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<html> <head> <title>MayaChemTools:Code:CalculatePhysicochemicalProperties.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: CalculatePhysicochemicalProperties.pl,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span> 5 <span class="c"># $Revision: 1.20 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$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">Molecule</span><span class="sc">;</span> 40 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> 41 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> 42 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptorsGenerator</span><span class="sc">;</span> 43 44 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span> 45 46 <span class="c"># Autoflush STDOUT</span> 47 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> 48 49 <span class="c"># Starting message...</span> 50 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> 51 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> 52 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 53 54 <span class="c"># Get the options and setup script...</span> 55 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 56 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 57 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span> 58 <span class="s">}</span> 59 60 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span> 61 <span class="i">@SDFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"sdf sd"</span><span class="s">)</span><span class="sc">;</span> 62 63 <span class="c"># Process options...</span> 64 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> 65 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> 66 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 67 68 <span class="c"># Setup information about input files...</span> 69 <span class="k">print</span> <span class="q">"Checking input SD file(s)...\n"</span><span class="sc">;</span> 70 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span> 71 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 72 73 <span class="c"># Process input files..</span> 74 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 75 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 76 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span> 77 <span class="s">}</span> 78 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span> 79 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> 80 <span class="k">print</span> <span class="q">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span> 81 <span class="i">CalculatePhysicochemicalProperties</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 82 <span class="s">}</span> 83 <span class="s">}</span> 84 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> 85 86 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 87 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span> 88 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 89 90 <span class="c">###############################################################################</span> 91 92 <span class="c"># Calculate physicochemical properties for a SD file...</span> 93 <span class="c">#</span> <a name="CalculatePhysicochemicalProperties-"></a> 94 <span class="k">sub </span><span class="m">CalculatePhysicochemicalProperties</span> <span class="s">{</span> 95 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 96 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$MoleculeFileIO</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$MolecularDescriptorsGenerator</span><span class="cm">,</span> <span class="i">$PhysicochemicalPropertiesDataRef</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span> 97 98 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> 99 100 <span class="c"># Setup output files...</span> 101 <span class="i">$NewSDFileRef</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$NewTextFileRef</span> = <span class="q">''</span><span class="sc">;</span> 102 <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">SetupAndOpenOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 103 104 <span class="c"># Setup molecular descriptor generator to calculate property values for specifed</span> 105 <span class="c"># property names...</span> 106 <span class="i">$MolecularDescriptorsGenerator</span> = <span class="i">SetupMolecularDescriptorsGenerator</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 107 108 <span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">4</span><span class="sc">;</span> 109 110 <span class="i">$MoleculeFileIO</span> = <span class="w">new</span> <span class="i">MoleculeFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span> 111 <span class="i">$MoleculeFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 112 113 <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Molecule</span> = <span class="i">$MoleculeFileIO</span><span class="i">->ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 114 <span class="i">$CmpdCount</span>++<span class="sc">;</span> 115 116 <span class="c"># Filter compound data before calculating physiochemical properties...</span> 117 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Filter</span>}<span class="s">)</span> <span class="s">{</span> 118 <span class="k">if</span> <span class="s">(</span><span class="i">CheckAndFilterCompound</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 119 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span> 120 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span> 121 <span class="s">}</span> 122 <span class="s">}</span> 123 124 <span class="c"># Calculate properties...</span> 125 <span class="i">$PhysicochemicalPropertiesDataRef</span> = <span class="i">CalculateMoleculeProperties</span><span class="s">(</span><span class="i">$MolecularDescriptorsGenerator</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 126 127 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$PhysicochemicalPropertiesDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 128 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span> 129 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'PropertiesCalculationFailed'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 130 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span> 131 <span class="s">}</span> 132 133 <span class="c"># Calculate any rule violations...</span> 134 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>} && <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span> 135 <span class="i">$RuleOf5ViolationsCount</span>++<span class="sc">;</span> 136 <span class="s">}</span> 137 138 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>} && <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span> 139 <span class="i">$RuleOf3ViolationsCount</span>++<span class="sc">;</span> 140 <span class="s">}</span> 141 142 <span class="c"># Write out calculate properties...</span> 143 <span class="i">WriteDataToOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$PhysicochemicalPropertiesDataRef</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span> 144 <span class="s">}</span> 145 <span class="i">$MoleculeFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 146 147 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} && <span class="i">$NewSDFileRef</span><span class="s">)</span> <span class="s">{</span> 148 <span class="k">close</span> <span class="i">$NewSDFileRef</span><span class="sc">;</span> 149 <span class="s">}</span> 150 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="i">$NewTextFileRef</span><span class="s">)</span> <span class="s">{</span> 151 <span class="k">close</span> <span class="i">$NewTextFileRef</span><span class="sc">;</span> 152 <span class="s">}</span> 153 154 <span class="i">WriteCalculationSummaryStatistics</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</span><span class="s">)</span><span class="sc">;</span> 155 <span class="s">}</span> 156 157 <span class="c"># Process compound being ignored due to problems in physicochemical properties calculation...</span> 158 <span class="c">#</span> <a name="ProcessIgnoredCompound-"></a> 159 <span class="k">sub </span><span class="m">ProcessIgnoredCompound</span> <span class="s">{</span> 160 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 161 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 162 163 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 164 <span class="i">$CmpdID</span> = <span class="i">SetupCmpdIDForTextFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 165 166 <span class="j">MODE:</span> <span class="s">{</span> 167 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNonElementalData$/i</span><span class="s">)</span> <span class="s">{</span> 168 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n"</span><span class="sc">;</span> 169 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span> 170 <span class="s">}</span> 171 172 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNoElementalData$/i</span><span class="s">)</span> <span class="s">{</span> 173 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n"</span><span class="sc">;</span> 174 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span> 175 <span class="s">}</span> 176 177 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^PropertiesCalculationFailed$/i</span><span class="s">)</span> <span class="s">{</span> 178 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Physicochemical properties calculation didn't succeed...\n\n"</span><span class="sc">;</span> 179 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span> 180 <span class="s">}</span> 181 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Physicochemical properties calculation didn't succeed...\n\n"</span><span class="sc">;</span> 182 <span class="s">}</span> 183 <span class="s">}</span> 184 185 <span class="c"># Check and filter compounds....</span> 186 <span class="c">#</span> <a name="CheckAndFilterCompound-"></a> 187 <span class="k">sub </span><span class="m">CheckAndFilterCompound</span> <span class="s">{</span> 188 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 189 <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span> 190 191 <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfElementsAndNonElements</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 192 193 <span class="k">if</span> <span class="s">(</span><span class="i">$NonElementCount</span><span class="s">)</span> <span class="s">{</span> 194 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'ContainsNonElementalData'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 195 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 196 <span class="s">}</span> 197 198 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ElementCount</span><span class="s">)</span> <span class="s">{</span> 199 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'ContainsNoElementalData'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 200 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 201 <span class="s">}</span> 202 203 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 204 <span class="s">}</span> 205 206 <span class="c"># Write out compounds physicochemical properties calculation summary statistics...</span> 207 <span class="c">#</span> <a name="WriteCalculationSummaryStatistics-"></a> 208 <span class="k">sub </span><span class="m">WriteCalculationSummaryStatistics</span> <span class="s">{</span> 209 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$RuleOf5ViolationsCount</span><span class="cm">,</span> <span class="i">$RuleOf3ViolationsCount</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 210 <span class="k">my</span><span class="s">(</span><span class="i">$ProcessedCmpdCount</span><span class="s">)</span><span class="sc">;</span> 211 212 <span class="i">$ProcessedCmpdCount</span> = <span class="i">$CmpdCount</span> - <span class="i">$IgnoredCmpdCount</span><span class="sc">;</span> 213 214 <span class="k">print</span> <span class="q">"\nNumber of compounds: $CmpdCount\n"</span><span class="sc">;</span> 215 <span class="k">print</span> <span class="q">"Number of compounds processed successfully during physicochemical properties calculation: $ProcessedCmpdCount\n"</span><span class="sc">;</span> 216 <span class="k">print</span> <span class="q">"Number of compounds ignored during physicochemical properties calculation: $IgnoredCmpdCount\n"</span><span class="sc">;</span> 217 218 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span> 219 <span class="k">print</span> <span class="q">"Number of compounds with one or more RuleOf5 violations: $RuleOf5ViolationsCount\n"</span><span class="sc">;</span> 220 <span class="s">}</span> 221 222 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span> 223 <span class="k">print</span> <span class="q">"Number of compounds with one or more RuleOf3 violations: $RuleOf3ViolationsCount\n"</span><span class="sc">;</span> 224 <span class="s">}</span> 225 226 <span class="s">}</span> 227 228 <span class="c"># Open output files...