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| author | deepakjadmin |
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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:Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: TopologicalPharmacophoreAtomPairsFingerprints.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> | |
| 18 5 <span class="c"># $Revision: 1.34 $</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">Fingerprints::Fingerprints</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">Molecule</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> | |
| 50 37 | |
| 51 38 <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> | |
| 52 39 | |
| 53 40 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> | |
| 54 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 55 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 56 43 | |
| 57 44 <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> | |
| 58 45 | |
| 59 46 <span class="c"># Setup class variables...</span> | |
| 60 47 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 61 48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 62 49 | |
| 63 50 <span class="c"># Overload Perl functions...</span> | |
| 64 51 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyTopologicalPharmacophoreAtomPairsFingerprints'</span><span class="sc">;</span> | |
| 65 52 | |
| 66 53 <span class="c"># Class constructor...</span> | |
| 67 <a name="new-"></a> 54 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 68 55 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 69 56 | |
| 70 57 <span class="c"># Initialize object...</span> | |
| 71 58 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 72 59 <span class="k">bless</span> <span class="i">$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> | |
| 73 60 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 74 61 | |
| 75 62 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 76 63 | |
| 77 64 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 78 65 <span class="s">}</span> | |
| 79 66 | |
| 80 67 <span class="c"># Initialize object data...</span> | |
| 81 68 <span class="c">#</span> | |
| 82 <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprints-"></a> 69 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span> | |
| 83 70 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 84 71 | |
| 85 72 <span class="c"># Type of fingerprint...</span> | |
| 86 73 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'TopologicalPharmacophoreAtomPairs'</span><span class="sc">;</span> | |
| 87 74 | |
| 88 75 <span class="c"># Type of vector...</span> | |
| 89 76 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> | |
| 90 77 | |
| 91 78 <span class="c"># AtomPairsSetSizeToUse...</span> | |
| 92 79 <span class="c">#</span> | |
| 93 80 <span class="c"># ArbitrarySize - Corrresponds to atom pairs with non-zero count</span> | |
| 94 81 <span class="c"># FixedSize - Corresponds to all atom pairs with zero and non-zero count</span> | |
| 95 82 <span class="c">#</span> | |
| 96 83 <span class="c"># Possible values: ArbitrarySize or FixedSize. Default: ArbitrarySize</span> | |
| 97 84 <span class="c">#</span> | |
| 98 85 <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 99 86 | |
| 100 87 <span class="c"># Type of FingerprintsVector...</span> | |
| 101 88 <span class="c">#</span> | |
| 102 89 <span class="c"># OrderedNumericalValues - For ArbitrarySize value of AtomPairsSetSizeToUse</span> | |
| 103 90 <span class="c"># NumericalValues - For FixedSize value of AtomPairsSetSizeToUse</span> | |
| 104 91 <span class="c">#</span> | |
| 105 92 <span class="c"># Possible values: OrderedNumericalValues or NumericalValues. Default: NumericalValues</span> | |
| 106 93 <span class="c">#</span> | |
| 107 94 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 108 95 | |
| 109 96 <span class="c"># Vector values precision for real values which might be generated after</span> | |
| 110 97 <span class="c"># normalization and fuzzification...</span> | |
| 111 98 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="n">2</span><span class="sc">;</span> | |
| 112 99 | |
| 113 100 <span class="c"># Minimum and maximum bond distance between pharmacophore atom paris...</span> | |
| 114 101 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 115 102 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> | |
| 116 103 | |
| 117 104 <span class="c"># Initialize atom types and weight information...</span> | |
| 118 105 <span class="i">$This</span><span class="i">->_InitializePharmacophoreAtomTypesAndWeightInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 119 106 | |
| 120 107 <span class="c"># Normalization methodology to use for scaling the occurance count of pharmacophore atom</span> | |
| 121 108 <span class="c"># pairs at various distances.</span> | |
| 122 109 <span class="c">#</span> | |
| 123 110 <span class="c"># Possible values: None, ByHeavyAtomsCount, ByAtomTypesCount. Default: None</span> | |
