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<html> <head> <title>MayaChemTools:Code:MolecularDescriptors::MolecularComplexityDescriptors.pm</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> <a name="package-MolecularDescriptors::MolecularComplexityDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularComplexityDescriptors</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: MolecularComplexityDescriptors.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> 5 <span class="c"># $Revision: 1.15 $</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">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> 38 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> 39 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> 40 <span class="k">use</span> <span class="w">Fingerprints::AtomTypesFingerprints</span><span class="sc">;</span> 41 <span class="k">use</span> <span class="w">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span> 42 <span class="k">use</span> <span class="w">Fingerprints::MACCSKeys</span><span class="sc">;</span> 43 <span class="k">use</span> <span class="w">Fingerprints::PathLengthFingerprints</span><span class="sc">;</span> 44 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="sc">;</span> 45 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="sc">;</span> 46 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="sc">;</span> 47 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span> 48 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="sc">;</span> 49 50 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> 51 52 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> 53 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 54 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames GetMolecularComplexityTypeAbbreviation)</span><span class="sc">;</span> 55 56 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> 57 58 <span class="c"># Setup class variables...</span> 59 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> 60 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 61 62 <span class="c"># Overload Perl functions...</span> 63 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyMolecularComplexityDescriptors'</span><span class="sc">;</span> 64 65 <span class="c"># Class constructor...</span> <a name="new-"></a> 66 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 67 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 68 69 <span class="c"># Initialize object...</span> 70 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 71 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> 72 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 73 74 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 75 76 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 77 <span class="s">}</span> 78 79 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 80 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 81 <span class="c">#Class name...</span> 82 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 83 84 <span class="c"># Descriptor names...</span> 85 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'MolecularComplexity'</span><span class="s">)</span><span class="sc">;</span> 86 87 <span class="s">}</span> 88 89 <span class="c"># Get descriptor names as an array.</span> 90 <span class="c">#</span> 91 <span class="c"># This functionality can be either invoked as a class function or an</span> 92 <span class="c"># object method.</span> 93 <span class="c">#</span> <a name="GetDescriptorNames-"></a> 94 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> 95 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> 96 <span class="s">}</span> 97 98 <span class="c"># Initialize object data...</span> 99 <span class="c">#</span> <a name="_InitializeMolecularComplexityDescriptors-"></a> 100 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptors</span> <span class="s">{</span> 101 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 102 103 <span class="c"># Type of MolecularDescriptor...</span> 104 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'MolecularComplexity'</span><span class="sc">;</span> 105 106 <span class="c">#</span> 107 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span> 108 <span class="c"># corresponding to number of bits-set or unique keys [ Ref 117-119 ] in molecular</span> 109 <span class="c"># fingerprints. The following types of fingerprints based molecular complexity measures</span> 110 <span class="c"># are supported:</span> 111 <span class="c">#</span> 112 <span class="c"># AtomTypesFingerprints</span> 113 <span class="c"># ExtendedConnectivityFingerprints</span> 114 <span class="c"># MACCSKeys</span> 115 <span class="c"># PathLengthFingerprints</span> 116 <span class="c"># TopologicalAtomPairsFingerprints</span> 117 <span class="c"># TopologicalAtomTripletsFingerprints</span> 118 <span class="c"># TopologicalAtomTorsionsFingerprints</span> 119 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> 120 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> 121 <span class="c">#</span> 122 <span class="c"># Default: MACCSKeys</span> 123 <span class="c">#</span> 124 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">''</span><span class="sc">;</span> 125 126 <span class="c"># Atom types to use for generating fingerprints...</span> 127 <span class="c">#</span> 128 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span> 129 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span> 130 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> 131 <span class="c">#</span> 132 <span class="c"># Notes:</span> 133 <span class="c"># . AtomicInvariantsAtomTypes for all supported MolecularComplexityType except for</span> 134 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints and TopologicalPharmacophoreAtomTripletsFingerprints</span> 135 <span class="c"># . This value is not used for MACCSKeys</span> 136 <span class="c"># . FunctionalClassAtomTypes is the only valid value during topological pharmacophore fingerprints.</span> 137 <span class="c">#</span> 138 <span class="c"># . Default values for AtomicInvariantsToUse and FunctionalClassesToUse are set appropriately</span> 139 <span class="c"># for different types of fingerprints as shown below.</span> 140 <span class="c">#</span> 141 <span class="c"># MolecularComplexityType AtomicInvariantsToUse</span> 142 <span class="c">#</span> 143 <span class="c"># AtomTypesFingerprints AS, X, BO, H, FC</span> 144 <span class="c"># TopologicalAtomPairsFingerprints AS, X, BO, H, FC</span> 145 <span class="c"># TopologicalAtomTripletsFingerprints AS, X, BO, H, FC</span> 146 <span class="c"># TopologicalAtomTorsionsFingerprints AS, X, BO, H, FC</span> 147 <span class="c">#</span> 148 <span class="c"># ExtendedConnectivityFingerprints AS, X, BO, H, FC, MN</span> 149 <span class="c"># PathLengthFingerprints AS</span> 150 <span class="c">#</span> 151 <span class="c"># Default for FunctionalClassesToUse for all fingerprints is set to:</span> 152 <span class="c">#</span> 153 <span class="c"># HBD, HBA, PI, NI, Ar, Hal</span> 154 <span class="c">#</span> 155 <span class="c"># except for the following two MolecularComplexityType fingerprints:</span> 156 <span class="c">#</span> 157 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints HBD, HBA, PI, NI, H</span> 158 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints HBD, HBA, PI, NI, H, Ar</span> 159 <span class="c">#</span> 160 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> 161 162 <span class="c"># Size of MACCS key set: 166 or 322...</span> 163 <span class="c">#</span> 164 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="n">166</span><span class="sc">;</span> 165 166 <span class="c"># Atomic neighborhoods radius for extended connectivity fingerprints...</span> 167 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span> 168 169 <span class="c"># Minimum and maximum path lengths to use for path length fingerprints...