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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:MolecularDescriptors::MolecularComplexityDescriptors.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
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| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
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| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-MolecularDescriptors::MolecularComplexityDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularComplexityDescriptors</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: MolecularComplexityDescriptors.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> | |
| 18 5 <span class="c"># $Revision: 1.15 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> | |
| 51 38 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> | |
| 52 39 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> | |
| 53 40 <span class="k">use</span> <span class="w">Fingerprints::AtomTypesFingerprints</span><span class="sc">;</span> | |
| 54 41 <span class="k">use</span> <span class="w">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span> | |
| 55 42 <span class="k">use</span> <span class="w">Fingerprints::MACCSKeys</span><span class="sc">;</span> | |
| 56 43 <span class="k">use</span> <span class="w">Fingerprints::PathLengthFingerprints</span><span class="sc">;</span> | |
| 57 44 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="sc">;</span> | |
| 58 45 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="sc">;</span> | |
| 59 46 <span class="k">use</span> <span class="w">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="sc">;</span> | |
| 60 47 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span> | |
| 61 48 <span class="k">use</span> <span class="w">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="sc">;</span> | |
| 62 49 | |
| 63 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> | |
| 64 51 | |
| 65 52 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> | |
| 66 53 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 67 54 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames GetMolecularComplexityTypeAbbreviation)</span><span class="sc">;</span> | |
| 68 55 | |
| 69 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> | |
| 70 57 | |
| 71 58 <span class="c"># Setup class variables...</span> | |
| 72 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> | |
| 73 60 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 74 61 | |
| 75 62 <span class="c"># Overload Perl functions...</span> | |
| 76 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> | |
| 77 64 | |
| 78 65 <span class="c"># Class constructor...</span> | |
| 79 <a name="new-"></a> 66 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 80 67 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 81 68 | |
| 82 69 <span class="c"># Initialize object...</span> | |
| 83 70 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 84 71 <span class="k">bless</span> <span class="i">$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> | |
| 85 72 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 86 73 | |
| 87 74 <span class="i">$This</span><span class="i">->_InitializeMolecularComplexityDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 88 75 | |
| 89 76 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 90 77 <span class="s">}</span> | |
| 91 78 | |
| 92 79 <span class="c"># Initialize class ...</span> | |
| 93 <a name="_InitializeClass-"></a> 80 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 94 81 <span class="c">#Class name...</span> | |
| 95 82 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 96 83 | |
| 97 84 <span class="c"># Descriptor names...</span> | |
| 98 85 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'MolecularComplexity'</span><span class="s">)</span><span class="sc">;</span> | |
| 99 86 | |
| 100 87 <span class="s">}</span> | |
| 101 88 | |
| 102 89 <span class="c"># Get descriptor names as an array.</span> | |
| 103 90 <span class="c">#</span> | |
| 104 91 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 105 92 <span class="c"># object method.</span> | |
| 106 93 <span class="c">#</span> | |
| 107 <a name="GetDescriptorNames-"></a> 94 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> | |
| 108 95 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> | |
| 109 96 <span class="s">}</span> | |
| 110 97 | |
| 111 98 <span class="c"># Initialize object data...</span> | |
| 112 99 <span class="c">#</span> | |
| 113 <a name="_InitializeMolecularComplexityDescriptors-"></a> 100 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptors</span> <span class="s">{</span> | |
| 114 101 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 115 102 | |
| 116 103 <span class="c"># Type of MolecularDescriptor...</span> | |
| 117 104 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'MolecularComplexity'</span><span class="sc">;</span> | |
| 118 105 | |
| 119 106 <span class="c">#</span> | |
| 120 107 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span> | |
| 121 108 <span class="c"># corresponding to number of bits-set or unique keys [ Ref 117-119 ] in molecular</span> | |
| 122 109 <span class="c"># fingerprints. The following types of fingerprints based molecular complexity measures</span> | |
| 123 110 <span class="c"># are supported:</span> | |
| 124 111 <span class="c">#</span> | |
| 125 112 <span class="c"># AtomTypesFingerprints</span> | |
| 126 113 <span class="c"># ExtendedConnectivityFingerprints</span> | |
| 127 114 <span class="c"># MACCSKeys</span> | |
| 128 115 <span class="c"># PathLengthFingerprints</span> | |
| 129 116 <span class="c"># TopologicalAtomPairsFingerprints</span> | |
| 130 117 <span class="c"># TopologicalAtomTripletsFingerprints</span> | |
| 131 118 <span class="c"># TopologicalAtomTorsionsFingerprints</span> | |
| 132 119 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> | |
| 133 120 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> | |
| 134 121 <span class="c">#</span> | |
| 135 122 <span class="c"># Default: MACCSKeys</span> | |
| 136 123 <span class="c">#</span> | |
| 137 124 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 138 125 | |
| 139 126 <span class="c"># Atom types to use for generating fingerprints...</span> | |
| 140 127 <span class="c">#</span> | |
| 141 128 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span> | |
| 142 129 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span> | |
| 143 130 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> | |
| 144 131 <span class="c">#</span> | |
| 145 132 <span class="c"># Notes:</span> | |
| 146 133 <span class="c"># . AtomicInvariantsAtomTypes for all supported MolecularComplexityType except for</span> | |
| 147 134 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints and TopologicalPharmacophoreAtomTripletsFingerprints</span> | |
| 148 135 <span class="c"># . This value is not used for MACCSKeys</span> | |
| 149 136 <span class="c"># . FunctionalClassAtomTypes is the only valid value during topological pharmacophore fingerprints.</span> | |
| 150 137 <span class="c">#</span> | |
| 151 138 <span class="c"># . Default values for AtomicInvariantsToUse and FunctionalClassesToUse are set appropriately</span> | |
| 152 139 <span class="c"># for different types of fingerprints as shown below.</span> | |
| 153 140 <span class="c">#</span> | |
| 154 141 <span class="c"># MolecularComplexityType AtomicInvariantsToUse</span> | |
| 155 142 <span class="c">#</span> | |
| 156 143 <span class="c"># AtomTypesFingerprints AS, X, BO, H, FC</span> | |
| 157 144 <span class="c"># TopologicalAtomPairsFingerprints AS, X, BO, H, FC</span> | |
| 158 145 <span class="c"># TopologicalAtomTripletsFingerprints AS, X, BO, H, FC</span> | |
| 159 146 <span class="c"># TopologicalAtomTorsionsFingerprints AS, X, BO, H, FC</span> | |
| 160 147 <span class="c">#</span> | |
| 161 148 <span class="c"># ExtendedConnectivityFingerprints AS, X, BO, H, FC, MN</span> | |
| 162 149 <span class="c"># PathLengthFingerprints AS</span> | |
| 163 150 <span class="c">#</span> | |
| 164 151 <span class="c"># Default for FunctionalClassesToUse for all fingerprints is set to:</span> | |
| 165 152 <span class="c">#</span> | |
| 166 153 <span class="c"># HBD, HBA, PI, NI, Ar, Hal</span> | |
| 167 154 <span class="c">#</span> | |
| 168 155 <span class="c"># except for the following two MolecularComplexityType fingerprints:</span> | |
| 169 156 <span class="c">#</span> | |
| 170 157 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints HBD, HBA, PI, NI, H</span> | |
| 171 158 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints HBD, HBA, PI, NI, H, Ar</span> | |
| 172 159 <span class="c">#</span> | |
| 173 160 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 174 161 | |
