="k">print</span> <span class="q">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span> 83 <span class="i">GenerateExtendedConnectivityFingerprints</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 84 <span class="s">}</span> 85 <span class="s">}</span> 86 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> 87 88 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 89 <span class="i">$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> 90 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 91 92 <span class="c">###############################################################################</span> 93 94 <span class="c"># Generate fingerprints for a SD file...</span> 95 <span class="c">#</span> <a name="GenerateExtendedConnectivityFingerprints-"></a> 96 <span class="k">sub </span><span class="m">GenerateExtendedConnectivityFingerprints</span> <span class="s">{</span> 97 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 98 <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">$Molecule</span><span class="cm">,</span> <span class="i">$ExtendedConnectivityFingerprints</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">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span> 99 100 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> 101 102 <span class="c"># Setup output files...</span> 103 <span class="c">#</span> 104 <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> 105 106 <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> 107 <span class="i">$MoleculeFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 108 109 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span> 110 <span class="i">$IgnoredCmpdCount</span> = <span class="n">0</span><span class="sc">;</span> 111 112 <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Molecule</span> = <span class="i">$MoleculeFileIO</span><span class="i">->ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 113 <span class="i">$CmpdCount</span>++<span class="sc">;</span> 114 115 <span class="c"># Filter compound data before calculating fingerprints...</span> 116 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Filter</span>}<span class="s">)</span> <span class="s">{</span> 117 <span class="k">if</span> <span class="s">(</span><span class="i">CheckAndFilterCompound</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 118 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span> 119 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span> 120 <span class="s">}</span> 121 <span class="s">}</span> 122 123 <span class="i">$ExtendedConnectivityFingerprints</span> = <span class="i">GenerateMoleculeFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 124 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ExtendedConnectivityFingerprints</span><span class="s">)</span> <span class="s">{</span> 125 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span> 126 <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> 127 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span> 128 <span class="s">}</span> 129 130 <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">$Molecule</span><span class="cm">,</span> <span class="i">$ExtendedConnectivityFingerprints</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">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span> 131 <span class="s">}</span> 132 <span class="i">$MoleculeFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 133 134 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span> 135 <span class="i">$NewFPSDFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 136 <span class="s">}</span> 137 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span> 138 <span class="i">$NewFPTextFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 139 <span class="s">}</span> 140 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span> 141 <span class="i">$NewFPFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 142 <span class="s">}</span> 143 144 <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> 145 <span class="s">}</span> 146 147 <span class="c"># Process compound being ignored due to problems in fingerprints geneation...</span> 148 <span class="c">#</span> <a name="ProcessIgnoredCompound-"></a> 149 <span class="k">sub </span><span class="m">ProcessIgnoredCompound</span> <span class="s">{</span> 150 <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">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 151 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 152 153 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 154 <span class="i">$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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 155 156 <span class="j">MODE:</span> <span class="s">{</span> 157 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNonElementalData$/i</span><span class="s">)</span> <span class="s">{</span> 158 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n"</span><span class="sc">;</span> 159 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span> 160 <span class="s">}</span> 161 162 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNoElementalData$/i</span><span class="s">)</span> <span class="s">{</span> 163 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n"</span><span class="sc">;</span> 164 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span> 165 <span class="s">}</span> 166 167 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^FingerprintsGenerationFailed$/i</span><span class="s">)</span> <span class="s">{</span> 168 <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> 169 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span> 170 <span class="s">}</span> 171 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"</span><span class="sc">;</span> 172 <span class="s">}</span> 173 <span class="s">}</span> 174 175 <span class="c"># Check and filter compounds....