</span> 170 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="n">1</span><span class="sc">;</span> 171 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="n">8</span><span class="sc">;</span> 172 173 <span class="c"># By default bond symbols are included in atom path strings used to generate path length</span> 174 <span class="c"># fingerprints... ...</span> 175 <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} = <span class="n">1</span><span class="sc">;</span> 176 177 <span class="c"># Minimum and maximum bond distance between atom pairs during topological</span> 178 <span class="c"># atom pairs/triplets fingerprints...</span> 179 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span> 180 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> 181 182 <span class="c"># Determines whether to apply triangle inequality to distance triplets...</span> 183 <span class="c">#</span> 184 <span class="c"># Default for TopologicalAtomTripletsFingerprints: 0</span> 185 <span class="c"># Default for TopologicalPharmacophoreAtomTripletsFingerprints: 1</span> 186 <span class="c">#</span> 187 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="q">''</span><span class="sc">;</span> 188 189 <span class="c"># Distance bin size used for binning distances during generation of</span> 190 <span class="c"># topological pharmacophore atom triplets fingerprints...</span> 191 <span class="c">#</span> 192 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="n">2</span><span class="sc">;</span> 193 194 <span class="c"># Normalization methodology to use for scaling the number of bits-set or unique keys</span> 195 <span class="c"># for:</span> 196 <span class="c">#</span> 197 <span class="c"># ExtendedConnectivityFingerprints</span> 198 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> 199 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> 200 <span class="c">#</span> 201 <span class="c"># This option is gnored for all other types of fingerprints.</span> 202 <span class="c">#</span> 203 <span class="c"># Possible values during extended connectivity fingerprints: None or ByHeavyAtomsCount. Default:</span> 204 <span class="c"># None.</span> 205 <span class="c">#</span> 206 <span class="c"># Possible values during topological pharmacophore atom pairs and tripletes fingerprints: None,</span> 207 <span class="c"># or ByPossibleKeysCount. Default: None. ByPossibleKeysCount corresponds to total number of</span> 208 <span class="c"># possible topological pharmacophore atom pairs or triplets in a molecule.</span> 209 <span class="c">#</span> 210 <span class="c">#</span> 211 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="q">'None'</span><span class="sc">;</span> 212 213 <span class="c"># Intialize descriptor names and values...</span> 214 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> 215 216 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 217 <span class="s">}</span> 218 219 <span class="c"># Initialize object properties...</span> 220 <span class="c">#</span> <a name="_InitializeMolecularComplexityDescriptorsProperties-"></a> 221 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptorsProperties</span> <span class="s">{</span> 222 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 223 224 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span> 225 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> 226 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 227 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 228 <span class="s">}</span> 229 230 <span class="c"># Make sure MolecularComplexityType is set...</span> 231 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span> 232 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">'MACCSKeys'</span><span class="sc">;</span> 233 <span class="s">}</span> 234 235 <span class="c"># Make sure AtomIdentifierType is set...</span> 236 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} !~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span> 237 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> 238 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 239 <span class="s">}</span> 240 <span class="s">}</span> 241 242 <span class="c"># Make sure UseTriangleInequality is set...</span> 243 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalAtomTripletsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> 244 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">UseTriangleInequality</span>}<span class="s">)</span> <span class="s">{</span> 245 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 246 <span class="s">}</span> 247 <span class="s">}</span> 248 249 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 250 <span class="s">}</span> 251 252 <span class="c"># Initialize atom identifer type...</span> 253 <span class="c">#</span> <a name="_InitializeAtomIdentifierType-"></a> 254 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierType</span> <span class="s">{</span> 255 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 256 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIdentifierType</span><span class="s">)</span><span class="sc">;</span> 257 258 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span> 259 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 260 <span class="s">}</span> 261 262 <span class="i">$AtomIdentifierType</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> ? <span class="q">'FunctionalClassAtomTypes'</span> <span class="co">:</span> <span class="q">'AtomicInvariantsAtomTypes'</span><span class="sc">;</span> 263 264 <span class="i">$This</span><span class="i">->SetAtomIdentifierType</span><span class="s">(</span><span class="i">$AtomIdentifierType</span><span class="s">)</span><span class="sc">;</span> 265 266 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 267 <span class="s">}</span> 268 269 <span class="c"># Get abbreviation for specified molecular complexity type or using descriptors object...</span> 270 <span class="c">#</span> 271 <span class="c"># This functionality can be either invoked as a class function or an</span> 272 <span class="c"># object method.</span> 273 <span class="c">#</span> <a name="GetMolecularComplexityTypeAbbreviation-"></a> 274 <span class="k">sub </span><span class="m">GetMolecularComplexityTypeAbbreviation</span> <span class="s">{</span> 275 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 276 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ComplexityType</span><span class="cm">,</span> <span class="i">%ComplexityTypeToAbbrev</span><span class="s">)</span><span class="sc">;</span> 277 278 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecularComplexityDescriptors</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 279 <span class="i">$This</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> 280 <span class="i">$ComplexityType</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span> 281 <span class="s">}</span> 282 <span class="k">else</span> <span class="s">{</span> 283 <span class="i">$ComplexityType</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> 284 <span class="s">}</span> 285 286 <span class="i">%ComplexityTypeToAbbrev</span> = <span class="s">(</span><span class="k">lc</span> <span class="q">'AtomTypesFingerprints'</span> <span class="cm">=></span> <span class="q">'ATFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'ExtendedConnectivityFingerprints'</span> <span class="cm">=></span> <span class="q">'ECFP'</span><span class="cm">,</span> 287 <span class="k">lc</span> <span class="q">'MACCSKeys'</span> <span class="cm">=></span> <span class="q">'MACCSKeys'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'PathLengthFingerprints'</span> <span class="cm">=></span> <span class="q">'PLFP'</span><span class="cm">,</span> 288 <span class="k">lc</span> <span class="q">'TopologicalAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TAPFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'TopologicalAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span> 289 <span class="k">lc</span> <span class="q">'TopologicalAtomTorsionsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span> 290 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPAPFP'</span><span class="cm">,</span> 291 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPATFP'</span><span class="s">)</span><span class="sc">;</span> 292 293 <span class="k">return</span> <span class="k">exists</span> <span class="i">$ComplexityTypeToAbbrev</span>{<span class="k">lc</span> <span class="i">$ComplexityType</span>} ? <span class="i">$ComplexityTypeToAbbrev</span>{<span class="k">lc</span> <span class="i">$ComplexityType</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> 294 <span class="s">}</span> 295 296 <span class="c"># Set MACCS key set size...