</span> 229 <span class="c">#</span> <a name="SetupAndOpenOutputFiles-"></a> 230 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span> 231 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 232 <span class="k">my</span><span class="s">(</span><span class="i">$NewSDFile</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span> 233 234 <span class="i">$NewSDFileRef</span> = <span class="q">''</span><span class="sc">;</span> 235 <span class="i">$NewTextFileRef</span> = <span class="q">''</span><span class="sc">;</span> 236 237 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> 238 <span class="i">$NewSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 239 <span class="k">print</span> <span class="q">"Generating SD file $NewSDFile...\n"</span><span class="sc">;</span> 240 <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">">$NewSDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewSDFile: $! \n"</span><span class="sc">;</span> 241 <span class="i">$NewSDFileRef</span> = \<span class="i">*NEWSDFILE</span><span class="sc">;</span> 242 <span class="s">}</span> 243 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span> 244 <span class="i">$NewTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 245 <span class="k">print</span> <span class="q">"Generating text file $NewTextFile...\n"</span><span class="sc">;</span> 246 <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">">$NewTextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewTextFile: $! \n"</span><span class="sc">;</span> 247 <span class="i">WriteTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> \<span class="i">*NEWTEXTFILE</span><span class="s">)</span><span class="sc">;</span> 248 <span class="i">$NewTextFileRef</span> = \<span class="i">*NEWTEXTFILE</span><span class="sc">;</span> 249 <span class="s">}</span> 250 <span class="k">return</span> <span class="s">(</span><span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span><span class="sc">;</span> 251 <span class="s">}</span> 252 253 <span class="c"># Write calculated physicochemical properties and other data to appropriate output files...</span> 254 <span class="c">#</span> <a name="WriteDataToOutputFiles-"></a> 255 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span> 256 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$PhysicochemicalPropertiesDataRef</span><span class="cm">,</span> <span class="i">$NewSDFileRef</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 257 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="s">)</span><span class="sc">;</span> 258 259 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> 260 <span class="c"># Retrieve input compound string used to create molecule and write it out</span> 261 <span class="c"># without last line containing a delimiter...</span> 262 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span> 263 <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">->GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 264 <span class="i">$CmpdString</span> =~ <span class="q">s/\$\$\$\$$//</span><span class="sc">;</span> 265 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"$CmpdString"</span><span class="sc">;</span> 266 267 <span class="c"># Write out calculated physicochemical properties data...</span> 268 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="s">)</span> <span class="s">{</span> 269 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="i">$PropertyName</span>}<span class="sc">;</span> 270 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <$PropertyName>\n$PropertyValue\n\n"</span><span class="sc">;</span> 271 <span class="s">}</span> 272 273 <span class="c"># Write out RuleOf5 violations for molecule....</span> 274 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span> 275 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf5Violations</span>}<span class="sc">;</span> 276 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <RuleOf5Violations>\n$PropertyValue\n\n"</span><span class="sc">;</span> 277 <span class="s">}</span> 278 279 <span class="c"># Write out RuleOf3 violations for molecule....</span> 280 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span> 281 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf3Violations</span>}<span class="sc">;</span> 282 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"> <RuleOf3Violations>\n$PropertyValue\n\n"</span><span class="sc">;</span> 283 <span class="s">}</span> 284 285 <span class="c"># Write out delimiter...</span> 286 <span class="k">print</span> <span class="i">$NewSDFileRef</span> <span class="q">"\$\$\$\$\n"</span><span class="sc">;</span> 287 <span class="s">}</span> 288 289 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span> 290 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="cm">,</span> <span class="i">$DataFieldLabel</span><span class="cm">,</span> <span class="i">$DataFieldValue</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span><span class="s">)</span><span class="sc">;</span> 291 292 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 293 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 294 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span> 295 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">SetupCmpdIDForTextFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span> 296 <span class="s">}</span> 297 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> 298 <span class="i">@LineWords</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span> 299 <span class="s">}</span> 300 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span> 301 <span class="i">@LineWords</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span> 302 <span class="s">}</span> 303 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> 304 <span class="i">@LineWords</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span> 305 <span class="s">}</span> 306 307 <span class="c"># Append calculated physicochemical properties data...</span> 308 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="s">)</span> <span class="s">{</span> 309 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="i">$PropertyName</span>}<span class="sc">;</span> 310 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span> 311 <span class="s">}</span> 312 313 <span class="c"># Write out RuleOf5 violations for molecule....</span> 314 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span> 315 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf5Violations</span>}<span class="sc">;</span> 316 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span> 317 <span class="s">}</span> 318 319 <span class="c"># Write out RuleOf3 violations for molecule....</span> 320 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span> 321 <span class="i">$PropertyValue</span> = <span class="i">$PhysicochemicalPropertiesDataRef</span>->{<span class="w">RuleOf3Violations</span>}<span class="sc">;</span> 322 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span> 323 <span class="s">}</span> 324 325 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> 326 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span> 327 <span class="s">}</span> 328 <span class="s">}</span> 329 330 <span class="c"># Write out approriate column labels to text file...</span> <a name="WriteTextFileCoulmnLabels-"></a> 331 <span class="k">sub </span><span class="m">WriteTextFileCoulmnLabels</span> <span class="s">{</span> 332 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 333 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span> 334 335 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 336 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> 337 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span> 338 <span class="s">}</span> 339 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span> 340 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span> 341 <span class="s">}</span> 342 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> 343 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span> 344 <span class="s">}</span> 345 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span> 346 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span> 347 <span class="s">}</span> 348 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span><span class="sc">;</span> 349 350 <span class="c"># Append physicochemical properties column labels...</span> 351 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="sc">;</span> 352 353 <span class="c"># Write out RuleOf5 violations label...</span> 354 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span> 355 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">'RuleOf5Violations'</span><span class="sc">;</span> 356 <span class="s">}</span> 357 358 <span class="c"># Write out RuleOf3 violations label...</span> 359 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span> 360 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">'RuleOf3Violations'</span><span class="sc">;</span> 361 <span class="s">}</span> 362 363 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> 364 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span> 365 <span class="s">}</span> 366 367 <span class="c"># Generate compound ID for text files..</span> 368 <span class="c">#</span> <a name="SetupCmpdIDForTextFiles-"></a> 369 <span class="k">sub </span><span class="m">SetupCmpdIDForTextFiles</span> <span class="s">{</span> 370 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 371 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span> 372 373 <span class="i">$CmpdID</span> = <span class="q">''</span><span class="sc">;</span> 374 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolNameOrLabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span> 375 <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span> 376 <span class="i">$MolName</span> = <span class="i">$Molecule</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 377 <span class="i">$CmpdID</span> = <span class="i">$MolName</span> ? <span class="i">$MolName</span> <span class="co">:</span> <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span> 378 <span class="s">}</span> 379 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^LabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span> 380 <span class="i">$CmpdID</span> = <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span> 381 <span class="s">}</span> 382 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span> 383 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span> 384 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span> 385 <span class="i">$CmpdID</span> = <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$SpecifiedDataField</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$SpecifiedDataField</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> 386 <span class="s">}</span> 387 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolName$/i</span><span class="s">)</span> <span class="s">{</span> 388 <span class="i">$CmpdID</span> = <span class="i">$Molecule</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 389 <span class="s">}</span> 390 <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span> 391 <span class="s">}</span> 392 393 <span class="c"># Calculate physicochemical properties for molecule...</span> 394 <span class="c">#</span> <a name="CalculateMoleculeProperties-"></a> 395 <span class="k">sub </span><span class="m">CalculateMoleculeProperties</span> <span class="s">{</span> 396 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularDescriptorsGenerator</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 397 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="cm">,</span> <span class="i">$MolecularDescriptorsObject</span><span class="cm">,</span> <span class="i">%CalculatedPhysicochemicalProperties</span><span class="s">)</span><span class="sc">;</span> 398 399 <span class="i">%CalculatedPhysicochemicalProperties</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 400 401 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span> 402 <span class="i">$Molecule</span><span class="i">->KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 403 <span class="s">}</span> 404 405 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">->DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 406 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 407 <span class="s">}</span> 408 <span class="i">$Molecule</span><span class="i">->SetAromaticityModel</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>}<span class="s">)</span><span class="sc">;</span> 409 <span class="i">$Molecule</span><span class="i">->DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 410 411 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AddHydrogens</span>}<span class="s">)</span> <span class="s">{</span> 412 <span class="i">$Molecule</span><span class="i">->AddHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 413 <span class="s">}</span> 414 415 <span class="c"># Calculate physicochemical properties...