| 175 162 <span class="c"># Size of MACCS key set: 166 or 322...</span> | |
| 176 163 <span class="c">#</span> | |
| 177 164 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="n">166</span><span class="sc">;</span> | |
| 178 165 | |
| 179 166 <span class="c"># Atomic neighborhoods radius for extended connectivity fingerprints...</span> | |
| 180 167 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span> | |
| 181 168 | |
| 182 169 <span class="c"># Minimum and maximum path lengths to use for path length fingerprints...</span> | |
| 183 170 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 184 171 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="n">8</span><span class="sc">;</span> | |
| 185 172 | |
| 186 173 <span class="c"># By default bond symbols are included in atom path strings used to generate path length</span> | |
| 187 174 <span class="c"># fingerprints... ...</span> | |
| 188 175 <span class="i">$This</span>->{<span class="w">UseBondSymbols</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 189 176 | |
| 190 177 <span class="c"># Minimum and maximum bond distance between atom pairs during topological</span> | |
| 191 178 <span class="c"># atom pairs/triplets fingerprints...</span> | |
| 192 179 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 193 180 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> | |
| 194 181 | |
| 195 182 <span class="c"># Determines whether to apply triangle inequality to distance triplets...</span> | |
| 196 183 <span class="c">#</span> | |
| 197 184 <span class="c"># Default for TopologicalAtomTripletsFingerprints: 0</span> | |
| 198 185 <span class="c"># Default for TopologicalPharmacophoreAtomTripletsFingerprints: 1</span> | |
| 199 186 <span class="c">#</span> | |
| 200 187 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 201 188 | |
| 202 189 <span class="c"># Distance bin size used for binning distances during generation of</span> | |
| 203 190 <span class="c"># topological pharmacophore atom triplets fingerprints...</span> | |
| 204 191 <span class="c">#</span> | |
| 205 192 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="n">2</span><span class="sc">;</span> | |
| 206 193 | |
| 207 194 <span class="c"># Normalization methodology to use for scaling the number of bits-set or unique keys</span> | |
| 208 195 <span class="c"># for:</span> | |
| 209 196 <span class="c">#</span> | |
| 210 197 <span class="c"># ExtendedConnectivityFingerprints</span> | |
| 211 198 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> | |
| 212 199 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> | |
| 213 200 <span class="c">#</span> | |
| 214 201 <span class="c"># This option is gnored for all other types of fingerprints.</span> | |
| 215 202 <span class="c">#</span> | |
| 216 203 <span class="c"># Possible values during extended connectivity fingerprints: None or ByHeavyAtomsCount. Default:</span> | |
| 217 204 <span class="c"># None.</span> | |
| 218 205 <span class="c">#</span> | |
| 219 206 <span class="c"># Possible values during topological pharmacophore atom pairs and tripletes fingerprints: None,</span> | |
| 220 207 <span class="c"># or ByPossibleKeysCount. Default: None. ByPossibleKeysCount corresponds to total number of</span> | |
| 221 208 <span class="c"># possible topological pharmacophore atom pairs or triplets in a molecule.</span> | |
| 222 209 <span class="c">#</span> | |
| 223 210 <span class="c">#</span> | |
| 224 211 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="q">'None'</span><span class="sc">;</span> | |
| 225 212 | |
| 226 213 <span class="c"># Intialize descriptor names and values...</span> | |
| 227 214 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> | |
| 228 215 | |
| 229 216 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 230 217 <span class="s">}</span> | |
| 231 218 | |
| 232 219 <span class="c"># Initialize object properties...</span> | |
| 233 220 <span class="c">#</span> | |
| 234 <a name="_InitializeMolecularComplexityDescriptorsProperties-"></a> 221 <span class="k">sub </span><span class="m">_InitializeMolecularComplexityDescriptorsProperties</span> <span class="s">{</span> | |
| 235 222 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 236 223 | |
| 237 224 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 238 225 <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> | |
| 239 226 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 240 227 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 241 228 <span class="s">}</span> | |
| 242 229 | |
| 243 230 <span class="c"># Make sure MolecularComplexityType is set...</span> | |
| 244 231 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 245 232 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="q">'MACCSKeys'</span><span class="sc">;</span> | |
| 246 233 <span class="s">}</span> | |
| 247 234 | |
| 248 235 <span class="c"># Make sure AtomIdentifierType is set...</span> | |
| 249 236 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} !~ <span class="q">/^MACCSKeys$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 250 237 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 251 238 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 252 239 <span class="s">}</span> | |
| 253 240 <span class="s">}</span> | |
| 254 241 | |
| 255 242 <span class="c"># Make sure UseTriangleInequality is set...</span> | |
| 256 243 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalAtomTripletsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 257 244 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">UseTriangleInequality</span>}<span class="s">)</span> <span class="s">{</span> | |
| 258 245 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 259 246 <span class="s">}</span> | |
| 260 247 <span class="s">}</span> | |
| 261 248 | |
| 262 249 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 263 250 <span class="s">}</span> | |
| 264 251 | |
| 265 252 <span class="c"># Initialize atom identifer type...</span> | |
| 266 253 <span class="c">#</span> | |
| 267 <a name="_InitializeAtomIdentifierType-"></a> 254 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierType</span> <span class="s">{</span> | |
| 268 255 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 269 256 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIdentifierType</span><span class="s">)</span><span class="sc">;</span> | |
| 270 257 | |
| 271 258 <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> | |
| 272 259 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 273 260 <span class="s">}</span> | |
| 274 261 | |
| 275 262 <span class="i">$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> | |
| 276 263 | |
| 277 264 <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> | |
| 278 265 | |
| 279 266 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 280 267 <span class="s">}</span> | |
| 281 268 | |
| 282 269 <span class="c"># Get abbreviation for specified molecular complexity type or using descriptors object...</span> | |
| 283 270 <span class="c">#</span> | |
| 284 271 <span class="c"># This functionality can be either invoked as a class function or an</span> | |
| 285 272 <span class="c"># object method.</span> | |
| 286 273 <span class="c">#</span> | |
| 287 <a name="GetMolecularComplexityTypeAbbreviation-"></a> 274 <span class="k">sub </span><span class="m">GetMolecularComplexityTypeAbbreviation</span> <span class="s">{</span> | |
| 288 275 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 289 276 <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> | |
| 290 277 | |
| 291 278 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecularComplexityDescriptors</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 292 279 <span class="i">$This</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> | |
| 293 280 <span class="i">$ComplexityType</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span> | |
| 294 281 <span class="s">}</span> | |
| 295 282 <span class="k">else</span> <span class="s">{</span> | |
| 296 283 <span class="i">$ComplexityType</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> | |
| 297 284 <span class="s">}</span> | |
| 298 285 | |
| 299 286 <span class="i">%ComplexityTypeToAbbrev</span> = <span class="s">(</span><span class="k">lc</span> <span class="q">'AtomTypesFingerprints'</span> <span class="cm">=></span> <span class="q">'ATFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'ExtendedConnectivityFingerprints'</span> <span class="cm">=></span> <span class="q">'ECFP'</span><span class="cm">,</span> | |
| 300 287 <span class="k">lc</span> <span class="q">'MACCSKeys'</span> <span class="cm">=></span> <span class="q">'MACCSKeys'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'PathLengthFingerprints'</span> <span class="cm">=></span> <span class="q">'PLFP'</span><span class="cm">,</span> | |