</span> 297 <span class="c">#</span> <a name="SetMACCSKeysSize-"></a> 298 <span class="k">sub </span><span class="m">SetMACCSKeysSize</span> <span class="s">{</span> 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 300 301 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 302 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: Size value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> 303 <span class="s">}</span> 304 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(166|322)/i</span><span class="s">)</span> <span class="s">{</span> 305 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: The current release of MayaChemTools doesn't support MDL MACCS $Value keys..."</span><span class="sc">;</span> 306 <span class="s">}</span> 307 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="i">$Value</span><span class="sc">;</span> 308 309 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 310 <span class="s">}</span> 311 312 <span class="c"># Set minimum path length...</span> 313 <span class="c">#</span> <a name="SetMinPathLength-"></a> 314 <span class="k">sub </span><span class="m">SetMinPathLength</span> <span class="s">{</span> 315 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 316 317 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 318 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinPathLength: MinPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> 319 <span class="s">}</span> 320 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span> 321 322 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 323 <span class="s">}</span> 324 325 <span class="c"># Set maximum path length...</span> 326 <span class="c">#</span> <a name="SetMaxPathLength-"></a> 327 <span class="k">sub </span><span class="m">SetMaxPathLength</span> <span class="s">{</span> 328 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 329 330 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 331 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxPathLength: MaxPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> 332 <span class="s">}</span> 333 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span> 334 335 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 336 <span class="s">}</span> 337 338 <span class="c"># Set minimum bond distance between atom pairs during topological and topological</span> 339 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span> 340 <span class="c">#</span> <a name="SetMinDistance-"></a> 341 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span> 342 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 343 344 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 345 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> 346 <span class="s">}</span> 347 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> 348 349 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 350 <span class="s">}</span> 351 352 <span class="c"># Set maximum bond distance between atom pairs during topological and topological</span> 353 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span> 354 <span class="c">#</span> <a name="SetMaxDistance-"></a> 355 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span> 356 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 357 358 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 359 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> 360 <span class="s">}</span> 361 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> 362 363 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 364 <span class="s">}</span> 365 366 <span class="c"># Set atom neighborhood radius...</span> 367 <span class="c">#</span> <a name="SetNeighborhoodRadius-"></a> 368 <span class="k">sub </span><span class="m">SetNeighborhoodRadius</span> <span class="s">{</span> 369 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 370 371 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 372 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> 373 <span class="s">}</span> 374 375 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span> 376 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span> 377 <span class="s">}</span> 378 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span> 379 380 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 381 <span class="s">}</span> 382 383 <span class="c"># Set molecular complexity type...</span> 384 <span class="c">#</span> <a name="SetMolecularComplexityType-"></a> 385 <span class="k">sub </span><span class="m">SetMolecularComplexityType</span> <span class="s">{</span> 386 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 387 388 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|MACCSKeys|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> 389 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecularComplexityType: MolecularComplexityType value, $Value, is not valid. Supported values: AtomTypesFingerprints, ExtendedConnectivityFingerprints, MACCSKeys, PathLengthFingerprints, TopologicalAtomPairsFingerprints, TopologicalAtomTripletsFingerprints, TopologicalAtomTorsionsFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints..."</span><span class="sc">;</span> 390 <span class="s">}</span> 391 392 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="i">$Value</span><span class="sc">;</span> 393 394 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 395 <span class="s">}</span> 396 397 <span class="c"># Set distance bin size for binning pharmacophore atom pair distances in atom triplets...</span> 398 <span class="c">#</span> <a name="SetDistanceBinSize-"></a> 399 <span class="k">sub </span><span class="m">SetDistanceBinSize</span> <span class="s">{</span> 400 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 401 402 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 403 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDistanceBinSize: DistanceBinSize value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> 404 <span class="s">}</span> 405 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="i">$Value</span><span class="sc">;</span> 406 407 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 408 <span class="s">}</span> 409 410 <span class="c"># Set normalization methodology to use for scaling the number of bits-set or unique keys</span> 411 <span class="c"># in fingerprints...</span> 412 <span class="c">#</span> <a name="SetNormalizationMethodology-"></a> 413 <span class="k">sub </span><span class="m">SetNormalizationMethodology</span> <span class="s">{</span> 414 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 415 416 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount|ByPossibleKeysCount|None)$/i</span><span class="s">)</span> <span class="s">{</span> 417 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid. Supported values: None, ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span> 418 <span class="s">}</span> 419 420 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span> 421 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} !~ <span class="q">/^(ExtendedConnectivityFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> 422 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: Normalization is not supported for MolecularComplexityType: $This->{MolecularComplexityType}. Valid MolecularComplexityType values: ExtendedConnectivityFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints...\n"</span><span class="sc">;</span> 423 <span class="s">}</span> 424 425 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span> && <span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount|None)$/i</span><span class="s">)</span> <span class="s">{</span> 426 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByHeavyAtomsCount..."</span><span class="sc">;</span> 427 <span class="s">}</span> 428 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span> && <span class="i">$Value</span> !~ <span class="q">/^(ByPossibleKeysCount|None)$/i</span><span class="s">)</span> <span class="s">{</span> 430 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByPossibleKeysCount..."</span><span class="sc">;</span> 431 <span class="s">}</span> 432 <span class="s">}</span> 433 434 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span> 435 436 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 437 <span class="s">}</span> 438 439 <span class="c"># Set intial atom identifier type..</span> 440 <span class="c">#</span> <a name="SetAtomIdentifierType-"></a> 441 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> 442 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IdentifierType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 443 444 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> 445 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes."</span><span class="sc">;</span> 446 <span class="s">}</span> 447 448 <span class="c"># FunctionalClassAtomTypes is the only valid atom identifier type for pharmacophore fingerprints...</span> 449 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> 450 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 451 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported type for $This->{MolecularComplexityType} complexity type: FunctionalClassAtomTypes."</span><span class="sc">;</span> 452 <span class="s">}</span> 453 <span class="s">}</span> 454 455 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> 456 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span> 457 <span class="s">}</span> 458 459 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> 460 461 <span class="c"># Initialize identifier type information...</span> 462 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 463 464 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 465 <span class="s">}</span> 466 467 <span class="c"># Calculate molecular complexity [ Ref 117-119 ] of a molecule using its fingerprints.</span> 468 <span class="c">#</span> 469 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span> 470 <span class="c"># corresponding to the number of bits-set or unique keys in molecular fingerprints. The</span> 471 <span class="c"># following types of fingerprints based molecular complexity measures are supported:</span> 472 <span class="c">#</span> 473 <span class="c"># AtomTypesFingerprints</span> 474 <span class="c"># ExtendedConnectivityFingerprints</span> 475 <span class="c"># MACCSKeys</span> 476 <span class="c"># PathLengthFingerprints</span> 477 <span class="c"># TopologicalAtomPairsFingerprints</span> 478 <span class="c"># TopologicalAtomTripletsFingerprints</span> 479 <span class="c"># TopologicalAtomTorsionsFingerprints</span> 480 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> 481 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> 482 <span class="c">#</span> 483 <span class="c"># After the molecular complexity value has been calculated, it can also be normalized by</span> 484 <span class="c"># by scaling the number of bits-set or unique keys for following types of fingerprints:</span> 485 <span class="c">#</span> 486 <span class="c"># ExtendedConnectivityFingerprints</span> 487 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> 488 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> 489 <span class="c">#</span> 490 <span class="c"># Two types of normalization methodologies are supported: by heavy atoms count for</span> 491 <span class="c"># extended connectivity fingerprints; by possible keys count for topological pharmacophore</span> 492 <span class="c"># atom pairs and triplets fingerprints.</span> 493 <span class="c">#</span> <a name="GenerateDescriptors-"></a> 494 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> 495 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 496 497 <span class="c"># Initialize descriptor values...</span> 498 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 499 500 <span class="c"># Check availability of molecule...</span> 501 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> 502 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> 503 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 504 <span class="s">}</span> 505 506 <span class="c"># Calculate descriptor values...</span> 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 508 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate MolecularComplexity values corresponding to assigned MolecularComplexity atom types..."</span><span class="sc">;</span> 509 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 510 <span class="s">}</span> 511 512 <span class="c"># Set final descriptor values...</span> 513 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 514 515 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 516 <span class="s">}</span> 517 518 <span class="c"># Calculate molecular complexity value...</span> 519 <span class="c">#</span> <a name="_CalculateDescriptorValues-"></a> 520 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> 521 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 522 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span> 523 524 <span class="c"># Setup fingerprints object and generate fingerprints...</span> 525 <span class="i">$MethodName</span> = <span class="q">"_Setup"</span> . <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span> 526 <span class="i">$FingerprintsObject</span> = <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 527 528 <span class="i">$FingerprintsObject</span><span class="i">->GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 529 530 <span class="c"># Make sure atom types fingerprints generation is successful...</span> 531 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsObject</span><span class="i">->IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 532 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 533 <span class="s">}</span> 534 535 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 536 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 537 <span class="s">}</span> 538 539 <span class="c"># Normalize molecular complexity...</span> 540 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> 541 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_NormalizeMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 542 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 543 <span class="s">}</span> 544 <span class="s">}</span> 545 546 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 547 <span class="s">}</span> 548 549 <span class="c"># Setup atom types fingerprints...</span> 550 <span class="c">#</span> <a name="_SetupAtomTypesFingerprints-"></a> 551 <span class="k">sub </span><span class="m">_SetupAtomTypesFingerprints</span> <span class="s">{</span> 552 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 553 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 554 555 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::AtomTypesFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'AtomTypesCount'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> 556 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 557 558 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> 559 <span class="s">}</span> 560 561 <span class="c"># Setup extended connectivity fingerprints...