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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/code/CalculatePhysicochemicalProperties.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1330 @@ +<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>