| 301 288 <span class="k">lc</span> <span class="q">'TopologicalAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TAPFP'</span><span class="cm">,</span> <span class="k">lc</span> <span class="q">'TopologicalAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span> | |
| 302 289 <span class="k">lc</span> <span class="q">'TopologicalAtomTorsionsFingerprints'</span> <span class="cm">=></span> <span class="q">'TATFP'</span><span class="cm">,</span> | |
| 303 290 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomPairsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPAPFP'</span><span class="cm">,</span> | |
| 304 291 <span class="k">lc</span> <span class="q">'TopologicalPharmacophoreAtomTripletsFingerprints'</span> <span class="cm">=></span> <span class="q">'TPATFP'</span><span class="s">)</span><span class="sc">;</span> | |
| 305 292 | |
| 306 293 <span class="k">return</span> <span class="k">exists</span> <span class="i">$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">$ComplexityType</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> | |
| 307 294 <span class="s">}</span> | |
| 308 295 | |
| 309 296 <span class="c"># Set MACCS key set size...</span> | |
| 310 297 <span class="c">#</span> | |
| 311 <a name="SetMACCSKeysSize-"></a> 298 <span class="k">sub </span><span class="m">SetMACCSKeysSize</span> <span class="s">{</span> | |
| 312 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 313 300 | |
| 314 301 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 315 302 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: Size value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 316 303 <span class="s">}</span> | |
| 317 304 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(166|322)/i</span><span class="s">)</span> <span class="s">{</span> | |
| 318 305 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMACCSKeysSize: The current release of MayaChemTools doesn't support MDL MACCS $Value keys..."</span><span class="sc">;</span> | |
| 319 306 <span class="s">}</span> | |
| 320 307 <span class="i">$This</span>->{<span class="w">MACCSKeysSize</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 321 308 | |
| 322 309 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 323 310 <span class="s">}</span> | |
| 324 311 | |
| 325 312 <span class="c"># Set minimum path length...</span> | |
| 326 313 <span class="c">#</span> | |
| 327 <a name="SetMinPathLength-"></a> 314 <span class="k">sub </span><span class="m">SetMinPathLength</span> <span class="s">{</span> | |
| 328 315 <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> | |
| 329 316 | |
| 330 317 <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> | |
| 331 318 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinPathLength: MinPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 332 319 <span class="s">}</span> | |
| 333 320 <span class="i">$This</span>->{<span class="w">MinPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 334 321 | |
| 335 322 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 336 323 <span class="s">}</span> | |
| 337 324 | |
| 338 325 <span class="c"># Set maximum path length...</span> | |
| 339 326 <span class="c">#</span> | |
| 340 <a name="SetMaxPathLength-"></a> 327 <span class="k">sub </span><span class="m">SetMaxPathLength</span> <span class="s">{</span> | |
| 341 328 <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> | |
| 342 329 | |
| 343 330 <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> | |
| 344 331 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxPathLength: MaxPathLength value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 345 332 <span class="s">}</span> | |
| 346 333 <span class="i">$This</span>->{<span class="w">MaxPathLength</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 347 334 | |
| 348 335 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 349 336 <span class="s">}</span> | |
| 350 337 | |
| 351 338 <span class="c"># Set minimum bond distance between atom pairs during topological and topological</span> | |
| 352 339 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span> | |
| 353 340 <span class="c">#</span> | |
| 354 <a name="SetMinDistance-"></a> 341 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span> | |
| 355 342 <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> | |
| 356 343 | |
| 357 344 <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> | |
| 358 345 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 359 346 <span class="s">}</span> | |
| 360 347 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 361 348 | |
| 362 349 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 363 350 <span class="s">}</span> | |
| 364 351 | |
| 365 352 <span class="c"># Set maximum bond distance between atom pairs during topological and topological</span> | |
| 366 353 <span class="c"># pharmacophore atom pairs/triplets fingerprints...</span> | |
| 367 354 <span class="c">#</span> | |
| 368 <a name="SetMaxDistance-"></a> 355 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span> | |
| 369 356 <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> | |
| 370 357 | |
| 371 358 <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> | |
| 372 359 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 373 360 <span class="s">}</span> | |
| 374 361 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 375 362 | |
| 376 363 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 377 364 <span class="s">}</span> | |
| 378 365 | |
| 379 366 <span class="c"># Set atom neighborhood radius...</span> | |
| 380 367 <span class="c">#</span> | |
| 381 <a name="SetNeighborhoodRadius-"></a> 368 <span class="k">sub </span><span class="m">SetNeighborhoodRadius</span> <span class="s">{</span> | |
| 382 369 <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> | |
| 383 370 | |
| 384 371 <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> | |
| 385 372 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> | |
| 386 373 <span class="s">}</span> | |
| 387 374 | |
| 388 375 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span> | |
| 389 376 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span> | |
| 390 377 <span class="s">}</span> | |
| 391 378 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 392 379 | |
| 393 380 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 394 381 <span class="s">}</span> | |
| 395 382 | |
| 396 383 <span class="c"># Set molecular complexity type...</span> | |
| 397 384 <span class="c">#</span> | |
| 398 <a name="SetMolecularComplexityType-"></a> 385 <span class="k">sub </span><span class="m">SetMolecularComplexityType</span> <span class="s">{</span> | |
| 399 386 <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> | |
| 400 387 | |
| 401 388 <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> | |
| 402 389 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecularComplexityType: MolecularComplexityType value, $Value, is not valid. Supported values: AtomTypesFingerprints, ExtendedConnectivityFingerprints, MACCSKeys, PathLengthFingerprints, TopologicalAtomPairsFingerprints, TopologicalAtomTripletsFingerprints, TopologicalAtomTorsionsFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints..."</span><span class="sc">;</span> | |
| 403 390 <span class="s">}</span> | |
| 404 391 | |
| 405 392 <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 406 393 | |
| 407 394 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 408 395 <span class="s">}</span> | |
| 409 396 | |
| 410 397 <span class="c"># Set distance bin size for binning pharmacophore atom pair distances in atom triplets...</span> | |
| 411 398 <span class="c">#</span> | |
| 412 <a name="SetDistanceBinSize-"></a> 399 <span class="k">sub </span><span class="m">SetDistanceBinSize</span> <span class="s">{</span> | |
| 413 400 <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> | |
| 414 401 | |
| 415 402 <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> | |
| 416 403 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDistanceBinSize: DistanceBinSize value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 417 404 <span class="s">}</span> | |
| 418 405 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 419 406 | |
| 420 407 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 421 408 <span class="s">}</span> | |
| 422 409 | |
| 423 410 <span class="c"># Set normalization methodology to use for scaling the number of bits-set or unique keys</span> | |
| 424 411 <span class="c"># in fingerprints...</span> | |
| 425 412 <span class="c">#</span> | |
| 426 <a name="SetNormalizationMethodology-"></a> 413 <span class="k">sub </span><span class="m">SetNormalizationMethodology</span> <span class="s">{</span> | |