| 124 111 <span class="c">#</span> | |
| 125 112 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="q">'None'</span><span class="sc">;</span> | |
| 126 113 | |
| 127 114 <span class="c"># Initialize fuzzification parameters...</span> | |
| 128 115 <span class="c">#</span> | |
| 129 116 <span class="i">$This</span><span class="i">->_InitializeFuzzificationInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 130 117 | |
| 131 118 <span class="c"># Pharmacophore types assigned to each heavy atom...</span> | |
| 132 119 <span class="c">#</span> | |
| 133 120 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 134 121 | |
| 135 122 <span class="c"># Assigned Atom types count of each type in the molecule...</span> | |
| 136 123 <span class="c">#</span> | |
| 137 124 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 138 125 | |
| 139 126 <span class="c"># All pharmacophore atom pairs between minimum and maximum distance...</span> | |
| 140 127 <span class="c">#</span> | |
| 141 128 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 142 129 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 143 130 <span class="s">}</span> | |
| 144 131 | |
| 145 132 <span class="c"># Inialize pharmacophore atom types and weight information...</span> | |
| 146 133 <span class="c">#</span> | |
| 147 <a name="_InitializePharmacophoreAtomTypesAndWeightInformation-"></a> 134 <span class="k">sub </span><span class="m">_InitializePharmacophoreAtomTypesAndWeightInformation</span> <span class="s">{</span> | |
| 148 135 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 149 136 | |
| 150 137 <span class="c"># Default pharmacophore atom types to use for atom pairs fingerprint generation</span> | |
| 151 138 <span class="c"># are: HBD, HBA, PI, NI, H</span> | |
| 152 139 <span class="c">#</span> | |
| 153 140 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 154 141 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="k">sort</span> <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="s">)</span><span class="sc">;</span> | |
| 155 142 | |
| 156 143 <span class="c"># Weight of the various pharmacophore atom types to use for their contribution to atom</span> | |
| 157 144 <span class="c"># pair interaction. It allows to increase the importance of specific pharmacophore atom</span> | |
| 158 145 <span class="c"># types in the generted fingerprints.</span> | |
| 159 146 <span class="c">#</span> | |
| 160 147 <span class="c"># A value of 0 eliminates the contribution by a particular pharmacophore atom</span> | |
| 161 148 <span class="c"># type and 2 doubles its contribution.</span> | |
| 162 149 <span class="c">#</span> | |
| 163 150 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span><span class="sc">;</span> | |
| 164 151 | |
| 165 152 <span class="i">%AvailableAtomTypes</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 166 153 | |
| 167 154 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 168 155 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span> <span class="s">{</span> | |
| 169 156 <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 170 157 <span class="s">}</span> | |
| 171 158 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 172 159 <span class="s">}</span> | |
| 173 160 | |
| 174 161 <span class="c"># Initialize fuzzification information...</span> | |
| 175 162 <span class="c">#</span> | |
| 176 <a name="_InitializeFuzzificationInformation-"></a> 163 <span class="k">sub </span><span class="m">_InitializeFuzzificationInformation</span> <span class="s">{</span> | |
| 177 164 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 178 165 | |
| 179 166 <span class="c"># To fuzz or not to fuzz atom pairs count. Default: No fuzzication</span> | |
| 180 167 <span class="c">#</span> | |
| 181 168 <span class="i">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 182 169 | |
| 183 170 <span class="c"># When to fuzz atom pair count...</span> | |
| 184 171 <span class="c">#</span> | |
| 185 172 <span class="c"># Possible values: BeforeNormalization or AfterNormalization. Default: AfterNormalization</span> | |
| 186 173 <span class="c">#</span> | |
| 187 174 <span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} = <span class="q">'AfterNormalization'</span><span class="sc">;</span> | |
| 188 175 | |
| 189 176 <span class="c"># How to fuzz atom pair count...</span> | |
| 190 177 <span class="c">#</span> | |
| 191 178 <span class="c"># Possible values: FuzzyBinning or FuzzyBinSmoothing. Default: FuzzyBinning</span> | |
| 192 179 <span class="c">#</span> | |
| 193 180 <span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} = <span class="q">'FuzzyBinning'</span><span class="sc">;</span> | |
| 194 181 | |
| 195 182 <span class="c"># By how much to fuzz atom pairs count...</span> | |
| 196 183 <span class="c">#</span> | |
| 197 184 <span class="i">$This</span>->{<span class="w">FuzzFactor</span>} = <span class="n">0.15</span><span class="sc">;</span> | |
| 198 185 | |