</span> 416 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetMolecule</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 417 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 418 419 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MolecularDescriptorsGenerator</span><span class="i">->IsDescriptorsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 420 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 421 <span class="s">}</span> 422 423 <span class="i">%CalculatedPhysicochemicalProperties</span> = <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 424 425 <span class="c"># Count RuleOf3 violations...</span> 426 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>}<span class="s">)</span> <span class="s">{</span> 427 <span class="i">CalculateRuleViolationsCount</span><span class="s">(</span><span class="q">'RuleOf3Violations'</span><span class="cm">,</span> \<span class="i">%CalculatedPhysicochemicalProperties</span><span class="s">)</span><span class="sc">;</span> 428 <span class="s">}</span> 429 430 <span class="c"># Count RuleOf5 violations...</span> 431 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>}<span class="s">)</span> <span class="s">{</span> 432 <span class="i">CalculateRuleViolationsCount</span><span class="s">(</span><span class="q">'RuleOf5Violations'</span><span class="cm">,</span> \<span class="i">%CalculatedPhysicochemicalProperties</span><span class="s">)</span><span class="sc">;</span> 433 <span class="s">}</span> 434 435 <span class="k">return</span> \<span class="i">%CalculatedPhysicochemicalProperties</span><span class="sc">;</span> 436 <span class="s">}</span> 437 438 <span class="c"># Setup molecular descriptor generator to calculate property values for specifed</span> 439 <span class="c"># property names...</span> 440 <span class="c">#</span> <a name="SetupMolecularDescriptorsGenerator-"></a> 441 <span class="k">sub </span><span class="m">SetupMolecularDescriptorsGenerator</span> <span class="s">{</span> 442 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$MolecularDescriptorsGenerator</span><span class="s">)</span><span class="sc">;</span> 443 444 <span class="i">$MolecularDescriptorsGenerator</span> = <span class="w">new</span> <span class="i">MolecularDescriptors::MolecularDescriptorsGenerator</span><span class="s">(</span><span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Specify'</span><span class="cm">,</span> <span class="q">'DescriptorNames'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}}<span class="s">)</span><span class="sc">;</span> 445 446 <span class="c"># Setup molecular desciptor calculation parameters...</span> 447 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'MolecularWeight'</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'ExactMass'</span><span class="s">)</span>}<span class="s">)</span> <span class="s">)</span> <span class="s">{</span> 448 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetDescriptorClassParameters</span><span class="s">(</span><span class="q">'DescriptorClassName'</span> <span class="cm">=></span> <span class="q">'WeightAndMassDescriptors'</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">PrecisionParametersMap</span>}}<span class="s">)</span><span class="sc">;</span> 449 <span class="s">}</span> 450 451 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'RotatableBonds'</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 452 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetDescriptorClassParameters</span><span class="s">(</span><span class="q">'DescriptorClassName'</span> <span class="cm">=></span> <span class="q">'RotatableBondsDescriptors'</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RotatableBondsParametersMap</span>}}<span class="s">)</span><span class="sc">;</span> 453 <span class="s">}</span> 454 455 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'HydrogenBondDonors'</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'HydrogenBondAcceptors'</span><span class="s">)</span>}<span class="s">)</span> <span class="s">)</span> <span class="s">{</span> 456 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetDescriptorClassParameters</span><span class="s">(</span><span class="q">'DescriptorClassName'</span> <span class="cm">=></span> <span class="q">'HydrogenBondsDescriptors'</span><span class="cm">,</span> <span class="q">'HydrogenBondsType'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">HydrogenBonds</span>}<span class="s">)</span><span class="sc">;</span> 457 <span class="s">}</span> 458 459 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'TPSA'</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 460 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetDescriptorClassParameters</span><span class="s">(</span><span class="q">'DescriptorClassName'</span> <span class="cm">=></span> <span class="q">'TPSADescriptors'</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">TPSAParametersMap</span>}}<span class="s">)</span><span class="sc">;</span> 461 <span class="s">}</span> 462 463 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="q">'MolecularComplexity'</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 464 <span class="i">$MolecularDescriptorsGenerator</span><span class="i">->SetDescriptorClassParameters</span><span class="s">(</span><span class="q">'DescriptorClassName'</span> <span class="cm">=></span> <span class="q">'MolecularComplexityDescriptors'</span><span class="cm">,</span> <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}}<span class="s">)</span><span class="sc">;</span> 465 <span class="s">}</span> 466 467 <span class="k">return</span> <span class="i">$MolecularDescriptorsGenerator</span><span class="sc">;</span> 468 <span class="s">}</span> 469 470 <span class="c"># Calculate RuleOf3 or RuleOf5 violations count...</span> 471 <span class="c">#</span> <a name="CalculateRuleViolationsCount-"></a> 472 <span class="k">sub </span><span class="m">CalculateRuleViolationsCount</span> <span class="s">{</span> 473 <span class="k">my</span><span class="s">(</span><span class="i">$RuleViolationsType</span><span class="cm">,</span> <span class="i">$CalculatedPropertiesMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 474 <span class="k">my</span><span class="s">(</span><span class="i">$RuleViolationsCount</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="s">)</span><span class="sc">;</span> 475 476 <span class="i">$RuleViolationsCount</span> = <span class="n">0</span><span class="sc">;</span> 477 478 <span class="j">RULEVIOLATIONSTYPE:</span> <span class="s">{</span> 479 <span class="k">if</span> <span class="s">(</span><span class="i">$RuleViolationsType</span> =~ <span class="q">/^RuleOf3Violations$/i</span><span class="s">)</span> <span class="s">{</span> 480 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span> 481 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculatedPropertiesMapRef</span>->{<span class="i">$PropertyName</span>} > <span class="i">$OptionsInfo</span>{<span class="w">RuleOf3MaxPropertyValuesMap</span>}{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span> 482 <span class="i">$RuleViolationsCount</span>++<span class="sc">;</span> 483 <span class="s">}</span> 484 <span class="s">}</span> 485 <span class="k">last</span> <span class="j">RULEVIOLATIONSTYPE</span><span class="sc">;</span> 486 <span class="s">}</span> 487 488 <span class="k">if</span> <span class="s">(</span><span class="i">$RuleViolationsType</span> =~ <span class="q">/^RuleOf5Violations$/i</span><span class="s">)</span> <span class="s">{</span> 489 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span> 490 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculatedPropertiesMapRef</span>->{<span class="i">$PropertyName</span>} > <span class="i">$OptionsInfo</span>{<span class="w">RuleOf5MaxPropertyValuesMap</span>}{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span> 491 <span class="i">$RuleViolationsCount</span>++<span class="sc">;</span> 492 <span class="s">}</span> 493 <span class="s">}</span> 494 <span class="k">last</span> <span class="j">RULEVIOLATIONSTYPE</span><span class="sc">;</span> 495 <span class="s">}</span> 496 497 <span class="k">die</span> <span class="q">"Warning: Unknown rule violation type: $RuleViolationsType..."</span><span class="sc">;</span> 498 <span class="s">}</span> 499 500 <span class="c"># Set rule violation count...</span> 501 <span class="i">$CalculatedPropertiesMapRef</span>->{<span class="i">$RuleViolationsType</span>} = <span class="i">$RuleViolationsCount</span><span class="sc">;</span> 502 503 <span class="s">}</span> 504 505 <span class="c"># Retrieve information about SD files...</span> 506 <span class="c">#</span> <a name="RetrieveSDFilesInfo-"></a> 507 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span> 508 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$TextOutFileExt</span><span class="cm">,</span> <span class="i">$SDOutFileExt</span><span class="cm">,</span> <span class="i">$NewSDFileName</span><span class="cm">,</span> <span class="i">$NewTextFileName</span><span class="cm">,</span> <span class="i">$CheckDataField</span><span class="cm">,</span> <span class="i">$CollectDataFields</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span><span class="sc">;</span> 509 510 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 511 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 512 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 513 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 514 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 515 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 516 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 517 518 <span class="i">$CheckDataField</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 519 <span class="i">$CollectDataFields</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^(All|Common)$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 520 521 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span> 522 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 523 524 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> 525 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 526 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 527 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 528 529 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 530 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 531 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span> 532 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 533 <span class="s">}</span> 534 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 535 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span> 536 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 537 <span class="s">}</span> 538 539 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span> 540 <span class="c"># Make sure data field exists in SD file..</span> 541 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$SpecifiedDataField</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldValues</span><span class="s">)</span><span class="sc">;</span> 542 543 <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 544 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $SDFile: $! \n"</span><span class="sc">;</span> 545 <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span> 546 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> 547 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span> 548 <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span> 549 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span> 550 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span> 551 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n"</span><span class="sc">;</span> 552 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 553 <span class="s">}</span> 554 <span class="s">}</span> 555 556 <span class="i">$AllDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span> 557 <span class="i">$CommonDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span> 558 <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span> 559 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span> 560 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $SDFile: $! \n"</span><span class="sc">;</span> 561 <span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span> = <span class="i">GetAllAndCommonCmpdDataHeaderLabels</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span> 562 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> 563 <span class="s">}</span> 564 565 <span class="c"># Setup output file names...</span> 566 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> 567 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span> 568 569 <span class="i">$TextOutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span> 570 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span> 571 <span class="i">$TextOutFileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span> 572 <span class="s">}</span> 573 <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span> 574 575 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 576 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> 577 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> 578 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> 579 <span class="s">}</span> 580 <span class="k">else</span> <span class="s">{</span> 581 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> 582 <span class="s">}</span> 583 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> 584 <span class="s">}</span> 585 <span class="k">else</span> <span class="s">{</span> 586 <span class="i">$OutFileRoot</span> = <span class="q">"${FileName}PhysicochemicalProperties"</span><span class="sc">;</span> 587 <span class="s">}</span> 588 589 <span class="i">$NewSDFileName</span> = <span class="q">"${OutFileRoot}.