</span> 176 <span class="c">#</span> <a name="CheckAndFilterCompound-"></a> 177 <span class="k">sub </span><span class="m">CheckAndFilterCompound</span> <span class="s">{</span> 178 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 179 <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span> 180 181 <span class="s">(</span><span class="i">$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> 182 183 <span class="k">if</span> <span class="s">(</span><span class="i">$NonElementCount</span><span class="s">)</span> <span class="s">{</span> 184 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'ContainsNonElementalData'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 185 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 186 <span class="s">}</span> 187 188 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ElementCount</span><span class="s">)</span> <span class="s">{</span> 189 <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> 190 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 191 <span class="s">}</span> 192 193 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 194 <span class="s">}</span> 195 196 <span class="c"># Write out compounds fingerprints generation summary statistics...</span> 197 <span class="c">#</span> <a name="WriteFingerprintsGenerationSummaryStatistics-"></a> 198 <span class="k">sub </span><span class="m">WriteFingerprintsGenerationSummaryStatistics</span> <span class="s">{</span> 199 <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> 200 <span class="k">my</span><span class="s">(</span><span class="i">$ProcessedCmpdCount</span><span class="s">)</span><span class="sc">;</span> 201 202 <span class="i">$ProcessedCmpdCount</span> = <span class="i">$CmpdCount</span> - <span class="i">$IgnoredCmpdCount</span><span class="sc">;</span> 203 204 <span class="k">print</span> <span class="q">"\nNumber of compounds: $CmpdCount\n"</span><span class="sc">;</span> 205 <span class="k">print</span> <span class="q">"Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n"</span><span class="sc">;</span> 206 <span class="k">print</span> <span class="q">"Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n"</span><span class="sc">;</span> 207 <span class="s">}</span> 208 209 <span class="c"># Open output files...</span> 210 <span class="c">#</span> <a name="SetupAndOpenOutputFiles-"></a> 211 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span> 212 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 213 <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> 214 215 <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">$NewFPFileIO</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> 216 217 <span class="c"># Setup common parameters for fingerprints file IO objects...</span> 218 <span class="c">#</span> 219 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 220 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(ExtendedConnectivity|ExtendedConnectivityCount)$/i</span><span class="s">)</span> <span class="s">{</span> 221 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Write'</span><span class="cm">,</span> <span class="q">'Overwrite'</span> <span class="cm">=></span> <span class="i">$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">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>}<span class="s">)</span><span class="sc">;</span> 222 <span class="s">}</span> 223 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> 224 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Write'</span><span class="cm">,</span> <span class="q">'Overwrite'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="q">'FingerprintsBitVectorString'</span><span class="cm">,</span> <span class="q">'BitStringFormat'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">BitStringFormat</span>}<span class="cm">,</span> <span class="q">'BitsOrder'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">BitsOrder</span>}<span class="s">)</span><span class="sc">;</span> 225 <span class="s">}</span> 226 227 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> 228 <span class="i">$NewFPSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 229 <span class="k">print</span> <span class="q">"Generating SD file $NewFPSDFile...\n"</span><span class="sc">;</span> 230 <span class="i">$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> 231 <span class="i">$NewFPSDFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 232 <span class="s">}</span> 233 234 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span> 235 <span class="i">$NewFPFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 236 <span class="k">print</span> <span class="q">"Generating FP file $NewFPFile...\n"</span><span class="sc">;</span> 237 <span class="i">$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">$NewFPFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span> 238 <span class="i">$NewFPFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 239 <span class="s">}</span> 240 241 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span> 242 <span class="k">my</span><span class="s">(</span><span class="i">$ColLabelsRef</span><span class="s">)</span><span class="sc">;</span> 243 244 <span class="i">$NewFPTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 245 <span class="i">$ColLabelsRef</span> = <span class="i">SetupFPTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 246 247 <span class="k">print</span> <span class="q">"Generating text file $NewFPTextFile...\n"</span><span class="sc">;</span> 248 <span class="i">$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> 249 <span class="i">$NewFPTextFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 250 <span class="s">}</span> 251 252 <span class="k">return</span> <span class="s">(</span><span class="i">$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> 253 <span class="s">}</span> 254 255 <span class="c"># Write fingerpritns and other data to appropriate output files...