| 199 186 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 200 187 <span class="s">}</span> | |
| 201 188 | |
| 202 189 <span class="c"># Initialize class ...</span> | |
| 203 <a name="_InitializeClass-"></a> 190 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 204 191 <span class="c">#Class name...</span> | |
| 205 192 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 206 193 <span class="s">}</span> | |
| 207 194 | |
| 208 195 <span class="c"># Initialize object properties....</span> | |
| 209 <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties-"></a> 196 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties</span> <span class="s">{</span> | |
| 210 197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 211 198 | |
| 212 199 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 213 200 <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> | |
| 214 201 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 215 202 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 216 203 <span class="s">}</span> | |
| 217 204 | |
| 218 205 <span class="c"># Make sure molecule object was specified...</span> | |
| 219 206 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
| 220 207 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> | |
| 221 208 <span class="s">}</span> | |
| 222 209 | |
| 223 210 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 224 211 | |
| 225 212 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 226 213 <span class="s">}</span> | |
| 227 214 | |
| 228 215 <span class="c"># Initialize fingerprints vector...</span> | |
| 229 216 <span class="c">#</span> | |
| 230 <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector-"></a> 217 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector</span> <span class="s">{</span> | |
| 231 218 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 232 219 | |
| 233 220 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span> | |
| 234 221 <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="q">'ArbitrarySize'</span><span class="sc">;</span> | |
| 235 222 <span class="s">}</span> | |
| 236 223 | |
| 237 224 <span class="c"># Vector type and type of values...</span> | |
| 238 225 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> | |
| 239 226 | |
| 240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 241 228 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'OrderedNumericalValues'</span><span class="sc">;</span> | |
| 242 229 <span class="s">}</span> | |
| 243 230 <span class="k">else</span> <span class="s">{</span> | |
| 244 231 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> | |
| 245 232 <span class="s">}</span> | |
| 246 233 | |
| 247 234 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 248 235 <span class="s">}</span> | |
| 249 236 | |
| 250 237 <span class="c"># Set atom parits set size to use...</span> | |
| 251 238 <span class="c">#</span> | |
| 252 <a name="SetAtomPairsSetSizeToUse-"></a> 239 <span class="k">sub </span><span class="m">SetAtomPairsSetSizeToUse</span> <span class="s">{</span> | |
| 253 240 <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> | |
| 254 241 | |
| 255 242 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span> | |
| 256 243 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomPairsSetSizeToUse: Can't change size: It's already set..."</span><span class="sc">;</span> | |
| 257 244 <span class="s">}</span> | |
| 258 245 | |
| 259 246 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ArbitrarySize|FixedSize)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 260 247 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomPairsSetSizeToUse: Unknown AtomPairsSetSizeToUse value: $Value; Supported values: ArbitrarySize or FixedSize"</span><span class="sc">;</span> | |
| 261 248 <span class="s">}</span> | |
| 262 249 | |
| 263 250 <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 264 251 | |
| 265 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 266 253 <span class="s">}</span> | |
| 267 254 | |
| 268 255 <span class="c"># Disable change of AvailableAtomTypes...</span> | |
| 269 256 <span class="c">#</span> | |
| 270 <a name="SetAvailableAtomTypes-"></a> 257 <span class="k">sub </span><span class="m">SetAvailableAtomTypes</span> <span class="s">{</span> | |
| 271 258 <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> | |
| 272 259 | |
| 273 260 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAvailableAtomTypes: AvailableAtomTypes value can't be set..."</span><span class="sc">;</span> | |
| 274 261 | |
| 275 262 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 276 263 <span class="s">}</span> | |
| 277 264 | |
| 278 265 <span class="c"># Set atom types to use for atom pairs...</span> | |
| 279 266 <span class="c">#</span> | |
| 280 <a name="SetAtomTypesToUse-"></a> 267 <span class="k">sub </span><span class="m">SetAtomTypesToUse</span> <span class="s">{</span> | |