${SDOutFileExt}"</span><span class="sc">;</span> 590 <span class="i">$NewTextFileName</span> = <span class="q">"${OutFileRoot}.${TextOutFileExt}"</span><span class="sc">;</span> 591 592 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> 593 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span> 594 <span class="k">warn</span> <span class="q">"Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n"</span><span class="sc">;</span> 595 <span class="k">print</span> <span class="q">"Specify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span> 596 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 597 <span class="s">}</span> 598 <span class="s">}</span> 599 600 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span> 601 <span class="c"># Check SD and text outout files...</span> 602 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span> 603 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span> 604 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n"</span><span class="sc">;</span> 605 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 606 <span class="s">}</span> 607 <span class="s">}</span> 608 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span> 609 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewTextFileName</span><span class="s">)</span> <span class="s">{</span> 610 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n"</span><span class="sc">;</span> 611 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 612 <span class="s">}</span> 613 <span class="s">}</span> 614 <span class="s">}</span> 615 616 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> 617 618 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> 619 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span> 620 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span> 621 622 <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span> 623 <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span> 624 <span class="s">}</span> 625 <span class="s">}</span> 626 627 <span class="c"># Process option values...</span> <a name="ProcessOptions-"></a> 628 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> 629 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 630 631 <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span> 632 633 <span class="c"># Process property name related options...</span> 634 <span class="i">ProcessPropertyNamesOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 635 636 <span class="c"># Setup RuleOf3 and RuleOf5 violation calculations...</span> 637 <span class="i">$OptionsInfo</span>{<span class="w">RuleOf3Violations</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 638 <span class="i">$OptionsInfo</span>{<span class="w">RuleOf5Violations</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 639 640 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span> 641 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span> 642 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span> 643 644 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span> 645 <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 646 647 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 648 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">''</span><span class="sc">;</span> 649 650 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span> 651 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span> 652 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span> 653 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n"</span><span class="sc">;</span> 654 <span class="s">}</span> 655 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span> 656 <span class="s">}</span> 657 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^(LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span> 658 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>} ? <span class="i">$Options</span>{<span class="w">compoundid</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span> 659 <span class="s">}</span> 660 <span class="s">}</span> 661 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span> 662 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span> 663 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n"</span><span class="sc">;</span> 664 <span class="s">}</span> 665 <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span> 666 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span> 667 <span class="s">}</span> 668 669 <span class="c"># Types of hydrogen bonds...</span> 670 <span class="i">$OptionsInfo</span>{<span class="w">HydrogenBonds</span>} = <span class="i">$Options</span>{<span class="w">hydrogenbonds</span>}<span class="sc">;</span> 671 672 <span class="c"># Process precision value parameters...</span> 673 <span class="i">ProcessPrecisionOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 674 675 <span class="c"># Process rotatable bonds parameters...</span> 676 <span class="i">ProcessRotatableBondsOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 677 678 <span class="c"># Process TPSA parameters...</span> 679 <span class="i">ProcessTPSAOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 680 681 <span class="c"># Process molecular complexity parameters...</span> 682 <span class="i">ProcessMolecularComplexityOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 683 684 <span class="i">$OptionsInfo</span>{<span class="w">Filter</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 685 686 <span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 687 688 <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span> 689 <span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(SD|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 690 <span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(Text|Both)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 691 692 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/tab/i</span> <span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span><span class="s">)</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span> 693 <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 694 695 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 696 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 697 <span class="s">}</span> 698 699 <span class="c"># Process property name related options...</span> 700 <span class="c">#</span> <a name="ProcessPropertyNamesOption-"></a> 701 <span class="k">sub </span><span class="m">ProcessPropertyNamesOption</span> <span class="s">{</span> 702 703 <span class="c"># Setup supported physicochemical properties...</span> 704 <span class="k">my</span><span class="s">(</span><span class="i">$SupportedProperty</span><span class="s">)</span><span class="sc">;</span> 705 706 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 707 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 708 709 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 710 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 711 712 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 713 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 714 715 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">DefaultPropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 716 717 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}} = <span class="q">qw(MolecularWeight ExactMass HeavyAtoms Rings AromaticRings MolecularVolume RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP SMR TPSA Fsp3Carbons Sp3Carbons MolecularComplexity)</span><span class="sc">;</span> 718 719 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}} = <span class="q">qw(MolecularWeight HydrogenBondDonors HydrogenBondAcceptors SLogP)</span><span class="sc">;</span> 720 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="q">'MolecularWeight'</span> <span class="cm">=></span> <span class="n">500</span><span class="cm">,</span> <span class="q">'HydrogenBondDonors'</span> <span class="cm">=></span> <span class="n">5</span><span class="cm">,</span> <span class="q">'HydrogenBondAcceptors'</span> <span class="cm">=></span> <span class="n">10</span><span class="cm">,</span> <span class="q">'SLogP'</span> <span class="cm">=></span> <span class="n">5</span><span class="s">)</span><span class="sc">;</span> 721 722 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}} = <span class="q">qw(MolecularWeight RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA)</span><span class="sc">;</span> 723 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3MaxPropertyValuesMap</span>}} = <span class="s">(</span><span class="q">'MolecularWeight'</span> <span class="cm">=></span> <span class="n">300</span><span class="cm">,</span> <span class="q">'RotatableBonds'</span> <span class="cm">=></span> <span class="n">3</span><span class="cm">,</span> <span class="q">'HydrogenBondDonors'</span> <span class="cm">=></span> <span class="n">3</span><span class="cm">,</span> <span class="q">'HydrogenBondAcceptors'</span> <span class="cm">=></span> <span class="n">3</span><span class="cm">,</span> <span class="q">'SLogP'</span> <span class="cm">=></span> <span class="n">3</span><span class="cm">,</span> <span class="q">'TPSA'</span> <span class="cm">=></span> <span class="n">60</span><span class="s">)</span><span class="sc">;</span> 724 725 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">DefaultPropertyNames</span>}} = <span class="q">qw(MolecularWeight HeavyAtoms MolecularVolume RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA)</span><span class="sc">;</span> 726 727 <span class="k">for</span> <span class="i">$SupportedProperty</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}}<span class="s">)</span> <span class="s">{</span> 728 <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$SupportedProperty</span><span class="s">)</span>} = <span class="i">$SupportedProperty</span><span class="sc">;</span> 729 <span class="s">}</span> 730 731 <span class="c"># Process specified properties....</span> 732 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="cm">,</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">%SpecifiedPropertyNamesMap</span><span class="s">)</span><span class="sc">;</span> 733 734 <span class="i">@SpecifiedPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 735 <span class="i">%SpecifiedPropertyNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 736 737 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 738 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 739 740 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> 741 <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}}<span class="sc">;</span> 742 <span class="s">}</span> 743 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf5$/i</span><span class="s">)</span> <span class="s">{</span> 744 <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}}<span class="sc">;</span> 745 <span class="s">}</span> 746 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf3$/i</span><span class="s">)</span> <span class="s">{</span> 747 <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}}<span class="sc">;</span> 748 <span class="s">}</span> 749 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 750 <span class="i">@SpecifiedPropertyNames</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">DefaultPropertyNames</span>}}<span class="sc">;</span> 751 <span class="s">}</span> 752 <span class="k">else</span> <span class="s">{</span> 753 <span class="c"># Comma delimited lisr of specified property names...</span> 754 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">@UnsupportedPropertyNames</span><span class="s">)</span><span class="sc">;</span> 755 756 <span class="i">$Mode</span> = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> 757 <span class="i">$Mode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 758 759 <span class="i">@PropertyNames</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$Mode</span><span class="sc">;</span> 760 <span class="i">@UnsupportedPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 761 762 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@PropertyNames</span><span class="s">)</span> <span class="s">{</span> 763 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 764 <span class="k">push</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span> 765 <span class="s">}</span> 766 <span class="k">else</span> <span class="s">{</span> 767 <span class="k">push</span> <span class="i">@UnsupportedPropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span> 768 <span class="s">}</span> 769 <span class="s">}</span> 770 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedPropertyNames</span><span class="s">)</span> <span class="s">{</span> 771 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedPropertyNames</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 772 <span class="k">warn</span> <span class="q">"Error: The physicochemical property names specified - "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@UnsupportedPropertyNames</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">" - for option \"-m --mode\" are not valid.