</span> 256 <span class="c">#</span> <a name="WriteDataToOutputFiles-"></a> 257 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span> 258 <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">$Molecule</span><span class="cm">,</span> <span class="i">$ExtendedConnectivityFingerprints</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">$NewFPFileIO</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 259 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 260 261 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="k">undef</span><span class="sc">;</span> 262 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span> || <span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span> 263 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 264 <span class="s">}</span> 265 266 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span> 267 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span> 268 269 <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">->GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 270 <span class="i">$NewFPSDFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span> 271 <span class="s">}</span> 272 273 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span> 274 <span class="k">my</span><span class="s">(</span><span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span> 275 276 <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 277 <span class="i">$NewFPTextFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="cm">,</span> <span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span> 278 <span class="s">}</span> 279 280 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span> 281 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span> 282 283 <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> 284 <span class="i">$NewFPFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="cm">,</span> <span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span> 285 <span class="s">}</span> 286 <span class="s">}</span> 287 288 <span class="c"># Generate approriate column labels for FPText output file...</span> 289 <span class="c">#</span> <a name="SetupFPTextFileCoulmnLabels-"></a> 290 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnLabels</span> <span class="s">{</span> 291 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 292 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span> 293 294 <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 295 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> 296 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span> 297 <span class="s">}</span> 298 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span> 299 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span> 300 <span class="s">}</span> 301 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> 302 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span> 303 <span class="s">}</span> 304 <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> 305 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span> 306 <span class="s">}</span> 307 <span class="c"># Add fingerprints label...</span> 308 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="sc">;</span> 309 310 <span class="k">return</span> \<span class="i">@ColLabels</span><span class="sc">;</span> 311 <span class="s">}</span> 312 313 <span class="c"># Generate column values FPText output file..</span> 314 <span class="c">#</span> <a name="SetupFPTextFileCoulmnValues-"></a> 315 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnValues</span> <span class="s">{</span> 316 <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> 317 <span class="k">my</span><span class="s">(</span><span class="i">@ColValues</span><span class="s">)</span><span class="sc">;</span> 318 319 <span class="i">@ColValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 320 <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> 321 <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 322 <span class="s">}</span> 323 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> 324 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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">$FileIndex</span>]}<span class="sc">;</span> 325 <span class="s">}</span> 326 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span> 327 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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">$FileIndex</span>]}<span class="sc">;</span> 328 <span class="s">}</span> 329 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> 330 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$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> 331 <span class="s">}</span> 332 333 <span class="k">return</span> \<span class="i">@ColValues</span><span class="sc">;</span> 334 <span class="s">}</span> 335 336 <span class="c"># Generate compound ID for FP and FPText output files..</span> 337 <span class="c">#</span> <a name="SetupCmpdIDForOutputFiles-"></a> 338 <span class="k">sub </span><span class="m">SetupCmpdIDForOutputFiles</span> <span class="s">{</span> 339 <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">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 340 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span> 341 342 <span class="i">$CmpdID</span> = <span class="q">''</span><span class="sc">;</span> 343 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolNameOrLabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span> 344 <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span> 345 <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> 346 <span class="i">$CmpdID</span> = <span class="i">$MolName</span> ? <span class="i">$MolName</span> <span class="co">:</span> <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span> 347 <span class="s">}</span> 348 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^LabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span> 349 <span class="i">$CmpdID</span> = <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span> 350 <span class="s">}</span> 351 <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> 352 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span> 353 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span> 354 <span class="i">$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> 355 <span class="s">}</span> 356 <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> 357 <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> 358 <span class="s">}</span> 359 <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span> 360 <span class="s">}</span> 361 362 <span class="c"># Generate fingerprints for molecule...