| 427 414 <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> | |
| 428 415 | |
| 429 416 <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> | |
| 430 417 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid. Supported values: None, ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span> | |
| 431 418 <span class="s">}</span> | |
| 432 419 | |
| 433 420 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 434 421 <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> | |
| 435 422 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: Normalization is not supported for MolecularComplexityType: $This->{MolecularComplexityType}. Valid MolecularComplexityType values: ExtendedConnectivityFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints...\n"</span><span class="sc">;</span> | |
| 436 423 <span class="s">}</span> | |
| 437 424 | |
| 438 425 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 439 426 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByHeavyAtomsCount..."</span><span class="sc">;</span> | |
| 440 427 <span class="s">}</span> | |
| 441 428 | |
| 442 429 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 443 430 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid for MolecularComplexityType: $This->{MolecularComplexityType}. Supported values: None or ByPossibleKeysCount..."</span><span class="sc">;</span> | |
| 444 431 <span class="s">}</span> | |
| 445 432 <span class="s">}</span> | |
| 446 433 | |
| 447 434 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 448 435 | |
| 449 436 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 450 437 <span class="s">}</span> | |
| 451 438 | |
| 452 439 <span class="c"># Set intial atom identifier type..</span> | |
| 453 440 <span class="c">#</span> | |
| 454 <a name="SetAtomIdentifierType-"></a> 441 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> | |
| 455 442 <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> | |
| 456 443 | |
| 457 444 <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> | |
| 458 445 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes."</span><span class="sc">;</span> | |
| 459 446 <span class="s">}</span> | |
| 460 447 | |
| 461 448 <span class="c"># FunctionalClassAtomTypes is the only valid atom identifier type for pharmacophore fingerprints...</span> | |
| 462 449 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 463 450 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 464 451 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported type for $This->{MolecularComplexityType} complexity type: FunctionalClassAtomTypes."</span><span class="sc">;</span> | |
| 465 452 <span class="s">}</span> | |
| 466 453 <span class="s">}</span> | |
| 467 454 | |
| 468 455 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 469 456 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span> | |
| 470 457 <span class="s">}</span> | |
| 471 458 | |
| 472 459 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> | |
| 473 460 | |
| 474 461 <span class="c"># Initialize identifier type information...</span> | |
| 475 462 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 476 463 | |
| 477 464 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 478 465 <span class="s">}</span> | |
| 479 466 | |
| 480 467 <span class="c"># Calculate molecular complexity [ Ref 117-119 ] of a molecule using its fingerprints.</span> | |
| 481 468 <span class="c">#</span> | |
| 482 469 <span class="c"># The current release of MayaChemTools supports calculation of molecular complexity</span> | |
| 483 470 <span class="c"># corresponding to the number of bits-set or unique keys in molecular fingerprints. The</span> | |
| 484 471 <span class="c"># following types of fingerprints based molecular complexity measures are supported:</span> | |
| 485 472 <span class="c">#</span> | |
| 486 473 <span class="c"># AtomTypesFingerprints</span> | |
| 487 474 <span class="c"># ExtendedConnectivityFingerprints</span> | |
| 488 475 <span class="c"># MACCSKeys</span> | |
| 489 476 <span class="c"># PathLengthFingerprints</span> | |
| 490 477 <span class="c"># TopologicalAtomPairsFingerprints</span> | |
| 491 478 <span class="c"># TopologicalAtomTripletsFingerprints</span> | |
| 492 479 <span class="c"># TopologicalAtomTorsionsFingerprints</span> | |
| 493 480 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> | |
| 494 481 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> | |
| 495 482 <span class="c">#</span> | |
| 496 483 <span class="c"># After the molecular complexity value has been calculated, it can also be normalized by</span> | |
| 497 484 <span class="c"># by scaling the number of bits-set or unique keys for following types of fingerprints:</span> | |
| 498 485 <span class="c">#</span> | |
| 499 486 <span class="c"># ExtendedConnectivityFingerprints</span> | |
| 500 487 <span class="c"># TopologicalPharmacophoreAtomPairsFingerprints</span> | |
| 501 488 <span class="c"># TopologicalPharmacophoreAtomTripletsFingerprints</span> | |
| 502 489 <span class="c">#</span> | |
| 503 490 <span class="c"># Two types of normalization methodologies are supported: by heavy atoms count for</span> | |
| 504 491 <span class="c"># extended connectivity fingerprints; by possible keys count for topological pharmacophore</span> | |
| 505 492 <span class="c"># atom pairs and triplets fingerprints.</span> | |
| 506 493 <span class="c">#</span> | |
| 507 <a name="GenerateDescriptors-"></a> 494 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> | |
| 508 495 <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> | |
| 509 496 | |
| 510 497 <span class="c"># Initialize descriptor values...</span> | |
| 511 498 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 512 499 | |
| 513 500 <span class="c"># Check availability of molecule...</span> | |
| 514 501 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
| 515 502 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> | |
| 516 503 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 517 504 <span class="s">}</span> | |
| 518 505 | |
| 519 506 <span class="c"># Calculate descriptor values...</span> | |
| 520 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 521 508 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate MolecularComplexity values corresponding to assigned MolecularComplexity atom types..."</span><span class="sc">;</span> | |
| 522 509 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 523 510 <span class="s">}</span> | |
| 524 511 | |
| 525 512 <span class="c"># Set final descriptor values...</span> | |
| 526 513 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 527 514 | |
| 528 515 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 529 516 <span class="s">}</span> | |
| 530 517 | |
| 531 518 <span class="c"># Calculate molecular complexity value...</span> | |
| 532 519 <span class="c">#</span> | |
| 533 <a name="_CalculateDescriptorValues-"></a> 520 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> | |
| 534 521 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 535 522 <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> | |
| 536 523 | |
| 537 524 <span class="c"># Setup fingerprints object and generate fingerprints...</span> | |
| 538 525 <span class="i">$MethodName</span> = <span class="q">"_Setup"</span> . <span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>}<span class="sc">;</span> | |
| 539 526 <span class="i">$FingerprintsObject</span> = <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 540 527 | |
| 541 528 <span class="i">$FingerprintsObject</span><span class="i">->GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 542 529 | |
| 543 530 <span class="c"># Make sure atom types fingerprints generation is successful...</span> | |
| 544 531 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsObject</span><span class="i">->IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 545 532 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 546 533 <span class="s">}</span> | |
| 547 534 | |
| 548 535 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 549 536 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 550 537 <span class="s">}</span> | |
| 551 538 | |
| 552 539 <span class="c"># Normalize molecular complexity...</span> | |
| 553 540 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 554 541 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_NormalizeMolecularComplexity</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 555 542 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 556 543 <span class="s">}</span> | |
| 557 544 <span class="s">}</span> | |
| 558 545 | |
| 559 546 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 560 547 <span class="s">}</span> | |
| 561 548 | |
| 562 549 <span class="c"># Setup atom types fingerprints...</span> | |