| 281 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 282 269 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$SpecifiedAtomType</span><span class="cm">,</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@AtomTypesToUse</span><span class="s">)</span><span class="sc">;</span> | |
| 283 270 | |
| 284 271 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
| 285 272 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomTypesToUse: No values specified..."</span><span class="sc">;</span> | |
| 286 273 <span class="k">return</span><span class="sc">;</span> | |
| 287 274 <span class="s">}</span> | |
| 288 275 | |
| 289 276 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 290 277 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
| 291 278 | |
| 292 279 <span class="i">@SpecifiedAtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 293 280 <span class="i">@AtomTypesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 294 281 | |
| 295 282 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
| 296 283 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
| 297 284 <span class="s">}</span> | |
| 298 285 <span class="k">else</span> <span class="s">{</span> | |
| 299 286 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
| 300 287 <span class="s">}</span> | |
| 301 288 | |
| 302 289 <span class="c"># Make sure specified AtomTypes are valid...</span> | |
| 303 290 <span class="k">for</span> <span class="i">$SpecifiedAtomType</span> <span class="s">(</span><span class="i">@SpecifiedAtomTypes</span><span class="s">)</span> <span class="s">{</span> | |
| 304 291 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 305 292 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesToUse: Specified atom type, $SpecifiedAtomType, is not supported...\n "</span><span class="sc">;</span> | |
| 306 293 <span class="s">}</span> | |
| 307 294 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomType</span><span class="sc">;</span> | |
| 308 295 <span class="k">push</span> <span class="i">@AtomTypesToUse</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span> | |
| 309 296 <span class="s">}</span> | |
| 310 297 | |
| 311 298 <span class="c"># Set atom types to use...</span> | |
| 312 299 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 313 300 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="cm">,</span> <span class="k">sort</span> <span class="i">@AtomTypesToUse</span><span class="sc">;</span> | |
| 314 301 | |
| 315 302 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 316 303 <span class="s">}</span> | |
| 317 304 | |
| 318 305 <span class="c"># Set vector values precision for real values which might be generated after</span> | |
| 319 306 <span class="c"># normalization and fuzzification...</span> | |
| 320 307 <span class="c">#</span> | |
| 321 <a name="SetValuesPrecision-"></a> 308 <span class="k">sub </span><span class="m">SetValuesPrecision</span> <span class="s">{</span> | |
| 322 309 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 323 310 | |
| 324 311 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 325 312 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetValuesPrecision: ValuesPrecision value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 326 313 <span class="s">}</span> | |
| 327 314 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 328 315 | |
| 329 316 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 330 317 <span class="s">}</span> | |
| 331 318 | |
| 332 319 <span class="c"># Set minimum distance for pharmacophore atom pairs...</span> | |
| 333 320 <span class="c">#</span> | |
| 334 <a name="SetMinDistance-"></a> 321 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span> | |
| 335 322 <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> | |
| 336 323 | |
| 337 324 <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> | |
| 338 325 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> | |
| 339 326 <span class="s">}</span> | |
| 340 327 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 341 328 | |
| 342 329 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 343 330 <span class="s">}</span> | |
| 344 331 | |
| 345 332 <span class="c"># Set maximum distance for pharmacophore atom pairs...</span> | |
| 346 333 <span class="c">#</span> | |
| 347 <a name="SetMaxDistance-"></a> 334 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span> | |
| 348 335 <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> | |
| 349 336 | |
| 350 337 <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> | |
| 351 338 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 352 339 <span class="s">}</span> | |
| 353 340 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 354 341 | |
| 355 342 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 356 343 <span class="s">}</span> | |
| 357 344 | |
| 358 345 <span class="c"># Set normalization methodology to use for scaling the occurance count of pharmacophore atom</span> | |
| 359 346 <span class="c"># pairs over distance range beween minimum and maximum distance.</span> | |
| 360 347 <span class="c">#</span> | |