</span> 363 <span class="c">#</span> <a name="GenerateMoleculeFingerprints-"></a> 364 <span class="k">sub </span><span class="m">GenerateMoleculeFingerprints</span> <span class="s">{</span> 365 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 366 <span class="k">my</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="s">)</span><span class="sc">;</span> 367 368 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span> 369 <span class="i">$Molecule</span><span class="i">->KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 370 <span class="s">}</span> 371 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">->DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 372 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 373 <span class="s">}</span> 374 <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> 375 <span class="i">$Molecule</span><span class="i">->DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 376 377 <span class="i">$ExtendedConnectivityFingerprints</span> = <span class="k">undef</span><span class="sc">;</span> 378 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(ExtendedConnectivity|ExtendedConnectivityCount)$/i</span> <span class="s">)</span> <span class="s">{</span> 379 <span class="i">$ExtendedConnectivityFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">'NeighborhoodRadius'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">NeighborhoodRadius</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> 380 <span class="s">}</span> 381 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> 382 <span class="i">$ExtendedConnectivityFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">'NeighborhoodRadius'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">NeighborhoodRadius</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'Size'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Size</span>}<span class="cm">,</span> <span class="q">'UsePerlCoreRandom'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span><span class="sc">;</span> 383 <span class="s">}</span> 384 <span class="k">else</span> <span class="s">{</span> 385 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits\n"</span><span class="sc">;</span> 386 <span class="s">}</span> 387 <span class="i">SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="s">)</span><span class="sc">;</span> 388 389 <span class="c"># Generate fingerprints...</span> 390 <span class="i">$ExtendedConnectivityFingerprints</span><span class="i">->GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 391 392 <span class="c"># Make sure fingerprints generation is successful...</span> 393 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ExtendedConnectivityFingerprints</span><span class="i">->IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 394 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 395 <span class="s">}</span> 396 397 <span class="k">return</span> <span class="i">$ExtendedConnectivityFingerprints</span><span class="sc">;</span> 398 <span class="s">}</span> 399 400 <span class="c"># Set atom identifier type to use for generating fingerprints...</span> 401 <span class="c">#</span> <a name="SetAtomIdentifierTypeValuesToUse-"></a> 402 <span class="k">sub </span><span class="m">SetAtomIdentifierTypeValuesToUse</span> <span class="s">{</span> 403 <span class="k">my</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 404 405 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 406 <span class="i">$ExtendedConnectivityFingerprints</span><span class="i">->SetAtomicInvariantsToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}}<span class="s">)</span><span class="sc">;</span> 407 <span class="s">}</span> 408 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 409 <span class="i">$ExtendedConnectivityFingerprints</span><span class="i">->SetFunctionalClassesToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span> 410 <span class="s">}</span> 411 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> 412 <span class="c"># Nothing to do for now...</span> 413 <span class="s">}</span> 414 <span class="k">else</span> <span class="s">{</span> 415 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span> 416 <span class="s">}</span> 417 <span class="s">}</span> 418 419 <span class="c"># Retrieve information about SD files...</span> 420 <span class="c">#</span> <a name="RetrieveSDFilesInfo-"></a> 421 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span> 422 <span class="k">my</span><span class="s">(</span><span class="i">$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">$CommonDataFieldsRef</span><span class="s">)</span><span class="sc">;</span> 423 424 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 425 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 426 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 427 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 428 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 429 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 430 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 431 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 432 433 <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> 434 <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> 435 436 <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> 437 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 438 439 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> 440 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 441 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 442 <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 443 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 444 445 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 446 <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> 447 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span> 448 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 449 <span class="s">}</span> 450 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 451 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span> 452 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 453 <span class="s">}</span> 454 455 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span> 456 <span class="c"># Make sure data field exists in SD file..