</span> 562 <span class="c">#</span> <a name="_SetupExtendedConnectivityFingerprints-"></a> 563 <span class="k">sub </span><span class="m">_SetupExtendedConnectivityFingerprints</span> <span class="s">{</span> 564 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 565 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 566 567 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'ExtendedConnectivity'</span><span class="cm">,</span> <span class="q">'NeighborhoodRadius'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> 568 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 569 570 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> 571 <span class="s">}</span> 572 573 <span class="c"># Setup MACCS keys...</span> 574 <span class="c">#</span> <a name="_SetupMACCSKeys-"></a> 575 <span class="k">sub </span><span class="m">_SetupMACCSKeys</span> <span class="s">{</span> 576 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 577 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 578 579 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::MACCSKeys</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'MACCSKeyBits'</span><span class="cm">,</span> <span class="q">'Size'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>}<span class="s">)</span><span class="sc">;</span> 580 581 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> 582 <span class="s">}</span> 583 584 <span class="c"># Set up path length fingerprints...</span> 585 <span class="c">#</span> <a name="_SetupPathLengthFingerprints-"></a> 586 <span class="k">sub </span><span class="m">_SetupPathLengthFingerprints</span> <span class="s">{</span> 587 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 588 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 589 590 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::PathLengthFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'PathLengthCount'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'MinLength'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinPathLength</span>}<span class="cm">,</span> <span class="q">'MaxLength'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxPathLength</span>}<span class="cm">,</span> <span class="q">'AllowRings'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'AllowSharedBonds'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'UseBondSymbols'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="cm">,</span> <span class="q">'UseUniquePaths'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> 591 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 592 593 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> 594 <span class="s">}</span> 595 596 <span class="c"># Setup topological atom pairs fingerprints...</span> 597 <span class="c">#</span> <a name="_SetupTopologicalAtomPairsFingerprints-"></a> 598 <span class="k">sub </span><span class="m">_SetupTopologicalAtomPairsFingerprints</span> <span class="s">{</span> 599 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 600 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 601 602 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> 603 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 604 605 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> 606 <span class="s">}</span> 607 608 <span class="c"># Setup topological atom triplets fingerprints...</span> 609 <span class="c">#</span> <a name="_SetupTopologicalAtomTripletsFingerprints-"></a> 610 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTripletsFingerprints</span> <span class="s">{</span> 611 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 612 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 613 614 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> 615 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 616 617 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> 618 <span class="s">}</span> 619 620 <span class="c"># Setup topological atom torsions fingerprints...</span> 621 <span class="c">#</span> <a name="_SetupTopologicalAtomTorsionsFingerprints-"></a> 622 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTorsionsFingerprints</span> <span class="s">{</span> 623 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 624 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 625 626 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> 627 628 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 629 630 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> 631 <span class="s">}</span> 632 633 <span class="c"># Setup TopologicalPharmacophoreAtomPairsFingerprints...</span> 634 <span class="c">#</span> <a name="_SetupTopologicalPharmacophoreAtomPairsFingerprints-"></a> 635 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span> 636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 637 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$AtomPairsSetSizeToUse</span><span class="s">)</span><span class="sc">;</span> 638 639 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span> 640 <span class="i">$AtomPairsSetSizeToUse</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> ? <span class="q">'FixedSize'</span> <span class="co">:</span> <span class="q">'ArbitrarySize'</span><span class="sc">;</span> 641 642 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomPairsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$AtomPairsSetSizeToUse</span><span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">'NormalizationMethodology'</span> <span class="cm">=></span> <span class="q">'None'</span><span class="cm">,</span> <span class="q">'ValuesPrecision'</span> <span class="cm">=></span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span> 643 644 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> 645 <span class="s">}</span> 646 647 <span class="c"># Setup TopologicalPharmacophoreAtomTripletsFingerprints...</span> 648 <span class="c">#</span> <a name="_SetupTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 649 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span> 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 651 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$AtomTripletsSetSizeToUse</span><span class="s">)</span><span class="sc">;</span> 652 653 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span> 654 <span class="i">$AtomTripletsSetSizeToUse</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> ? <span class="q">'FixedSize'</span> <span class="co">:</span> <span class="q">'ArbitrarySize'</span><span class="sc">;</span> 655 656 <span class="i">$FingerprintsObject</span> = <span class="i">new</span> <span class="i">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'AtomTripletsSetSizeToUse'</span> <span class="cm">=></span> <span class="i">$AtomTripletsSetSizeToUse</span><span class="cm">,</span> <span class="q">'MinDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="cm">,</span> <span class="q">'MaxDistance'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="cm">,</span> <span class="q">'DistanceBinSize'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="cm">,</span> <span class="q">'UseTriangleInequality'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>}<span class="cm">,</span> <span class="q">'AtomTypesToUse'</span> <span class="cm">=></span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span> 657 658 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> 659 <span class="s">}</span> 660 661 <span class="c"># Normalize molecular complexity value...</span> 662 <span class="c">#</span> <a name="_NormalizeMolecularComplexity-"></a> 663 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexity</span> <span class="s">{</span> 664 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 665 666 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span> && <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByHeavyAtomsCount$/i</span><span class="s">)</span> <span class="s">{</span> 667 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByHeavyAtomsCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 668 <span class="s">}</span> 669 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span> && <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> <span class="s">{</span> 670 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByPossibleKeysCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> 671 <span class="s">}</span> 672 <span class="k">else</span> <span class="s">{</span> 673 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_NormalizeMolecularComplexity: NormalizationMethodology value, $This->{NormalizationMethodology}, is not valid. Supported values: ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span> 674 <span class="s">}</span> 675 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 676 <span class="s">}</span> 677 678 <span class="c"># Normalize molecular complexity value by heavy atom count...