\n"</span><span class="sc">;</span> 773 <span class="s">}</span> 774 <span class="k">else</span> <span class="s">{</span> 775 <span class="k">warn</span> <span class="q">"Error: The physicochemical property name specified, @UnsupportedPropertyNames , for option \"-m --mode\" is not valid.\n"</span><span class="sc">;</span> 776 <span class="s">}</span> 777 <span class="k">die</span> <span class="q">"Allowed values:"</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNames</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 778 <span class="s">}</span> 779 <span class="k">if</span> <span class="s">(</span>!<span class="i">@SpecifiedPropertyNames</span><span class="s">)</span> <span class="s">{</span> 780 <span class="k">die</span> <span class="q">"Error: No valid physicochemical property names specified for option \"-m --mode\".\n"</span><span class="sc">;</span> 781 <span class="s">}</span> 782 <span class="s">}</span> 783 784 <span class="c"># Set up specified property names map...</span> 785 <span class="j">PROPERTY:</span> <span class="k">for</span> <span class="i">$SpecifiedPropertyName</span> <span class="s">(</span><span class="i">@SpecifiedPropertyNames</span><span class="s">)</span> <span class="s">{</span> 786 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 787 <span class="k">warn</span> <span class="q">"Warning: The physicochemical property name, $SpecifiedPropertyName, is specified multiple times as value of option \"-m --mode\" .\n"</span><span class="sc">;</span> 788 <span class="k">next</span> <span class="j">PROPERTY</span><span class="sc">;</span> 789 <span class="s">}</span> 790 <span class="c"># Canonical specified property name...</span> 791 <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>} = <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>}<span class="sc">;</span> 792 <span class="s">}</span> 793 794 <span class="c"># Make sure for calculation of RuleOf3Violations, all appropriate property names are specified...</span> 795 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} =~ <span class="q">/^Yes$/i</span> && <span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf5$/i</span><span class="s">)</span> <span class="s">{</span> 796 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ruleof3violations}, for \"--RuleOf3Violations\" option in \"RuleOf5\" \"-m --Mode\" is not valid. You must specify RuleOf3 value for \"-m --Mode\" to calculate RuleOf3 violations.\n"</span><span class="sc">;</span> 797 <span class="s">}</span> 798 799 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> <span class="s">{</span> 800 <span class="k">my</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="cm">,</span> <span class="i">@MissingRuleOf3Names</span><span class="s">)</span><span class="sc">;</span> 801 802 <span class="i">@MissingRuleOf3Names</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 803 <span class="j">PROPERTY:</span> <span class="k">for</span> <span class="i">$RuleOf3PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf3PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span> 804 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 805 <span class="k">next</span> <span class="j">PROPERTY</span><span class="sc">;</span> 806 <span class="s">}</span> 807 <span class="k">push</span> <span class="i">@MissingRuleOf3Names</span><span class="cm">,</span> <span class="i">$RuleOf3PropertyName</span><span class="sc">;</span> 808 809 <span class="c"># Add property name to specified properties names list and map...</span> 810 <span class="k">push</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">$RuleOf3PropertyName</span><span class="sc">;</span> 811 <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="s">)</span>} = <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf3PropertyName</span><span class="s">)</span>}<span class="sc">;</span> 812 <span class="s">}</span> 813 <span class="k">if</span> <span class="s">(</span><span class="i">@MissingRuleOf3Names</span><span class="s">)</span> <span class="s">{</span> 814 <span class="k">warn</span> <span class="q">"Warning: The following physicochemical property names not specified in \"-m --Mode\" option are required for calculating RuleOf3Violations and have been added to the list of property names: @MissingRuleOf3Names\n"</span><span class="sc">;</span> 815 <span class="s">}</span> 816 <span class="s">}</span> 817 818 <span class="c"># Make sure for calculation of RuleOf5Violations, all appropriate property names are specified...</span> 819 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} =~ <span class="q">/^Yes$/i</span> && <span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^RuleOf3$/i</span><span class="s">)</span> <span class="s">{</span> 820 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ruleof5violations}, for \"--RuleOf5Violations\" option in \"RuleOf3\" \"-m --Mode\" is not valid. You must specify RuleOf5 value for \"-m --Mode\" to calculate RuleOf5 violations.\n"</span><span class="sc">;</span> 821 <span class="s">}</span> 822 823 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> <span class="s">{</span> 824 <span class="k">my</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="cm">,</span> <span class="i">@MissingRuleOf5Names</span><span class="s">)</span><span class="sc">;</span> 825 826 <span class="i">@MissingRuleOf5Names</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 827 <span class="j">PROPERTY:</span> <span class="k">for</span> <span class="i">$RuleOf5PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">RuleOf5PropertyNames</span>}}<span class="s">)</span> <span class="s">{</span> 828 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 829 <span class="k">next</span> <span class="j">PROPERTY</span><span class="sc">;</span> 830 <span class="s">}</span> 831 <span class="k">push</span> <span class="i">@MissingRuleOf5Names</span><span class="cm">,</span> <span class="i">$RuleOf5PropertyName</span><span class="sc">;</span> 832 833 <span class="c"># Add property name to specified properties names list and map...</span> 834 <span class="k">push</span> <span class="i">@SpecifiedPropertyNames</span><span class="cm">,</span> <span class="i">$RuleOf5PropertyName</span><span class="sc">;</span> 835 <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="s">)</span>} = <span class="i">$OptionsInfo</span>{<span class="w">SupportedPropertyNamesMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$RuleOf5PropertyName</span><span class="s">)</span>}<span class="sc">;</span> 836 <span class="s">}</span> 837 <span class="k">if</span> <span class="s">(</span><span class="i">@MissingRuleOf5Names</span><span class="s">)</span> <span class="s">{</span> 838 <span class="k">warn</span> <span class="q">"Warning: The following physicochemical property names not specified in \"-m --Mode\" option are required for calculating RuleOf5Violations and have been added to the list of property names: @MissingRuleOf5Names\n"</span><span class="sc">;</span> 839 <span class="s">}</span> 840 <span class="s">}</span> 841 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> 842 843 <span class="c"># Setup canonical specified property names corresponding to supported names in mixed case...</span> 844 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedCanonicalPropertyNames</span><span class="s">)</span><span class="sc">;</span> 845 846 <span class="i">@SpecifiedCanonicalPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 847 <span class="k">for</span> <span class="i">$SpecifiedPropertyName</span> <span class="s">(</span><span class="i">@SpecifiedPropertyNames</span><span class="s">)</span> <span class="s">{</span> 848 <span class="k">push</span> <span class="i">@SpecifiedCanonicalPropertyNames</span><span class="cm">,</span> <span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedPropertyName</span><span class="s">)</span>}<span class="sc">;</span> 849 <span class="s">}</span> 850 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNames</span>}} = <span class="i">@SpecifiedCanonicalPropertyNames</span><span class="sc">;</span> 851 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedPropertyNamesMap</span>}} = <span class="i">%SpecifiedPropertyNamesMap</span><span class="sc">;</span> 852 853 <span class="c"># Based on specified property names, figure out whether hydrogens need to be added before</span> 854 <span class="c"># calculation of properties...</span> 855 <span class="c">#</span> 856 <span class="i">$OptionsInfo</span>{<span class="w">AddHydrogens</span>} = <span class="n">0</span><span class="sc">;</span> 857 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="q">'MolecularVolume'</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="q">'SLogP'</span><span class="s">)</span>}<span class="s">)</span> || <span class="k">exists</span><span class="s">(</span><span class="i">$SpecifiedPropertyNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="q">'SMR'</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 858 <span class="i">$OptionsInfo</span>{<span class="w">AddHydrogens</span>} = <span class="n">1</span><span class="sc">;</span> 859 <span class="s">}</span> 860 <span class="s">}</span> 861 862 <span class="c"># Process precision option...</span> 863 <span class="c">#</span> <a name="ProcessPrecisionOption-"></a> 864 <span class="k">sub </span><span class="m">ProcessPrecisionOption</span> <span class="s">{</span> 865 <span class="k">my</span><span class="s">(</span><span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">%PrecisionParametersMap</span><span class="cm">,</span> <span class="i">%PrecisionParameterNamesMap</span><span class="s">)</span><span class="sc">;</span> 866 867 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">PrecisionParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 868 869 <span class="i">%PrecisionParametersMap</span> = <span class="s">(</span><span class="q">'WeightPrecision'</span> <span class="cm">=></span> <span class="n">2</span><span class="cm">,</span> <span class="q">'MassPrecision'</span> <span class="cm">=></span> <span class="n">4</span><span class="s">)</span><span class="sc">;</span> 870 <span class="i">%PrecisionParameterNamesMap</span> = <span class="s">(</span><span class="q">'molecularweight'</span> <span class="cm">=></span> <span class="q">'WeightPrecision'</span><span class="cm">,</span> <span class="q">'exactmass'</span> <span class="cm">=></span> <span class="q">'MassPrecision'</span><span class="s">)</span><span class="sc">;</span> 871 872 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span> <span class="s">{</span> 873 <span class="c"># Process specified values...</span> 874 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedPrecision</span><span class="cm">,</span> <span class="i">@SpecifiedPrecisionValuePairs</span><span class="s">)</span><span class="sc">;</span> 875 876 <span class="i">$SpecifiedPrecision</span> = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span> 877 <span class="i">$SpecifiedPrecision</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 878 <span class="i">@SpecifiedPrecisionValuePairs</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$SpecifiedPrecision</span><span class="sc">;</span> 879 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedPrecisionValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 880 <span class="k">die</span> <span class="q">"Error: Invalid number of values specified using \"--Precision\" option: It must contain even number of values.\n"</span><span class="sc">;</span> 881 <span class="s">}</span> 882 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> < <span class="i">@SpecifiedPrecisionValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span> 883 <span class="i">$ParameterName</span> = <span class="i">$SpecifiedPrecisionValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span> 884 <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedPrecisionValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> 885 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$PrecisionParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 886 <span class="k">die</span> <span class="q">"Error: The precision parameter name specified, $ParameterName, for option \"--Precision\" is not valid.