| 563 550 <span class="c">#</span> | |
| 564 <a name="_SetupAtomTypesFingerprints-"></a> 551 <span class="k">sub </span><span class="m">_SetupAtomTypesFingerprints</span> <span class="s">{</span> | |
| 565 552 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 566 553 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 567 554 | |
| 568 555 <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">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 569 556 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 570 557 | |
| 571 558 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
| 572 559 <span class="s">}</span> | |
| 573 560 | |
| 574 561 <span class="c"># Setup extended connectivity fingerprints...</span> | |
| 575 562 <span class="c">#</span> | |
| 576 <a name="_SetupExtendedConnectivityFingerprints-"></a> 563 <span class="k">sub </span><span class="m">_SetupExtendedConnectivityFingerprints</span> <span class="s">{</span> | |
| 577 564 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 578 565 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 579 566 | |
| 580 567 <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> | |
| 581 568 <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> | |
| 582 569 | |
| 583 570 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
| 584 571 <span class="s">}</span> | |
| 585 572 | |
| 586 573 <span class="c"># Setup MACCS keys...</span> | |
| 587 574 <span class="c">#</span> | |
| 588 <a name="_SetupMACCSKeys-"></a> 575 <span class="k">sub </span><span class="m">_SetupMACCSKeys</span> <span class="s">{</span> | |
| 589 576 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 590 577 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 591 578 | |
| 592 579 <span class="i">$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> | |
| 593 580 | |
| 594 581 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
| 595 582 <span class="s">}</span> | |
| 596 583 | |
| 597 584 <span class="c"># Set up path length fingerprints...</span> | |
| 598 585 <span class="c">#</span> | |
| 599 <a name="_SetupPathLengthFingerprints-"></a> 586 <span class="k">sub </span><span class="m">_SetupPathLengthFingerprints</span> <span class="s">{</span> | |
| 600 587 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 601 588 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 602 589 | |
| 603 590 <span class="i">$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">$This</span>->{<span class="w">UseBondSymbols</span>}<span class="cm">,</span> <span class="q">'UseUniquePaths'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 604 591 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 605 592 | |
| 606 593 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
| 607 594 <span class="s">}</span> | |
| 608 595 | |
| 609 596 <span class="c"># Setup topological atom pairs fingerprints...</span> | |
| 610 597 <span class="c">#</span> | |
| 611 <a name="_SetupTopologicalAtomPairsFingerprints-"></a> 598 <span class="k">sub </span><span class="m">_SetupTopologicalAtomPairsFingerprints</span> <span class="s">{</span> | |
| 612 599 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 613 600 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 614 601 | |
| 615 602 <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">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span> | |
| 616 603 <span class="i">$This</span><span class="i">->_SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 617 604 | |
| 618 605 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
| 619 606 <span class="s">}</span> | |
| 620 607 | |
| 621 608 <span class="c"># Setup topological atom triplets fingerprints...</span> | |
| 622 609 <span class="c">#</span> | |
| 623 <a name="_SetupTopologicalAtomTripletsFingerprints-"></a> 610 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTripletsFingerprints</span> <span class="s">{</span> | |
| 624 611 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 625 612 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 626 613 | |
| 627 614 <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> | |
| 628 615 <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> | |
| 629 616 | |
| 630 617 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
| 631 618 <span class="s">}</span> | |
| 632 619 | |
| 633 620 <span class="c"># Setup topological atom torsions fingerprints...</span> | |
| 634 621 <span class="c">#</span> | |
| 635 <a name="_SetupTopologicalAtomTorsionsFingerprints-"></a> 622 <span class="k">sub </span><span class="m">_SetupTopologicalAtomTorsionsFingerprints</span> <span class="s">{</span> | |
| 636 623 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 637 624 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 638 625 | |
| 639 626 <span class="i">$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> | |
| 640 627 | |
| 641 628 <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> | |
| 642 629 | |
| 643 630 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
| 644 631 <span class="s">}</span> | |
| 645 632 | |
| 646 633 <span class="c"># Setup TopologicalPharmacophoreAtomPairsFingerprints...</span> | |
| 647 634 <span class="c">#</span> | |
| 648 <a name="_SetupTopologicalPharmacophoreAtomPairsFingerprints-"></a> 635 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span> | |
| 649 636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 650 637 <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> | |
| 651 638 | |
| 652 639 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span> | |
| 653 640 <span class="i">$AtomPairsSetSizeToUse</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByPossibleKeysCount$/i</span><span class="s">)</span> ? <span class="q">'FixedSize'</span> <span class="co">:</span> <span class="q">'ArbitrarySize'</span><span class="sc">;</span> | |
| 654 641 | |
| 655 642 <span class="i">$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">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">'NormalizationMethodology'</span> <span class="cm">=></span> <span class="q">'None'</span><span class="cm">,</span> <span class="q">'ValuesPrecision'</span> <span class="cm">=></span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span> | |
| 656 643 | |
| 657 644 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
| 658 645 <span class="s">}</span> | |
| 659 646 | |
| 660 647 <span class="c"># Setup TopologicalPharmacophoreAtomTripletsFingerprints...</span> | |
| 661 648 <span class="c">#</span> | |
| 662 <a name="_SetupTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 649 <span class="k">sub </span><span class="m">_SetupTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span> | |
| 663 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 664 651 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">$AtomTripletsSetSizeToUse</span><span class="s">)</span><span class="sc">;</span> | |
| 665 652 | |
| 666 653 <span class="c"># Use fixed size to get total number of possible keys for normalization...</span> | |
| 667 654 <span class="i">$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> | |
| 668 655 | |
| 669 656 <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> | |
| 670 657 | |
| 671 658 <span class="k">return</span> <span class="i">$FingerprintsObject</span><span class="sc">;</span> | |
| 672 659 <span class="s">}</span> | |
| 673 660 | |
| 674 661 <span class="c"># Normalize molecular complexity value...</span> | |
| 675 662 <span class="c">#</span> | |
| 676 <a name="_NormalizeMolecularComplexity-"></a> 663 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexity</span> <span class="s">{</span> | |
| 677 664 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 678 665 | |
| 679 666 <span class="k">if</span> <span class="s">(</span><span class="i">$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$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 680 667 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByHeavyAtomsCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 681 668 <span class="s">}</span> | |
| 682 669 <span class="k">elsif</span> <span class="s">(</span><span class="i">$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$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 683 670 <span class="k">return</span> <span class="i">$This</span><span class="i">->_NormalizeMolecularComplexityByPossibleKeysCount</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="s">)</span><span class="sc">;</span> | |
| 684 671 <span class="s">}</span> | |
| 685 672 <span class="k">else</span> <span class="s">{</span> | |
| 686 673 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_NormalizeMolecularComplexity: NormalizationMethodology value, $This->{NormalizationMethodology}, is not valid. Supported values: ByHeavyAtomsCount or ByPossibleKeysCount..."</span><span class="sc">;</span> | |