</span> 679 <span class="c">#</span> <a name="_NormalizeMolecularComplexityByHeavyAtomsCount-"></a> 680 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByHeavyAtomsCount</span> <span class="s">{</span> 681 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 682 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfHeavyAtoms</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span> 683 684 <span class="i">$NumOfHeavyAtoms</span> = <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetNumOfHeavyAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 685 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfHeavyAtoms</span><span class="s">)</span> <span class="s">{</span> 686 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 687 <span class="s">}</span> 688 689 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfHeavyAtoms</span><span class="sc">;</span> 690 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$NormalizedComplexity</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> 691 692 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 693 <span class="s">}</span> 694 695 <span class="c"># Normalize molecular complexity value by possible keys count...</span> 696 <span class="c">#</span> <a name="_NormalizeMolecularComplexityByPossibleKeysCount-"></a> 697 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByPossibleKeysCount</span> <span class="s">{</span> 698 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 699 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfPossibleKeys</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span> 700 701 <span class="i">$NumOfPossibleKeys</span> = <span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 702 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfPossibleKeys</span><span class="s">)</span> <span class="s">{</span> 703 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 704 <span class="s">}</span> 705 706 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfPossibleKeys</span><span class="sc">;</span> 707 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$NormalizedComplexity</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> 708 709 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 710 <span class="s">}</span> 711 712 <span class="c"># Calculate molecular complexity value using fingerprints objects...</span> 713 <span class="c">#</span> <a name="_CalculateMolecularComplexity-"></a> 714 <span class="k">sub </span><span class="m">_CalculateMolecularComplexity</span> <span class="s">{</span> 715 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 716 717 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span> 718 <span class="k">return</span> <span class="i">$This</span><span class="i">->_CalculateMolecularComplexityUsingFingerprintsBitVector</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 719 <span class="s">}</span> 720 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsVector$/i</span><span class="s">)</span> <span class="s">{</span> 721 <span class="k">return</span> <span class="i">$This</span><span class="i">->_CalculateMolecularComplexityUsingFingerprintsVector</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 722 <span class="s">}</span> 723 <span class="k">else</span> <span class="s">{</span> 724 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_CalculateMolecularComplexity: Fingerprints vector type is not valid. Supported values: FingerprintsBitVector or FingerprintsVector..."</span><span class="sc">;</span> 725 <span class="s">}</span> 726 727 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 728 <span class="s">}</span> 729 730 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span> 731 <span class="c">#</span> <a name="_CalculateMolecularComplexityUsingFingerprintsVector-"></a> 732 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsVector</span> <span class="s">{</span> 733 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 734 735 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="s">(</span><span class="i">$FingerprintsVector</span><span class="i">->GetType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^(OrderedNumericalValues|NumericalValues)$/i</span><span class="s">)</span> ? <span class="i">$FingerprintsVector</span><span class="i">->GetNumOfNonZeroValues</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="i">$FingerprintsVector</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 736 737 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 738 <span class="s">}</span> 739 740 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span> 741 <span class="c">#</span> <a name="_CalculateMolecularComplexityUsingFingerprintsBitVector-"></a> 742 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsBitVector</span> <span class="s">{</span> 743 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 744 745 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">$FingerprintsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 746 747 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 748 <span class="s">}</span> 749 750 <span class="c"># Setup final descriptor values...</span> 751 <span class="c">#</span> <a name="_SetFinalDescriptorValues-"></a> 752 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> 753 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 754 755 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> 756 757 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexity</span>}<span class="s">)</span><span class="sc">;</span> 758 759 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 760 <span class="s">}</span> 761 762 <span class="c"># Set atom identifier type to use for generating fingerprints...</span> 763 <span class="c">#</span> <a name="_SetAtomIdentifierTypeValuesToUse-"></a> 764 <span class="k">sub </span><span class="m">_SetAtomIdentifierTypeValuesToUse</span> <span class="s">{</span> 765 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 766 767 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 768 <span class="i">$FingerprintsObject</span><span class="i">->SetAtomicInvariantsToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="s">)</span><span class="sc">;</span> 769 <span class="s">}</span> 770 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 771 <span class="i">$FingerprintsObject</span><span class="i">->SetFunctionalClassesToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span> 772 <span class="s">}</span> 773 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> 774 <span class="c"># Nothing to do for now...</span> 775 <span class="s">}</span> 776 <span class="k">else</span> <span class="s">{</span> 777 <span class="w">croak</span> <span class="q">"Error: The value specified, $This->{AtomIdentifierType}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span> 778 <span class="s">}</span> 779 <span class="s">}</span> 780 781 <span class="c"># Initialize atom indentifier type information...