\n"</span><span class="sc">;</span> 887 <span class="s">}</span> 888 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 889 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--Precision\" is not valid. Allowed values: positive integer. \n"</span><span class="sc">;</span> 890 <span class="s">}</span> 891 <span class="i">$ParameterName</span> = <span class="i">$PrecisionParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span> 892 <span class="i">$PrecisionParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span> 893 <span class="s">}</span> 894 <span class="s">}</span> 895 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span> 896 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">PrecisionParametersMap</span>}} = <span class="i">%PrecisionParametersMap</span><span class="sc">;</span> 897 <span class="s">}</span> 898 899 <span class="c"># Process rotatable bonds option...</span> <a name="ProcessRotatableBondsOption-"></a> 900 <span class="k">sub </span><span class="m">ProcessRotatableBondsOption</span> <span class="s">{</span> 901 <span class="k">my</span><span class="s">(</span><span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">%RotatableBondsParametersMap</span><span class="cm">,</span> <span class="i">%RotatableBondsParameterNamesMap</span><span class="s">)</span><span class="sc">;</span> 902 903 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RotatableBondsParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 904 <span class="i">%RotatableBondsParametersMap</span> = <span class="s">(</span><span class="q">'IgnoreTerminalBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'IgnoreBondsToTripleBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'IgnoreAmideBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'IgnoreThioamideBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'IgnoreSulfonamideBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> 905 906 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%RotatableBondsParametersMap</span><span class="s">)</span> <span class="s">{</span> 907 <span class="i">$RotatableBondsParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>} = <span class="i">$ParameterName</span><span class="sc">;</span> 908 <span class="s">}</span> 909 910 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">rotatablebonds</span>}<span class="s">)</span> <span class="s">{</span> 911 <span class="c"># Process specified values...</span> 912 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedRotatableBonds</span><span class="cm">,</span> <span class="i">@SpecifiedRotatableBondsValuePairs</span><span class="s">)</span><span class="sc">;</span> 913 914 <span class="i">$SpecifiedRotatableBonds</span> = <span class="i">$Options</span>{<span class="w">rotatablebonds</span>}<span class="sc">;</span> 915 <span class="i">$SpecifiedRotatableBonds</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 916 <span class="i">@SpecifiedRotatableBondsValuePairs</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$SpecifiedRotatableBonds</span><span class="sc">;</span> 917 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedRotatableBondsValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 918 <span class="k">die</span> <span class="q">"Error: Invalid number of values specified using \"--RotatableBonds\" option: It must contain even number of values.\n"</span><span class="sc">;</span> 919 <span class="s">}</span> 920 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> < <span class="i">@SpecifiedRotatableBondsValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span> 921 <span class="i">$ParameterName</span> = <span class="i">$SpecifiedRotatableBondsValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span> 922 <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedRotatableBondsValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> 923 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$RotatableBondsParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 924 <span class="k">die</span> <span class="q">"Error: The rotatable bonds parameter name specified, $ParameterName, for option \"--RotatableBonds\" is not valid.\n"</span><span class="sc">;</span> 925 <span class="s">}</span> 926 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 927 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--RotatableBonds\" is not valid. Allowed values: Yes or No. \n"</span><span class="sc">;</span> 928 <span class="s">}</span> 929 <span class="i">$ParameterName</span> = <span class="i">$RotatableBondsParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span> 930 <span class="i">$ParameterValue</span> = <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 931 <span class="i">$RotatableBondsParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span> 932 <span class="s">}</span> 933 <span class="s">}</span> 934 <span class="i">$OptionsInfo</span>{<span class="w">RotatableBonds</span>} = <span class="i">$Options</span>{<span class="w">rotatablebonds</span>}<span class="sc">;</span> 935 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">RotatableBondsParametersMap</span>}} = <span class="i">%RotatableBondsParametersMap</span><span class="sc">;</span> 936 <span class="s">}</span> 937 938 <span class="c"># Process TPSA option...</span> 939 <span class="c">#</span> <a name="ProcessTPSAOption-"></a> 940 <span class="k">sub </span><span class="m">ProcessTPSAOption</span> <span class="s">{</span> 941 <span class="k">my</span><span class="s">(</span><span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">%TPSAParametersMap</span><span class="cm">,</span> <span class="i">%TPSAParameterNamesMap</span><span class="s">)</span><span class="sc">;</span> 942 943 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">TPSAParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 944 945 <span class="i">%TPSAParametersMap</span> = <span class="s">(</span><span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> 946 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%TPSAParametersMap</span><span class="s">)</span> <span class="s">{</span> 947 <span class="i">$TPSAParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>} = <span class="i">$ParameterName</span><span class="sc">;</span> 948 <span class="s">}</span> 949 950 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">tpsa</span>}<span class="s">)</span> <span class="s">{</span> 951 <span class="c"># Process specified values...</span> 952 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedTPSA</span><span class="cm">,</span> <span class="i">@SpecifiedTPSAValuePairs</span><span class="s">)</span><span class="sc">;</span> 953 954 <span class="i">$SpecifiedTPSA</span> = <span class="i">$Options</span>{<span class="w">tpsa</span>}<span class="sc">;</span> 955 <span class="i">$SpecifiedTPSA</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 956 <span class="i">@SpecifiedTPSAValuePairs</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$SpecifiedTPSA</span><span class="sc">;</span> 957 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedTPSAValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 958 <span class="k">die</span> <span class="q">"Error: Invalid number of values specified using \"--TPSA\" option: It must contain even number of values.\n"</span><span class="sc">;</span> 959 <span class="s">}</span> 960 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> < <span class="i">@SpecifiedTPSAValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span> 961 <span class="i">$ParameterName</span> = <span class="i">$SpecifiedTPSAValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span> 962 <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedTPSAValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> 963 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$TPSAParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 964 <span class="k">die</span> <span class="q">"Error: The TPSA parameter name specified, $ParameterName, for option \"--TPSA\" is not valid.\n"</span><span class="sc">;</span> 965 <span class="s">}</span> 966 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 967 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--TPSA\" is not valid. Allowed values: Yes or No. \n"</span><span class="sc">;</span> 968 <span class="s">}</span> 969 <span class="i">$ParameterName</span> = <span class="i">$TPSAParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span> 970 <span class="i">$ParameterValue</span> = <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 971 <span class="i">$TPSAParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span> 972 <span class="s">}</span> 973 <span class="s">}</span> 974 <span class="i">$OptionsInfo</span>{<span class="w">TPSA</span>} = <span class="i">$Options</span>{<span class="w">tpsa</span>}<span class="sc">;</span> 975 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">TPSAParametersMap</span>}} = <span class="i">%TPSAParametersMap</span><span class="sc">;</span> 976 <span class="s">}</span> 977 978 <span class="c"># Process molecular complexity parameters...</span> 979 <span class="c">#</span> <a name="ProcessMolecularComplexityOption-"></a> 980 <span class="k">sub </span><span class="m">ProcessMolecularComplexityOption</span> <span class="s">{</span> 981 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularComplexityType</span><span class="cm">,</span> <span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@ParameterValues</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="i">%ComplexityParametersMap</span><span class="cm">,</span> <span class="i">%ComplexityParameterNamesMap</span><span class="s">)</span><span class="sc">;</span> 982 983 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 984 985 <span class="i">%ComplexityParametersMap</span> = <span class="s">(</span><span class="q">'MolecularComplexityType'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span> 986 <span class="q">'AtomicInvariantsToUse'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span> 987 <span class="q">'MACCSKeysSize'</span> <span class="cm">=></span> <span class="q">'166'</span><span class="cm">,</span> <span class="q">'NeighborhoodRadius'</span> <span class="cm">=></span> <span class="q">'2'</span><span class="cm">,</span> 988 <span class="q">'MinPathLength'</span> <span class="cm">=></span> <span class="q">'1'</span><span class="cm">,</span> <span class="q">'MaxPathLength'</span> <span class="cm">=></span> <span class="q">'8'</span><span class="cm">,</span> <span class="q">'UseBondSymbols'</span> <span class="cm">=></span> <span class="q">'1'</span><span class="cm">,</span> 989 <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="q">'1'</span><span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="q">'10'</span><span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="q">''</span><span class="cm">,</span> 990 <span class="q">'DistanceBinSize'</span> <span class="cm">=></span> <span class="q">'2'</span><span class="cm">,</span> <span class="q">'NormalizationMethodology'</span> <span class="cm">=></span> <span class="q">'None'</span><span class="s">)</span><span class="sc">;</span> 991 992 <span class="i">%ComplexityParameterNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 993 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%ComplexityParametersMap</span><span class="s">)</span> <span class="s">{</span> 994 <span class="i">$ComplexityParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>} = <span class="i">$ParameterName</span><span class="sc">;</span> 995 <span class="s">}</span> 996 997 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">molecularcomplexity</span>}<span class="s">)</span> <span class="s">{</span> 998 <span class="c"># Process specified values...</span> 999 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SpecifiedComplexity</span><span class="cm">,</span> <span class="i">@SpecifiedComplexityValuePairs</span><span class="s">)</span><span class="sc">;</span> 1000 1001 <span class="i">$SpecifiedComplexity</span> = <span class="i">$Options</span>{<span class="w">molecularcomplexity</span>}<span class="sc">;</span> 1002 1003 <span class="i">@SpecifiedComplexityValuePairs</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$SpecifiedComplexity</span><span class="sc">;</span> 1004 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedComplexityValuePairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 1005 <span class="k">die</span> <span class="q">"Error: Invalid number of values specified using \"--MolecularComplexity\" option: It must contain even number of values.\n"</span><span class="sc">;</span> 1006 <span class="s">}</span> 1007 1008 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index</span> + <span class="n">1</span><span class="s">)</span> < <span class="i">@SpecifiedComplexityValuePairs</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span> <span class="s">)</span> <span class="s">{</span> 1009 <span class="i">$ParameterName</span> = <span class="i">$SpecifiedComplexityValuePairs</span>[<span class="i">$Index</span>]<span class="sc">;</span> 1010 <span class="i">$ParameterValue</span> = <span class="i">$SpecifiedComplexityValuePairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> 1011 1012 <span class="i">$ParameterName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span><span class="sc">;</span> 1013 <span class="i">$ParameterValue</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="sc">;</span> 1014 1015 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ComplexityParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 1016 <span class="k">die</span> <span class="q">"Error: The molecular complexity parameter name specified, $ParameterName, for option \"--MolecularComplexity\" is not valid.