</span> 457 <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> 458 459 <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 460 <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: $! \n"</span><span class="sc">;</span> 461 <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span> 462 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> 463 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span> 464 <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span> 465 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span> 466 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span> 467 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n"</span><span class="sc">;</span> 468 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 469 <span class="s">}</span> 470 <span class="s">}</span> 471 472 <span class="i">$AllDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span> 473 <span class="i">$CommonDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span> 474 <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span> 475 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span> 476 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $SDFile: $! \n"</span><span class="sc">;</span> 477 <span class="s">(</span><span class="i">$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> 478 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> 479 <span class="s">}</span> 480 481 <span class="c"># Setup output file names...</span> 482 <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">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> 483 <span class="s">(</span><span class="i">$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">$SDFile</span><span class="s">)</span><span class="sc">;</span> 484 485 <span class="i">$TextOutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span> 486 <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> 487 <span class="i">$TextOutFileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span> 488 <span class="s">}</span> 489 <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span> 490 <span class="i">$FPOutFileExt</span> = <span class="q">"fpf"</span><span class="sc">;</span> 491 492 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 493 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> 494 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> 495 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> 496 <span class="s">}</span> 497 <span class="k">else</span> <span class="s">{</span> 498 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> 499 <span class="s">}</span> 500 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> 501 <span class="s">}</span> 502 <span class="k">else</span> <span class="s">{</span> 503 <span class="i">$OutFileRoot</span> = <span class="q">"${FileName}ExtendedConnectivityFP"</span><span class="sc">;</span> 504 <span class="s">}</span> 505 506 <span class="i">$NewSDFileName</span> = <span class="q">"${OutFileRoot}.${SDOutFileExt}"</span><span class="sc">;</span> 507 <span class="i">$NewFPFileName</span> = <span class="q">"${OutFileRoot}.${FPOutFileExt}"</span><span class="sc">;</span> 508 <span class="i">$NewTextFileName</span> = <span class="q">"${OutFileRoot}.${TextOutFileExt}"</span><span class="sc">;</span> 509 510 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> 511 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span> 512 <span class="k">warn</span> <span class="q">"Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n"</span><span class="sc">;</span> 513 <span class="k">print</span> <span class="q">"Specify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span> 514 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 515 <span class="s">}</span> 516 <span class="s">}</span> 517 518 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span> 519 <span class="c"># Check SD and text outout files...</span> 520 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> 521 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span> 522 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n"</span><span class="sc">;</span> 523 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 524 <span class="s">}</span> 525 <span class="s">}</span> 526 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span> 527 <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> 528 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n"</span><span class="sc">;</span> 529 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 530 <span class="s">}</span> 531 <span class="s">}</span> 532 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span> 533 <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> 534 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n"</span><span class="sc">;</span> 535 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 536 <span class="s">}</span> 537 <span class="s">}</span> 538 <span class="s">}</span> 539 540 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> 541 542 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> 543 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span> 544 <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewFPFileName</span><span class="sc">;</span> 545 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span> 546 547 <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span> 548 <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span> 549 <span class="s">}</span> 550 <span class="s">}</span> 551 552 <span class="c"># Process option values...