</span> 782 <span class="c">#</span> 783 <span class="c"># Current supported values:</span> 784 <span class="c">#</span> 785 <span class="c"># AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,</span> 786 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> 787 <span class="c">#</span> <a name="_InitializeAtomIdentifierTypeInformation-"></a> 788 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> 789 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 790 791 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> 792 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 793 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 794 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 795 <span class="s">}</span> 796 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 797 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 798 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 799 <span class="s">}</span> 800 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> 801 <span class="c"># Nothing to do for now...</span> 802 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 803 <span class="s">}</span> 804 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 805 <span class="s">}</span> 806 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 807 <span class="s">}</span> 808 809 <span class="c"># Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes</span> 810 <span class="c"># class, to use for generating initial atom identifiers...</span> 811 <span class="c">#</span> 812 <span class="c"># Let:</span> 813 <span class="c"># AS = Atom symbol corresponding to element symbol</span> 814 <span class="c">#</span> 815 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> 816 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 817 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> 818 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 819 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 820 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 821 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> 822 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> 823 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> 824 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> 825 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> 826 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> 827 <span class="c">#</span> 828 <span class="c"># Then:</span> 829 <span class="c">#</span> 830 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> 831 <span class="c">#</span> 832 <span class="c"># AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></span> 833 <span class="c">#</span> 834 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span> 835 <span class="c"># optional.</span> 836 <span class="c">#</span> 837 <span class="c"># Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:</span> 838 <span class="c">#</span> 839 <span class="c"># AS, X<n>, BO<n>, H<n>, FC<+n/-n>, MN<n></span> 840 <span class="c">#</span> 841 <span class="c"># In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words</span> 842 <span class="c"># are also allowed:</span> 843 <span class="c">#</span> 844 <span class="c"># X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors</span> 845 <span class="c"># BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms</span> 846 <span class="c"># LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms</span> 847 <span class="c"># SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms</span> 848 <span class="c"># DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms</span> 849 <span class="c"># TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms</span> 850 <span class="c"># H : NumOfImplicitAndExplicitHydrogens</span> 851 <span class="c"># Ar : Aromatic</span> 852 <span class="c"># RA : RingAtom</span> 853 <span class="c"># FC : FormalCharge</span> 854 <span class="c"># MN : MassNumber</span> 855 <span class="c"># SM : SpinMultiplicity</span> 856 <span class="c">#</span> <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 857 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> 858 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 859 860 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 861 862 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> 863 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span> 864 <span class="s">}</span> 865 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 866 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="cm">,</span> <span class="q">'MN'</span><span class="s">)</span><span class="sc">;</span> 867 <span class="s">}</span> 868 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 869 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="s">)</span><span class="sc">;</span> 870 <span class="s">}</span> 871 872 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 873 <span class="s">}</span> 874 875 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> 876 <span class="c"># class, to use for generating initial atom identifiers...</span> 877 <span class="c">#</span> 878 <span class="c"># Let:</span> 879 <span class="c"># HBD: HydrogenBondDonor</span> 880 <span class="c"># HBA: HydrogenBondAcceptor</span> 881 <span class="c"># PI : PositivelyIonizable</span> 882 <span class="c"># NI : NegativelyIonizable</span> 883 <span class="c"># Ar : Aromatic</span> 884 <span class="c"># Hal : Halogen</span> 885 <span class="c"># H : Hydrophobic</span> 886 <span class="c"># RA : RingAtom</span> 887 <span class="c"># CA : ChainAtom</span> 888 <span class="c">#</span> 889 <span class="c"># Then:</span> 890 <span class="c">#</span> 891 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> 892 <span class="c">#</span> 893 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> 894 <span class="c">#</span> 895 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> 896 <span class="c">#</span> 897 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> 898 <span class="c">#</span> 899 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> 900 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> 901 <span class="c"># PositivelyIonizable: +, NH2</span> 902 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> 903 <span class="c">#</span> <a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 904 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> 905 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 906 907 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 908 909 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> 910 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> 911 <span class="s">}</span> 912 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 913 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="s">)</span><span class="sc">;</span> 914 <span class="s">}</span> 915 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 916 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="s">)</span><span class="sc">;</span> 917 <span class="s">}</span> 918 919 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 920 <span class="s">}</span> 921 922 <span class="c"># Set atomic invariants to use for generation of intial atom indentifiers...</span> 923 <span class="c">#</span> <a name="SetAtomicInvariantsToUse-"></a> 924 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> 925 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 926 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$SpecifiedAtomicInvariant</span><span class="cm">,</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span> 927 928 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 929 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> 930 <span class="k">return</span><span class="sc">;</span> 931 <span class="s">}</span> 932 933 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 934 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: AtomicInvariantsToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 935 <span class="k">return</span><span class="sc">;</span> 936 <span class="s">}</span> 937 938 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 939 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 940 941 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 942 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 943 944 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 945 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> 946 <span class="s">}</span> 947 <span class="k">else</span> <span class="s">{</span> 948 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 949 <span class="s">}</span> 950 951 <span class="c"># Make sure specified AtomicInvariants are valid...