\n"</span><span class="sc">;</span> 1017 <span class="s">}</span> 1018 <span class="i">$ParameterName</span> = <span class="i">$ComplexityParameterNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ParameterName</span><span class="s">)</span>}<span class="sc">;</span> 1019 1020 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^AtomicInvariantsToUse$/i</span><span class="s">)</span> <span class="s">{</span> 1021 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbolFound</span><span class="s">)</span><span class="sc">;</span> 1022 1023 <span class="i">$AtomSymbolFound</span> = <span class="n">0</span><span class="sc">;</span> 1024 <span class="i">@ParameterValues</span> = <span class="k">split</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="s">)</span><span class="sc">;</span> 1025 <span class="k">for</span> <span class="i">$ParameterValue</span> <span class="s">(</span><span class="i">@ParameterValues</span><span class="s">)</span> <span class="s">{</span> 1026 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1027 <span class="k">die</span> <span class="q">"Error: The atomic invariant specified, $ParameterValue, for AtomicInvariantsToUse in option \"--MolecularComplexity\" is not valid.\n"</span><span class="sc">;</span> 1028 <span class="s">}</span> 1029 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^(AS|AtomSymbol)$/i</span><span class="s">)</span> <span class="s">{</span> 1030 <span class="i">$AtomSymbolFound</span> = <span class="n">1</span><span class="sc">;</span> 1031 <span class="s">}</span> 1032 <span class="s">}</span> 1033 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSymbolFound</span><span class="s">)</span> <span class="s">{</span> 1034 <span class="k">die</span> <span class="q">"Error: The atomic invariants specified using AtomicInvariantsToUse in option \"--MolecularComplexity\" is not valid: AtomicInvariant atom symbol, AS or AtomSymbol, must be specified.\n"</span><span class="sc">;</span> 1035 <span class="s">}</span> 1036 <span class="i">$ParameterValue</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ParameterValues</span><span class="cm">,</span> <span class="q">","</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> 1037 <span class="s">}</span> 1038 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^FunctionalClassesToUse$/i</span><span class="s">)</span> <span class="s">{</span> 1039 <span class="i">@ParameterValues</span> = <span class="k">split</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="s">)</span><span class="sc">;</span> 1040 <span class="k">for</span> <span class="i">$ParameterValue</span> <span class="s">(</span><span class="i">@ParameterValues</span><span class="s">)</span> <span class="s">{</span> 1041 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1042 <span class="k">die</span> <span class="q">"Error: The functional class specified, $ParameterValue, for FunctionalClassesToUse in option \"--MolecularComplexity\" is not valid.\n"</span><span class="sc">;</span> 1043 <span class="s">}</span> 1044 <span class="s">}</span> 1045 <span class="i">$ParameterValue</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ParameterValues</span><span class="cm">,</span> <span class="q">","</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> 1046 <span class="s">}</span> 1047 <span class="k">else</span> <span class="s">{</span> 1048 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/ /</span><span class="s">)</span> <span class="s">{</span> 1049 <span class="i">$ParameterValue</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 1050 <span class="s">}</span> 1051 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 1052 <span class="i">$ParameterValue</span> = <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 1053 <span class="s">}</span> 1054 <span class="s">}</span> 1055 1056 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^MolecularComplexityType$/i</span><span class="s">)</span> <span class="s">{</span> 1057 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|MACCSKeys|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> 1058 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: AtomTypesFingerprints, ExtendedConnectivityFingerprints, MACCSKeys, PathLengthFingerprints, TopologicalAtomPairsFingerprints, TopologicalAtomTripletsFingerprints, TopologicalAtomTorsionsFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints..\n"</span><span class="sc">;</span> 1059 <span class="s">}</span> 1060 <span class="s">}</span> 1061 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^AtomIdentifierType$/i</span><span class="s">)</span> <span class="s">{</span> 1062 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> 1063 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes.\n"</span><span class="sc">;</span> 1064 <span class="s">}</span> 1065 <span class="s">}</span> 1066 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^(MACCSKeysSize|MinPathLength|MaxPathLength|MinDistance|MaxDistance|DistanceBinSize)$/i</span><span class="s">)</span> <span class="s">{</span> 1067 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1068 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: positive integer. \n"</span><span class="sc">;</span> 1069 <span class="s">}</span> 1070 <span class="s">}</span> 1071 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^NeighborhoodRadius$/i</span><span class="s">)</span> <span class="s">{</span> 1072 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsInteger</span><span class="s">(</span><span class="i">$ParameterValue</span><span class="s">)</span> && <span class="i">$ParameterValue</span> >=<span class="n">0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1073 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: 0 or positive integer. \n"</span><span class="sc">;</span> 1074 <span class="s">}</span> 1075 <span class="s">}</span> 1076 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/^NormalizationMethodology$/i</span><span class="s">)</span> <span class="s">{</span> 1077 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> !~ <span class="q">/^(None|ByHeavyAtomsCount|ByPossibleKeysCount)$/i</span><span class="s">)</span> <span class="s">{</span> 1078 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: None, ByHeavyAtomsCount, or ByPossibleKeysCount\n"</span><span class="sc">;</span> 1079 <span class="s">}</span> 1080 <span class="s">}</span> 1081 <span class="i">$ComplexityParametersMap</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span> 1082 <span class="s">}</span> 1083 1084 <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MACCSKeysSize</span>} !~ <span class="q">/^(166|322)$/i</span><span class="s">)</span> <span class="s">{</span> 1085 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ComplexityParametersMap{MACCSKeysSize}, for parameter name, MACCSKeysSize in option \"--MolecularComplexity\" is not valid. Allowed values: 166 or 322\n"</span><span class="sc">;</span> 1086 <span class="s">}</span> 1087 <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MinPathLength</span>} > <span class="i">$ComplexityParametersMap</span>{<span class="w">MaxPathLength</span>}<span class="s">)</span> <span class="s">{</span> 1088 <span class="k">die</span> <span class="q">"Error: The parameter value specified for MinPathLength, $ComplexityParametersMap{MinPathLength}, must be <= MaxPathLength, $ComplexityParametersMap{MaxPathLength} ...\n"</span><span class="sc">;</span> 1089 <span class="s">}</span> 1090 <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MinDistance</span>} > <span class="i">$ComplexityParametersMap</span>{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> 1091 <span class="k">die</span> <span class="q">"Error: The parameter value specified for MinDistance, $ComplexityParametersMap{MinDistance}, must be <= MaxDistance, $ComplexityParametersMap{MaxDistance} ...\n"</span><span class="sc">;</span> 1092 <span class="s">}</span> 1093 <span class="s">}</span> 1094 1095 <span class="c"># Set default parameter values...</span> 1096 1097 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">MolecularComplexityType</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1098 <span class="i">$ComplexityParametersMap</span>{<span class="w">MolecularComplexityType</span>} = <span class="q">'MACCSKeys'</span><span class="sc">;</span> 1099 <span class="s">}</span> 1100 <span class="i">$MolecularComplexityType</span> = <span class="i">$ComplexityParametersMap</span>{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span> 1101 1102 1103 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1104 <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} = <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> ? <span class="q">"FunctionalClassAtomTypes"</span> <span class="co">:</span> <span class="q">"AtomicInvariantsAtomTypes"</span><span class="sc">;</span> 1105 <span class="s">}</span> 1106 1107 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1108 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span> 1109 1110 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^(AtomTypesFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> 1111 <span class="i">$AtomicInvariantsToUse</span> = <span class="q">"AS,X,BO,H,FC"</span><span class="sc">;</span> 1112 <span class="s">}</span> 1113 <span class="k">elsif</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1114 <span class="i">$AtomicInvariantsToUse</span> = <span class="q">"AS,X,BO,H,FC,MN"</span><span class="sc">;</span> 1115 <span class="s">}</span> 1116 <span class="k">else</span> <span class="s">{</span> 1117 <span class="i">$AtomicInvariantsToUse</span> = <span class="q">"AS"</span><span class="sc">;</span> 1118 <span class="s">}</span> 1119 <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>} = <span class="i">$AtomicInvariantsToUse</span><span class="sc">;</span> 1120 <span class="s">}</span> 1121 1122 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1123 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span> 1124 1125 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1126 <span class="i">$FunctionalClassesToUse</span> = <span class="q">"HBD,HBA,PI,NI,H"</span><span class="sc">;</span> 1127 <span class="s">}</span> 1128 <span class="k">elsif</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1129 <span class="i">$FunctionalClassesToUse</span> = <span class="q">"HBD,HBA,PI,NI,H,Ar"</span><span class="sc">;</span> 1130 <span class="s">}</span> 1131 <span class="k">else</span> <span class="s">{</span> 1132 <span class="i">$FunctionalClassesToUse</span> = <span class="q">"HBD,HBA,PI,NI,H,Ar,Hal"</span><span class="sc">;</span> 1133 <span class="s">}</span> 1134 <span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>} = <span class="i">$FunctionalClassesToUse</span><span class="sc">;</span> 1135 <span class="s">}</span> 1136 1137 <span class="k">my</span><span class="s">(</span><span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span> 1138 <span class="i">@AtomicInvariantsToUse</span> = <span class="k">split</span> <span class="q">','</span><span class="cm">,</span> <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>}<span class="sc">;</span> 1139 <span class="i">$ComplexityParametersMap</span>{<span class="w">AtomicInvariantsToUse</span>} = \<span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> 1140 1141 <span class="k">my</span><span class="s">(</span><span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span> 1142 <span class="i">@FunctionalClassesToUse</span> = <span class="k">split</span> <span class="q">','</span><span class="cm">,</span> <span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>}<span class="sc">;</span> 1143 <span class="i">$ComplexityParametersMap</span>{<span class="w">FunctionalClassesToUse</span>} = \<span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> 1144 1145 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">UseTriangleInequality</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1146 <span class="i">$ComplexityParametersMap</span>{<span class="w">UseTriangleInequality</span>} = <span class="n">0</span><span class="sc">;</span> 1147 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1148 <span class="i">$ComplexityParametersMap</span>{<span class="w">UseTriangleInequality</span>} = <span class="n">1</span><span class="sc">;</span> 1149 <span class="s">}</span> 1150 <span class="s">}</span> 1151 1152 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> 1153 <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 1154 <span class="k">die</span> <span class="q">"Error: The parameter value specified for AtomIdentifierType, $ComplexityParametersMap{AtomIdentifierType}, in option \"--MolecularComplexity\" is not valid for MolecularComplexityType, $MolecularComplexityType: Allowed value: FunctionalClassAtomTypes...