</span> <a name="ProcessOptions-"></a> 553 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> 554 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 555 556 <span class="i">ProcessAtomIdentifierTypeOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 557 558 <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span> 559 560 <span class="i">$OptionsInfo</span>{<span class="w">BitsOrder</span>} = <span class="i">$Options</span>{<span class="w">bitsorder</span>}<span class="sc">;</span> 561 <span class="i">$OptionsInfo</span>{<span class="w">BitStringFormat</span>} = <span class="i">$Options</span>{<span class="w">bitstringformat</span>}<span class="sc">;</span> 562 563 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span> 564 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span> 565 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span> 566 567 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span> 568 <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 569 570 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 571 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">''</span><span class="sc">;</span> 572 573 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span> 574 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span> 575 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span> 576 <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> 577 <span class="s">}</span> 578 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span> 579 <span class="s">}</span> 580 <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> 581 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>} ? <span class="i">$Options</span>{<span class="w">compoundid</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span> 582 <span class="s">}</span> 583 <span class="s">}</span> 584 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> 585 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span> 586 <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> 587 <span class="s">}</span> 588 <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span> 589 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span> 590 <span class="s">}</span> 591 592 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>} = <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} ? <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} <span class="co">:</span> <span class="q">'ExtendedConnectivityFingerprints'</span><span class="sc">;</span> 593 594 <span class="i">$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> 595 596 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 597 598 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> 599 600 <span class="i">$OptionsInfo</span>{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Options</span>{<span class="w">neighborhoodradius</span>}<span class="sc">;</span> 601 602 <span class="i">$OptionsInfo</span>{<span class="w">UsePerlCoreRandom</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">useperlcorerandom</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 603 604 <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span> 605 <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 606 <span class="i">$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> 607 <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 608 609 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="i">$Options</span>{<span class="w">outdelim</span>}<span class="sc">;</span> 610 <span class="i">$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> 611 612 <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> 613 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 614 615 <span class="k">my</span><span class="s">(</span><span class="i">$Size</span><span class="cm">,</span> <span class="i">$MinSize</span><span class="cm">,</span> <span class="i">$MaxSize</span><span class="s">)</span><span class="sc">;</span> 616 <span class="i">$MinSize</span> = <span class="n">32</span><span class="sc">;</span> 617 <span class="i">$MaxSize</span> = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span> 618 <span class="i">$Size</span> = <span class="i">$Options</span>{<span class="w">size</span>}<span class="sc">;</span> 619 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span> && <span class="i">$Size</span> >= <span class="i">$MinSize</span> && <span class="i">$Size</span> <= <span class="i">$MaxSize</span> && <span class="i">IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$Size</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 620 <span class="k">die</span> <span class="q">"Error: Invalid size value, $Size, for \"-s, --size\" option. Allowed values: power of 2, >= minimum size of $MinSize, and <= maximum size of $MaxSize.\n"</span><span class="sc">;</span> 621 <span class="s">}</span> 622 <span class="i">$OptionsInfo</span>{<span class="w">Size</span>} = <span class="i">$Size</span><span class="sc">;</span> 623 624 <span class="c"># Setup default vector string format...</span> 625 <span class="c">#</span> 626 <span class="k">my</span><span class="s">(</span><span class="i">$VectorStringFormat</span><span class="s">)</span><span class="sc">;</span> 627 <span class="i">$VectorStringFormat</span> = <span class="q">''</span><span class="sc">;</span> 628 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="s">)</span> <span class="s">{</span> 629 <span class="i">$VectorStringFormat</span> = <span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="sc">;</span> 630 <span class="s">}</span> 631 <span class="k">else</span> <span class="s">{</span> 632 <span class="i">$VectorStringFormat</span> = <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^ExtendedConnectivity$/</span><span class="s">)</span> ? <span class="q">"ValuesString"</span> <span class="co">:</span> <span class="q">"IDsAndValuesString"</span><span class="sc">;</span> 633 <span class="s">}</span> 634 <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>} = <span class="i">$VectorStringFormat</span><span class="sc">;</span> 635 <span class="s">}</span> 636 637 <span class="c"># Process atom identifier type and related options...