</span> 952 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> 953 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 954 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> 955 <span class="s">}</span> 956 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> 957 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> 958 <span class="s">}</span> 959 960 <span class="c"># Set atomic invariants to use...</span> 961 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 962 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> 963 964 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 965 <span class="s">}</span> 966 967 <span class="c"># Set functional classes to use for generation of intial atom indentifiers...</span> 968 <span class="c">#</span> <a name="SetFunctionalClassesToUse-"></a> 969 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> 970 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 971 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="cm">,</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span> 972 973 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 974 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> 975 <span class="k">return</span><span class="sc">;</span> 976 <span class="s">}</span> 977 978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 979 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 980 <span class="k">return</span><span class="sc">;</span> 981 <span class="s">}</span> 982 983 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 984 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 985 986 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 987 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 988 989 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 990 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> 991 <span class="s">}</span> 992 <span class="k">else</span> <span class="s">{</span> 993 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 994 <span class="s">}</span> 995 996 <span class="c"># Make sure specified FunctionalClasses are valid...</span> 997 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> 998 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedFunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 999 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> 1000 <span class="s">}</span> 1001 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> 1002 <span class="s">}</span> 1003 1004 <span class="c"># Set functional classes to use...</span> 1005 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1006 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> 1007 1008 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1009 <span class="s">}</span> 1010 1011 <span class="c"># Return a string containg data for MolecularComplexityDescriptors object...</span> 1012 <span class="c">#</span> <a name="StringifyMolecularComplexityDescriptors-"></a>1013 <span class="k">sub </span><span class="m">StringifyMolecularComplexityDescriptors</span> <span class="s">{</span> 1014 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1015 <span class="k">my</span><span class="s">(</span><span class="i">$ComplexityDescriptorsString</span><span class="cm">,</span> <span class="i">$Nothing</span><span class="s">)</span><span class="sc">;</span> 1016 1017 <span class="i">$ComplexityDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; MolecularComplexityType: $This->{MolecularComplexityType}; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1018 1019 <span class="c"># Setup fingerprints specific information...</span> 1020 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span> 1021 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MACCSKeysSize = $This->{MACCSKeysSize}"</span><span class="sc">;</span> 1022 <span class="s">}</span> 1023 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1024 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; NeighborhoodRadius = $This->{NeighborhoodRadius}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span> 1025 <span class="s">}</span> 1026 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1027 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinPathLength = $This->{MinPathLength}; MaxPathLength = $This->{MaxPathLength}; UseBondSymbols: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> 1028 <span class="s">}</span> 1029 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1030 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span> 1031 <span class="s">}</span> 1032 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1033 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> 1034 <span class="s">}</span> 1035 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomTorsionsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1036 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span> 1037 <span class="s">}</span> 1038 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1039 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span> 1040 <span class="s">}</span> 1041 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> 1042 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; NormalizationMethodology = $This->{NormalizationMethodology}; DistanceBinSize: $This->{DistanceBinSize}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> 1043 <span class="s">}</span> 1044 1045 <span class="c"># Setup atom identifier information...</span> 1046 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> 1047 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomIdentifierType = $This->{AtomIdentifierType}"</span><span class="sc">;</span> 1048 1049 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 1050 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomicInvariants</span><span class="s">)</span><span class="sc">;</span> 1051 1052 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1053 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1054 1055 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> 1056 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> 1057 <span class="s">}</span> 1058 1059 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 1060 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 1061 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AvailableAtomicInvariants: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 1062 <span class="s">}</span> 1063 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 1064 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> 1065 1066 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1067 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1068 1069 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> 1070 <span class="k">push</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">"$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}"</span><span class="sc">;</span> 1071 <span class="s">}</span> 1072 1073 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 1074 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 1075 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AvailableFunctionalClasses: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 1076 <span class="s">}</span> 1077 <span class="s">}</span> 1078 <span class="k">return</span> <span class="i">$ComplexityDescriptorsString</span><span class="sc">;</span> 1079 <span class="s">}</span> 1080 1081 <span class="c"># Is it a MolecularComplexityDescriptors object?</span> <a name="_IsMolecularComplexityDescriptors-"></a>1082 <span class="k">sub </span><span class="m">_IsMolecularComplexityDescriptors</span> <span class="s">{</span> 1083 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1084 1085 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</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> 1086 <span class="s">}</span> 1087 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>