\n"</span><span class="sc">;</span> 1155 <span class="s">}</span> 1156 <span class="s">}</span> 1157 1158 <span class="c"># Set up approprate paremeter names for specified molecular complexity...</span> 1159 1160 <span class="i">@ParameterNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1161 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="q">'MolecularComplexityType'</span><span class="sc">;</span> 1162 1163 <span class="i">@AtomIdentifierTypeParameters</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1164 <span class="k">push</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span><span class="sc">;</span> 1165 <span class="k">if</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 1166 <span class="k">push</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="q">'AtomicInvariantsToUse'</span><span class="sc">;</span> 1167 <span class="s">}</span> 1168 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ComplexityParametersMap</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 1169 <span class="k">push</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span><span class="sc">;</span> 1170 <span class="s">}</span> 1171 1172 <span class="j">COMPLEXITYTYPE:</span> <span class="s">{</span> 1173 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^AtomTypesFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1174 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span> 1175 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span> 1176 <span class="s">}</span> 1177 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1178 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span> 1179 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'NeighborhoodRadius'</span><span class="cm">,</span> <span class="q">'NormalizationMethodology'</span><span class="s">)</span><span class="sc">;</span> 1180 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span> 1181 <span class="s">}</span> 1182 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span> 1183 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="q">'MACCSKeysSize'</span><span class="sc">;</span> 1184 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span> 1185 <span class="s">}</span> 1186 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1187 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span> 1188 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'MinPathLength'</span><span class="cm">,</span> <span class="q">'MaxPathLength'</span><span class="cm">,</span> <span class="q">'UseBondSymbols'</span><span class="s">)</span><span class="sc">;</span> 1189 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span> 1190 <span class="s">}</span> 1191 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1192 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span> 1193 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'MinDistance'</span><span class="cm">,</span> <span class="q">'MaxDistance'</span><span class="s">)</span><span class="sc">;</span> 1194 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span> 1195 <span class="s">}</span> 1196 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1197 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span> 1198 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'MinDistance'</span><span class="cm">,</span> <span class="q">'MaxDistance'</span><span class="cm">,</span> <span class="q">'UseTriangleInequality'</span><span class="s">)</span><span class="sc">;</span> 1199 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span> 1200 <span class="s">}</span> 1201 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalAtomTorsionsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1202 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="i">@AtomIdentifierTypeParameters</span><span class="sc">;</span> 1203 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span> 1204 <span class="s">}</span> 1205 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1206 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'AtomIdentifierType'</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span><span class="cm">,</span> <span class="q">'MinDistance'</span><span class="cm">,</span> <span class="q">'MaxDistance'</span><span class="cm">,</span> <span class="q">'NormalizationMethodology'</span><span class="s">)</span><span class="sc">;</span> 1207 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span> 1208 <span class="s">}</span> 1209 <span class="k">if</span> <span class="s">(</span><span class="i">$MolecularComplexityType</span> =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1210 <span class="k">push</span> <span class="i">@ParameterNames</span><span class="cm">,</span> <span class="s">(</span><span class="q">'AtomIdentifierType'</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span><span class="cm">,</span> <span class="q">'MinDistance'</span><span class="cm">,</span> <span class="q">'MaxDistance'</span><span class="cm">,</span> <span class="q">'UseTriangleInequality'</span><span class="cm">,</span> <span class="q">'NormalizationMethodology'</span><span class="cm">,</span> <span class="q">'DistanceBinSize'</span><span class="s">)</span><span class="sc">;</span> 1211 <span class="k">last</span> <span class="j">COMPLEXITYTYPE</span><span class="sc">;</span> 1212 <span class="s">}</span> 1213 <span class="k">die</span> <span class="q">"Error: The parameter value specified, $ParameterValue, for parameter name MolecularComplexityType using \"--MolecularComplexity\" is not valid.\n"</span><span class="sc">;</span> 1214 <span class="s">}</span> 1215 1216 <span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexity</span>} = <span class="i">$Options</span>{<span class="w">molecularcomplexity</span>}<span class="sc">;</span> 1217 1218 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1219 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="i">@ParameterNames</span><span class="s">)</span> <span class="s">{</span> 1220 <span class="i">$ParameterValue</span> = <span class="i">$ComplexityParametersMap</span>{<span class="i">$ParameterName</span>}<span class="sc">;</span> 1221 <span class="i">$OptionsInfo</span>{<span class="w">MolecularComplexityParametersMap</span>}{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span> 1222 <span class="s">}</span> 1223 <span class="s">}</span> 1224 1225 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> <a name="SetupScriptUsage-"></a>1226 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> 1227 1228 <span class="c"># Retrieve all the options...</span> 1229 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1230 1231 <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span> 1232 1233 <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span> 1234 <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span> 1235 <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span> 1236 1237 <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">'Yes'</span><span class="sc">;</span> 1238 1239 <span class="i">$Options</span>{<span class="w">hydrogenbonds</span>} = <span class="q">'HBondsType2'</span><span class="sc">;</span> 1240 1241 <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">'Yes'</span><span class="sc">;</span> 1242 1243 <span class="c"># Default mode values are set later...</span> 1244 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">''</span><span class="sc">;</span> 1245 1246 <span class="c"># Default moelcular complexity values are set later...</span> 1247 <span class="i">$Options</span>{<span class="w">molecularcomplexity</span>} = <span class="q">''</span><span class="sc">;</span> 1248 1249 <span class="c"># Default precision values are set later...</span> 1250 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="q">''</span><span class="sc">;</span> 1251 1252 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">'text'</span><span class="sc">;</span> 1253 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> 1254 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span> 1255 1256 <span class="c"># Default rotatable bond parameter values are set later...</span> 1257 <span class="i">$Options</span>{<span class="w">rotatablebonds</span>} = <span class="q">''</span><span class="sc">;</span> 1258 1259 <span class="i">$Options</span>{<span class="w">ruleof3violations</span>} = <span class="q">'No'</span><span class="sc">;</span> 1260 <span class="i">$Options</span>{<span class="w">ruleof5violations</span>} = <span class="q">'No'</span><span class="sc">;</span> 1261 1262 <span class="c"># Default TPSA paramater values are set later...</span> 1263 <span class="i">$Options</span>{<span class="w">tpsa</span>} = <span class="q">''</span><span class="sc">;</span> 1264 1265 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"aromaticitymodel=s"</span><span class="cm">,</span> <span class="q">"compoundid=s"</span><span class="cm">,</span> <span class="q">"compoundidlabel=s"</span><span class="cm">,</span> <span class="q">"compoundidmode=s"</span><span class="cm">,</span> <span class="q">"datafields=s"</span><span class="cm">,</span> <span class="q">"datafieldsmode|d=s"</span><span class="cm">,</span> <span class="q">"filter|f=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"hydrogenbonds=s"</span><span class="cm">,</span> <span class="q">"keeplargestcomponent|k=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"molecularcomplexity=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"output=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"precision=s"</span><span class="cm">,</span> <span class="q">"rotatablebonds=s"</span><span class="cm">,</span> <span class="q">"ruleof3violations=s"</span><span class="cm">,</span> <span class="q">"ruleof5violations=s"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"tpsa=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1266 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> 1267 <span class="s">}</span> 1268 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 1269 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 1270 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> 1271 <span class="s">}</span> 1272 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span> 1273 <span class="s">}</span> 1274 <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1275 <span class="k">my</span><span class="s">(</span><span class="i">@SupportedModels</span><span class="s">)</span> = <span class="i">Molecule::GetSupportedAromaticityModels</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1276 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"</span><span class="sc">;</span> 1277 <span class="s">}</span> 1278 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span> 1279 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span> 1280 <span class="s">}</span> 1281 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span> 1282 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"</span><span class="sc">;</span> 1283 <span class="s">}</span> 1284 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 1285 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 1286 <span class="s">}</span> 1287 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">hydrogenbonds</span>} !~ <span class="q">/^(HBondsType1|HydrogenBondsType1|HBondsType2|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span> 1288 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{hydrogenbonds}, for option \"--HydrogenBonds\" is not valid. Allowed values: HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2\n"</span><span class="sc">;</span> 1289 <span class="s">}</span> 1290 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 1291 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 1292 <span class="s">}</span> 1293 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|text|both)$/i</span><span class="s">)</span> <span class="s">{</span> 1294 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, text, or both\n"</span><span class="sc">;</span> 1295 <span class="s">}</span> 1296 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span> 1297 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span> 1298 <span class="s">}</span> 1299 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 1300 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 1301 <span class="s">}</span> 1302 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof3violations</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 1303 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ruleof3violations}, for option \"--RuleOf3Violations\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 1304 <span class="s">}</span> 1305 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ruleof5violations</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> 1306 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ruleof5violations}, for option \"--RuleOf5Violations\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> 1307 <span class="s">}</span> 1308 <span class="s">}</span> 1309 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>