| 687 674 <span class="s">}</span> | |
| 688 675 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 689 676 <span class="s">}</span> | |
| 690 677 | |
| 691 678 <span class="c"># Normalize molecular complexity value by heavy atom count...</span> | |
| 692 679 <span class="c">#</span> | |
| 693 <a name="_NormalizeMolecularComplexityByHeavyAtomsCount-"></a> 680 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByHeavyAtomsCount</span> <span class="s">{</span> | |
| 694 681 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 695 682 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfHeavyAtoms</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span> | |
| 696 683 | |
| 697 684 <span class="i">$NumOfHeavyAtoms</span> = <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetNumOfHeavyAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 698 685 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfHeavyAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 699 686 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 700 687 <span class="s">}</span> | |
| 701 688 | |
| 702 689 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfHeavyAtoms</span><span class="sc">;</span> | |
| 703 690 <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> | |
| 704 691 | |
| 705 692 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 706 693 <span class="s">}</span> | |
| 707 694 | |
| 708 695 <span class="c"># Normalize molecular complexity value by possible keys count...</span> | |
| 709 696 <span class="c">#</span> | |
| 710 <a name="_NormalizeMolecularComplexityByPossibleKeysCount-"></a> 697 <span class="k">sub </span><span class="m">_NormalizeMolecularComplexityByPossibleKeysCount</span> <span class="s">{</span> | |
| 711 698 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 712 699 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfPossibleKeys</span><span class="cm">,</span> <span class="i">$NormalizedComplexity</span><span class="s">)</span><span class="sc">;</span> | |
| 713 700 | |
| 714 701 <span class="i">$NumOfPossibleKeys</span> = <span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 715 702 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfPossibleKeys</span><span class="s">)</span> <span class="s">{</span> | |
| 716 703 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 717 704 <span class="s">}</span> | |
| 718 705 | |
| 719 706 <span class="i">$NormalizedComplexity</span> = <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} / <span class="i">$NumOfPossibleKeys</span><span class="sc">;</span> | |
| 720 707 <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> | |
| 721 708 | |
| 722 709 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 723 710 <span class="s">}</span> | |
| 724 711 | |
| 725 712 <span class="c"># Calculate molecular complexity value using fingerprints objects...</span> | |
| 726 713 <span class="c">#</span> | |
| 727 <a name="_CalculateMolecularComplexity-"></a> 714 <span class="k">sub </span><span class="m">_CalculateMolecularComplexity</span> <span class="s">{</span> | |
| 728 715 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 729 716 | |
| 730 717 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 731 718 <span class="k">return</span> <span class="i">$This</span><span class="i">->_CalculateMolecularComplexityUsingFingerprintsBitVector</span><span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 732 719 <span class="s">}</span> | |
| 733 720 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsObject</span><span class="i">->GetVectorType</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^FingerprintsVector$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 734 721 <span class="k">return</span> <span class="i">$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> | |
| 735 722 <span class="s">}</span> | |
| 736 723 <span class="k">else</span> <span class="s">{</span> | |
| 737 724 <span class="k">warn</span> <span class="q">"Warning: ${ClassName}->_CalculateMolecularComplexity: Fingerprints vector type is not valid. Supported values: FingerprintsBitVector or FingerprintsVector..."</span><span class="sc">;</span> | |
| 738 725 <span class="s">}</span> | |
| 739 726 | |
| 740 727 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 741 728 <span class="s">}</span> | |
| 742 729 | |
| 743 730 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span> | |
| 744 731 <span class="c">#</span> | |
| 745 <a name="_CalculateMolecularComplexityUsingFingerprintsVector-"></a> 732 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsVector</span> <span class="s">{</span> | |
| 746 733 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 747 734 | |
| 748 735 <span class="i">$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> | |
| 749 736 | |
| 750 737 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 751 738 <span class="s">}</span> | |
| 752 739 | |
| 753 740 <span class="c"># Calculate molecular complexity value using fingerprints vector...</span> | |
| 754 741 <span class="c">#</span> | |
| 755 <a name="_CalculateMolecularComplexityUsingFingerprintsBitVector-"></a> 742 <span class="k">sub </span><span class="m">_CalculateMolecularComplexityUsingFingerprintsBitVector</span> <span class="s">{</span> | |
| 756 743 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 757 744 | |
| 758 745 <span class="i">$This</span>->{<span class="w">MolecularComplexity</span>} = <span class="i">$FingerprintsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 759 746 | |
| 760 747 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 761 748 <span class="s">}</span> | |
| 762 749 | |
| 763 750 <span class="c"># Setup final descriptor values...</span> | |
| 764 751 <span class="c">#</span> | |
| 765 <a name="_SetFinalDescriptorValues-"></a> 752 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> | |
| 766 753 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 767 754 | |
| 768 755 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 769 756 | |
| 770 757 <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> | |
| 771 758 | |
| 772 759 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 773 760 <span class="s">}</span> | |
| 774 761 | |
| 775 762 <span class="c"># Set atom identifier type to use for generating fingerprints...</span> | |
| 776 763 <span class="c">#</span> | |
| 777 <a name="_SetAtomIdentifierTypeValuesToUse-"></a> 764 <span class="k">sub </span><span class="m">_SetAtomIdentifierTypeValuesToUse</span> <span class="s">{</span> | |
| 778 765 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 779 766 | |
| 780 767 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 781 768 <span class="i">$FingerprintsObject</span><span class="i">->SetAtomicInvariantsToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="s">)</span><span class="sc">;</span> | |
| 782 769 <span class="s">}</span> | |
| 783 770 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 784 771 <span class="i">$FingerprintsObject</span><span class="i">->SetFunctionalClassesToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span> | |
| 785 772 <span class="s">}</span> | |
| 786 773 <span class="k">elsif</span> <span class="s">(</span><span class="i">$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> | |
| 787 774 <span class="c"># Nothing to do for now...</span> | |
| 788 775 <span class="s">}</span> | |
| 789 776 <span class="k">else</span> <span class="s">{</span> | |
| 790 777 <span class="w">croak</span> <span class="q">"Error: The value specified, $This->{AtomIdentifierType}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span> | |
| 791 778 <span class="s">}</span> | |
| 792 779 <span class="s">}</span> | |
| 793 780 | |
| 794 781 <span class="c"># Initialize atom indentifier type information...</span> | |
| 795 782 <span class="c">#</span> | |
| 796 783 <span class="c"># Current supported values:</span> | |
| 797 784 <span class="c">#</span> | |
| 798 785 <span class="c"># AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,</span> | |
| 799 786 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> | |
| 800 787 <span class="c">#</span> | |
| 801 <a name="_InitializeAtomIdentifierTypeInformation-"></a> 788 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> | |
| 802 789 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 803 790 | |
| 804 791 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> | |
| 805 792 <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> | |
| 806 793 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 807 794 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 808 795 <span class="s">}</span> | |
| 809 796 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 810 797 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 811 798 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 812 799 <span class="s">}</span> | |