</span> 638 <span class="c">#</span> <a name="ProcessAtomIdentifierTypeOptions-"></a> 639 <span class="k">sub </span><span class="m">ProcessAtomIdentifierTypeOptions</span> <span class="s">{</span> 640 641 <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} = <span class="i">$Options</span>{<span class="w">atomidentifiertype</span>}<span class="sc">;</span> 642 643 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 644 <span class="i">ProcessAtomicInvariantsToUseOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 645 <span class="s">}</span> 646 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 647 <span class="i">ProcessFunctionalClassesToUse</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 648 <span class="s">}</span> 649 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> 650 <span class="c"># Nothing to do for now...</span> 651 <span class="s">}</span> 652 <span class="k">else</span> <span class="s">{</span> 653 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span> 654 <span class="s">}</span> 655 <span class="s">}</span> 656 657 <span class="c"># Process specified atomic invariants to use...</span> 658 <span class="c">#</span> <a name="ProcessAtomicInvariantsToUseOption-"></a> 659 <span class="k">sub </span><span class="m">ProcessAtomicInvariantsToUseOption</span> <span class="s">{</span> 660 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomSymbolSpecified</span><span class="cm">,</span> <span class="i">@AtomicInvariantsWords</span><span class="s">)</span><span class="sc">;</span> 661 662 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 663 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 664 <span class="k">die</span> <span class="q">"Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n"</span><span class="sc">;</span> 665 <span class="s">}</span> 666 <span class="i">$AtomSymbolSpecified</span> = <span class="n">0</span><span class="sc">;</span> 667 <span class="i">@AtomicInvariantsWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>}<span class="sc">;</span> 668 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsWords</span><span class="s">)</span> <span class="s">{</span> 669 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 670 <span class="k">die</span> <span class="q">"Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n "</span><span class="sc">;</span> 671 <span class="s">}</span> 672 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AS|AtomSymbol)$/i</span><span class="s">)</span> <span class="s">{</span> 673 <span class="i">$AtomSymbolSpecified</span> = <span class="n">1</span><span class="sc">;</span> 674 <span class="s">}</span> 675 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> 676 <span class="s">}</span> 677 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSymbolSpecified</span><span class="s">)</span> <span class="s">{</span> 678 <span class="k">die</span> <span class="q">"Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n "</span><span class="sc">;</span> 679 <span class="s">}</span> 680 <span class="s">}</span> 681 682 <span class="c"># Process specified functional classes invariants to use...</span> 683 <span class="c">#</span> <a name="ProcessFunctionalClassesToUse-"></a> 684 <span class="k">sub </span><span class="m">ProcessFunctionalClassesToUse</span> <span class="s">{</span> 685 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUseWords</span><span class="s">)</span><span class="sc">;</span> 686 687 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 688 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">functionalclassestouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 689 <span class="k">die</span> <span class="q">"Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n"</span><span class="sc">;</span> 690 <span class="s">}</span> 691 <span class="i">@FunctionalClassesToUseWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">functionalclassestouse</span>}<span class="sc">;</span> 692 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesToUseWords</span><span class="s">)</span> <span class="s">{</span> 693 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 694 <span class="k">die</span> <span class="q">"Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n "</span><span class="sc">;</span> 695 <span class="s">}</span> 696 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="sc">;</span> 697 <span class="s">}</span> 698 <span class="s">}</span> 699 700 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> <a name="SetupScriptUsage-"></a> 701 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> 702 703 <span class="c"># Retrieve all the options...</span> 704 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 705 706 <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span> 707 708 <span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} = <span class="q">'AtomicInvariantsAtomTypes'</span><span class="sc">;</span> 709 <span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>} = <span class="q">'AS,X,BO,H,FC,MN'</span><span class="sc">;</span> 710 <span class="i">$Options</span>{<span class="w">functionalclassestouse</span>} = <span class="q">'HBD,HBA,PI,NI,Ar,Hal'</span><span class="sc">;</span> 711 712 <span class="i">$Options</span>{<span class="w">bitsorder</span>} = <span class="q">'Ascending'</span><span class="sc">;</span> 713 <span class="i">$Options</span>{<span class="w">bitstringformat</span>} = <span class="q">'HexadecimalString'</span><span class="sc">;</span> 714 715 <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span> 716 <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span> 717 <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span> 718 719 <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">'Yes'</span><span class="sc">;</span> 720 721 <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">'Yes'</span><span class="sc">;</span> 722 723 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'ExtendedConnectivity'</span><span class="sc">;</span> 724 725 <span class="i">$Options</span>{<span class="w">neighborhoodradius</span>} = <span class="n">2</span><span class="sc">;</span> 726 727 <span class="i">$Options</span>{<span