| 813 800 <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> | |
| 814 801 <span class="c"># Nothing to do for now...</span> | |
| 815 802 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 816 803 <span class="s">}</span> | |
| 817 804 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
| 818 805 <span class="s">}</span> | |
| 819 806 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 820 807 <span class="s">}</span> | |
| 821 808 | |
| 822 809 <span class="c"># Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes</span> | |
| 823 810 <span class="c"># class, to use for generating initial atom identifiers...</span> | |
| 824 811 <span class="c">#</span> | |
| 825 812 <span class="c"># Let:</span> | |
| 826 813 <span class="c"># AS = Atom symbol corresponding to element symbol</span> | |
| 827 814 <span class="c">#</span> | |
| 828 815 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 829 816 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 830 817 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 831 818 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 832 819 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 833 820 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 834 821 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> | |
| 835 822 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> | |
| 836 823 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> | |
| 837 824 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> | |
| 838 825 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> | |
| 839 826 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> | |
| 840 827 <span class="c">#</span> | |
| 841 828 <span class="c"># Then:</span> | |
| 842 829 <span class="c">#</span> | |
| 843 830 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> | |
| 844 831 <span class="c">#</span> | |
| 845 832 <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> | |
| 846 833 <span class="c">#</span> | |
| 847 834 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span> | |
| 848 835 <span class="c"># optional.</span> | |
| 849 836 <span class="c">#</span> | |
| 850 837 <span class="c"># Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:</span> | |
| 851 838 <span class="c">#</span> | |
| 852 839 <span class="c"># AS, X<n>, BO<n>, H<n>, FC<+n/-n>, MN<n></span> | |
| 853 840 <span class="c">#</span> | |
| 854 841 <span class="c"># In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words</span> | |
| 855 842 <span class="c"># are also allowed:</span> | |
| 856 843 <span class="c">#</span> | |
| 857 844 <span class="c"># X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors</span> | |
| 858 845 <span class="c"># BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms</span> | |
| 859 846 <span class="c"># LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms</span> | |
| 860 847 <span class="c"># SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms</span> | |
| 861 848 <span class="c"># DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms</span> | |
| 862 849 <span class="c"># TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms</span> | |
| 863 850 <span class="c"># H : NumOfImplicitAndExplicitHydrogens</span> | |
| 864 851 <span class="c"># Ar : Aromatic</span> | |
| 865 852 <span class="c"># RA : RingAtom</span> | |
| 866 853 <span class="c"># FC : FormalCharge</span> | |
| 867 854 <span class="c"># MN : MassNumber</span> | |
| 868 855 <span class="c"># SM : SpinMultiplicity</span> | |
| 869 856 <span class="c">#</span> | |
| 870 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 857 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> | |
| 871 858 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 872 859 | |
| 873 860 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 874 861 | |
| 875 862 <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> | |
| 876 863 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span> | |
| 877 864 <span class="s">}</span> | |
| 878 865 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 879 866 <span class="i">@</span>{<span class="i">$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> | |
| 880 867 <span class="s">}</span> | |
| 881 868 <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> | |
| 882 869 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="s">)</span><span class="sc">;</span> | |
| 883 870 <span class="s">}</span> | |
| 884 871 | |
| 885 872 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 886 873 <span class="s">}</span> | |
| 887 874 | |
| 888 875 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> | |
| 889 876 <span class="c"># class, to use for generating initial atom identifiers...</span> | |
| 890 877 <span class="c">#</span> | |
| 891 878 <span class="c"># Let:</span> | |
| 892 879 <span class="c"># HBD: HydrogenBondDonor</span> | |
| 893 880 <span class="c"># HBA: HydrogenBondAcceptor</span> | |
| 894 881 <span class="c"># PI : PositivelyIonizable</span> | |
| 895 882 <span class="c"># NI : NegativelyIonizable</span> | |
| 896 883 <span class="c"># Ar : Aromatic</span> | |
| 897 884 <span class="c"># Hal : Halogen</span> | |
| 898 885 <span class="c"># H : Hydrophobic</span> | |
| 899 886 <span class="c"># RA : RingAtom</span> | |
| 900 887 <span class="c"># CA : ChainAtom</span> | |
| 901 888 <span class="c">#</span> | |
| 902 889 <span class="c"># Then:</span> | |
| 903 890 <span class="c">#</span> | |
| 904 891 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> | |
| 905 892 <span class="c">#</span> | |
| 906 893 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> | |
| 907 894 <span class="c">#</span> | |
| 908 895 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> | |
| 909 896 <span class="c">#</span> | |
| 910 897 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> | |
| 911 898 <span class="c">#</span> | |
| 912 899 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> | |
| 913 900 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> | |
| 914 901 <span class="c"># PositivelyIonizable: +, NH2</span> | |
| 915 902 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> | |
| 916 903 <span class="c">#</span> | |
| 917 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 904 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> | |
| 918 905 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 919 906 | |
| 920 907 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 921 908 | |
| 922 909 <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> | |
| 923 910 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> | |
| 924 911 <span class="s">}</span> | |
| 925 912 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 926 913 <span class="i">@</span>{<span class="i">$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> | |
| 927 914 <span class="s">}</span> | |
| 928 915 <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> | |
| 929 916 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="s">)</span><span class="sc">;</span> | |
| 930 917 <span class="s">}</span> | |
| 931 918 | |
| 932 919 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 933 920 <span class="s">}</span> | |
| 934 921 | |
| 935 922 <span class="c"># Set atomic invariants to use for generation of intial atom indentifiers...</span> | |
| 936 923 <span class="c">#</span> | |
| 937 <a name="SetAtomicInvariantsToUse-"></a> 924 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> | |
| 938 925 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 939 926 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 940 927 | |
| 941 928 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
| 942 929 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> | |
| 943 930 <span class="k">return</span><span class="sc">;</span> | |
| 944 931 <span class="s">}</span> | |
| 945 932 | |
| 946 933 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 947 934 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: AtomicInvariantsToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
| 948 935 <span class="k">return</span><span class="sc">;</span> | |
| 949 936 <span class="s">}</span> | |
| 950 937 | |
| 951 938 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 952 939 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
| 953 940 | |
| 954 941 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 955 942 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 956 943 | |
| 957 944 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
| 958 945 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
| 959 946 <span class="s">}</span> | |
| 960 947 <span class="k">else</span> <span class="s">{</span> | |
| 961 948 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