class="w">useperlcorerandom</span>} = <span class="q">'yes'</span><span class="sc">;</span> 728 729 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">'text'</span><span class="sc">;</span> 730 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> 731 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span> 732 733 <span class="i">$Options</span>{<span class="w">size</span>} = <span class="n">1024</span><span class="sc">;</span> 734 735 <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} = <span class="q">''</span><span class="sc">;</span> 736 737 <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">"atomidentifiertype|a=s"</span><span class="cm">,</span> <span class="q">"atomicinvariantstouse=s"</span><span class="cm">,</span> <span class="q">"functionalclassestouse=s"</span><span class="cm">,</span> <span class="q">"bitsorder=s"</span><span class="cm">,</span> <span class="q">"bitstringformat|b=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">"fingerprintslabel=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"keeplargestcomponent|k=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"neighborhoodradius|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">"size|s=i"</span><span class="cm">,</span> <span class="q">"useperlcorerandom=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> 738 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> 739 <span class="s">}</span> 740 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 741 <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> 742 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> 743 <span class="s">}</span> 744 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span> 745 <span class="s">}</span> 746 <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 747 <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> 748 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"</span><span class="sc">;</span> 749 <span class="s">}</span> 750 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> 751 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span> 752 <span class="s">}</span> 753 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">bitsorder</span>} !~ <span class="q">/^(Ascending|Descending)$/i</span><span class="s">)</span> <span class="s">{</span> 754 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{bitsorder}, for option \"--BitsOrder\" is not valid. Allowed values: Ascending or Descending\n"</span><span class="sc">;</span> 755 <span class="s">}</span> 756 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">bitstringformat</span>} !~ <span class="q">/^(BinaryString|HexadecimalString)$/i</span><span class="s">)</span> <span class="s">{</span> 757 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{bitstringformat}, for option \"-b, --bitstringformat\" is not valid. Allowed values: BinaryString or HexadecimalString\n"</span><span class="sc">;</span> 758 <span class="s">}</span> 759 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span> 760 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span> 761 <span class="s">}</span> 762 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span> 763 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"</span><span class="sc">;</span> 764 <span class="s">}</span> 765 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 766 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 767 <span class="s">}</span> 768 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 769 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 770 <span class="s">}</span> 771 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(ExtendedConnectivity|ExtendedConnectivityCount|ExtendedConnectivityBits)$/i</span><span class="s">)</span> <span class="s">{</span> 772 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: ExtendedConnectivity, ExtendedConnecticityCount, or ExtendedConnectivityBits\n"</span><span class="sc">;</span> 773 <span class="s">}</span> 774 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">neighborhoodradius</span>}<span class="s">)</span> && <span class="s">(</span><span class="i">$Options</span>{<span class="w">neighborhoodradius</span>} >= <span class="n">0</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 775 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{neighborhoodradius}, for option \"-n, --NeighborhoodRadius\" is not valid. Allowed values: >= 0 \n"</span><span class="sc">;</span> 776 <span class="s">}</span> 777 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|FP|text|all)$/i</span><span class="s">)</span> <span class="s">{</span> 778 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n"</span><span class="sc">;</span> 779 <span class="s">}</span> 780 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span> 781 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span> 782 <span class="s">}</span> 783 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 784 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 785 <span class="s">}</span> 786 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">size</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, $Options{size}, for option \"-s, --size\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> 788 <span class="s">}</span> 789 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">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> 790 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"</span><span class="sc">;</span> 791 <span class="s">}</span> 792 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">useperlcorerandom</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 793 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{useperlcorerandom}, for option \"--UsePerlCoreRandom\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 794 <span class="s">}</span> 795 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">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> 796 <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> 797 <span class="s">}</span> 798 <span class="s">}</span> 799 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>