| 962 949 <span class="s">}</span> | |
| 963 950 | |
| 964 951 <span class="c"># Make sure specified AtomicInvariants are valid...</span> | |
| 965 952 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> | |
| 966 953 <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> | |
| 967 954 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> | |
| 968 955 <span class="s">}</span> | |
| 969 956 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> | |
| 970 957 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> | |
| 971 958 <span class="s">}</span> | |
| 972 959 | |
| 973 960 <span class="c"># Set atomic invariants to use...</span> | |
| 974 961 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 975 962 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> | |
| 976 963 | |
| 977 964 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 978 965 <span class="s">}</span> | |
| 979 966 | |
| 980 967 <span class="c"># Set functional classes to use for generation of intial atom indentifiers...</span> | |
| 981 968 <span class="c">#</span> | |
| 982 <a name="SetFunctionalClassesToUse-"></a> 969 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> | |
| 983 970 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 984 971 <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> | |
| 985 972 | |
| 986 973 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
| 987 974 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> | |
| 988 975 <span class="k">return</span><span class="sc">;</span> | |
| 989 976 <span class="s">}</span> | |
| 990 977 | |
| 991 978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 992 979 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
| 993 980 <span class="k">return</span><span class="sc">;</span> | |
| 994 981 <span class="s">}</span> | |
| 995 982 | |
| 996 983 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 997 984 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
| 998 985 | |
| 999 986 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1000 987 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1001 988 | |
| 1002 989 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
| 1003 990 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
| 1004 991 <span class="s">}</span> | |
| 1005 992 <span class="k">else</span> <span class="s">{</span> | |
| 1006 993 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
| 1007 994 <span class="s">}</span> | |
| 1008 995 | |
| 1009 996 <span class="c"># Make sure specified FunctionalClasses are valid...</span> | |
| 1010 997 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> | |
| 1011 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> | |
| 1012 999 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> | |
| 1013 1000 <span class="s">}</span> | |
| 1014 1001 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> | |
| 1015 1002 <span class="s">}</span> | |
| 1016 1003 | |
| 1017 1004 <span class="c"># Set functional classes to use...</span> | |
| 1018 1005 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1019 1006 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> | |
| 1020 1007 | |
| 1021 1008 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1022 1009 <span class="s">}</span> | |
| 1023 1010 | |
| 1024 1011 <span class="c"># Return a string containg data for MolecularComplexityDescriptors object...</span> | |
| 1025 1012 <span class="c">#</span> | |
| 1026 <a name="StringifyMolecularComplexityDescriptors-"></a>1013 <span class="k">sub </span><span class="m">StringifyMolecularComplexityDescriptors</span> <span class="s">{</span> | |
| 1027 1014 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1028 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> | |
| 1029 1016 | |
| 1030 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> | |
| 1031 1018 | |
| 1032 1019 <span class="c"># Setup fingerprints specific information...</span> | |
| 1033 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> | |
| 1034 1021 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MACCSKeysSize = $This->{MACCSKeysSize}"</span><span class="sc">;</span> | |
| 1035 1022 <span class="s">}</span> | |
| 1036 1023 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^ExtendedConnectivityFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1037 1024 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; NeighborhoodRadius = $This->{NeighborhoodRadius}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span> | |
| 1038 1025 <span class="s">}</span> | |
| 1039 1026 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^PathLengthFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1040 1027 <span class="i">$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> | |
| 1041 1028 <span class="s">}</span> | |
| 1042 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> | |
| 1043 1030 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span> | |
| 1044 1031 <span class="s">}</span> | |
| 1045 1032 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1046 1033 <span class="i">$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> | |
| 1047 1034 <span class="s">}</span> | |
| 1048 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> | |
| 1049 1036 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}"</span><span class="sc">;</span> | |
| 1050 1037 <span class="s">}</span> | |
| 1051 1038 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomPairsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1052 1039 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; MinDistance = $This->{MinDistance}; MaxDistance = $This->{MaxDistance}; NormalizationMethodology = $This->{NormalizationMethodology}"</span><span class="sc">;</span> | |
| 1053 1040 <span class="s">}</span> | |
| 1054 1041 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularComplexityType</span>} =~ <span class="q">/^TopologicalPharmacophoreAtomTripletsFingerprints$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1055 1042 <span class="i">$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> | |
| 1056 1043 <span class="s">}</span> | |
| 1057 1044 | |
| 1058 1045 <span class="c"># Setup atom identifier information...</span> | |
| 1059 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> | |
| 1060 1047 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomIdentifierType = $This->{AtomIdentifierType}"</span><span class="sc">;</span> | |
| 1061 1048 | |
| 1062 1049 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1063 1050 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1064 1051 | |
| 1065 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> | |
| 1066 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> | |
| 1067 1054 | |
| 1068 1055 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 1069 1056 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> | |
| 1070 1057 <span class="s">}</span> | |
| 1071 1058 | |
| 1072 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> | |
| 1073 1060 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
| 1074 1061 <span class="i">$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> | |
| 1075 1062 <span class="s">}</span> | |
| 1076 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> | |
| 1077 1064 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> | |
| 1078 1065 | |
| 1079 1066 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1080 1067 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1081 1068 | |
| 1082 1069 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 1083 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> | |
| 1084 1071 <span class="s">}</span> | |
| 1085 1072 | |
| 1086 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> | |
| 1087 1074 <span class="i">$ComplexityDescriptorsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
| 1088 1075 <span class="i">$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> | |
| 1089 1076 <span class="s">}</span> | |
| 1090 1077 <span class="s">}</span> | |
| 1091 1078 <span class="k">return</span> <span class="i">$ComplexityDescriptorsString</span><span class="sc">;</span> | |
| 1092 1079 <span class="s">}</span> | |
| 1093 1080 | |
| 1094 1081 <span class="c"># Is it a MolecularComplexityDescriptors object?</span> | |
| 1095 <a name="_IsMolecularComplexityDescriptors-"></a>1082 <span class="k">sub </span><span class="m">_IsMolecularComplexityDescriptors</span> <span class="s">{</span> | |
| 1096 1083 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1097 1084 | |
| 1098 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> | |
| 1099 1086 <span class="s">}</span> | |
| 1100 1087 | |
| 1101 <a name="EOF-"></a></pre> | |
| 1102 <p> </p> | |
| 1103 <br /> | |
| 1104 <center> | |
| 1105 <img src="../../../images/h2o2.png"> | |
| 1106 </center> | |
| 1107 </body> | |
| 1108 </html> |