| 361 <a name="SetNormalizationMethodology-"></a> 348 <span class="k">sub </span><span class="m">SetNormalizationMethodology</span> <span class="s">{</span> | |
| 362 349 <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> | |
| 363 350 | |
| 364 351 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ByHeavyAtomsCount|ByAtomTypesCount|None)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 365 352 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid. Supported values: None, ByHeavyAtomsCount or ByAtomTypesCount..."</span><span class="sc">;</span> | |
| 366 353 <span class="s">}</span> | |
| 367 354 | |
| 368 355 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 369 356 | |
| 370 357 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 371 358 <span class="s">}</span> | |
| 372 359 | |
| 373 360 <span class="c"># Set weight of the various pharmacophore atom types to use for their contribution to atom</span> | |
| 374 361 <span class="c"># pair interaction using atom types label and value hash.</span> | |
| 375 362 <span class="c">#</span> | |
| 376 363 <span class="c"># It allows to increase the importance of specific pharmacophore atom</span> | |
| 377 364 <span class="c"># types in the generted fingerprints.</span> | |
| 378 365 <span class="c">#</span> | |
| 379 366 <span class="c"># A value of 0 eliminates the contribution by a particular pharmacophore atom</span> | |
| 380 367 <span class="c"># type and 2 doubles its contribution.</span> | |
| 381 368 <span class="c">#</span> | |
| 382 <a name="SetAtomTypesWeight-"></a> 369 <span class="k">sub </span><span class="m">SetAtomTypesWeight</span> <span class="s">{</span> | |
| 383 370 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%AtomTypesWeight</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 384 371 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span><span class="sc">;</span> | |
| 385 372 | |
| 386 373 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%AtomTypesWeight</span><span class="s">)</span> <span class="s">{</span> | |
| 387 374 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 388 375 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesWeight: AtomTypeWeight for $AtomType couldn't be set: Unknown atom type..."</span><span class="sc">;</span> | |
| 389 376 <span class="s">}</span> | |
| 390 377 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$Weight</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Weight</span> >= <span class="n">0</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 391 378 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesWeight: Specified weight value, $Weight, for AtomType, $AtomType, muts be >= 0..."</span><span class="sc">;</span> | |
| 392 379 <span class="s">}</span> | |
| 393 380 <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>} = <span class="i">$Weight</span><span class="sc">;</span> | |
| 394 381 <span class="s">}</span> | |
| 395 382 <span class="s">}</span> | |
| 396 383 | |
| 397 384 <span class="c"># Set fuzzification methodology to use for fuzzifying atom pairs count...</span> | |
| 398 385 <span class="c">#</span> | |
| 399 <a name="SetFuzzificationMethodology-"></a> 386 <span class="k">sub </span><span class="m">SetFuzzificationMethodology</span> <span class="s">{</span> | |
| 400 387 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 401 388 | |
| 402 389 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(FuzzyBinning|FuzzyBinSmoothing)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 403 390 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzificationMethodology: FuzzificationMethodology value, $Value, is not valid. Supported values: FuzzyBinning or FuzzyBinSmoothing..."</span><span class="sc">;</span> | |
| 404 391 <span class="s">}</span> | |
| 405 392 | |
| 406 393 <span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 407 394 | |
| 408 395 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 409 396 <span class="s">}</span> | |
| 410 397 | |
| 411 398 <span class="c"># Set fuzzification mode for fuzzifying atom pairs count...</span> | |
| 412 399 <span class="c">#</span> | |
| 413 <a name="SetFuzzificationMode-"></a> 400 <span class="k">sub </span><span class="m">SetFuzzificationMode</span> <span class="s">{</span> | |
| 414 401 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 415 402 | |
| 416 403 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(BeforeNormalization|AfterNormalization)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 417 404 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzificationMode: FuzzificationMode value, $Value, is not valid. Supported values: BeforeNormalization or AfterNormalization..."</span><span class="sc">;</span> | |
| 418 405 <span class="s">}</span> | |
| 419 406 | |
| 420 407 <span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 421 408 | |
| 422 409 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 423 410 <span class="s">}</span> | |
| 424 411 | |
| 425 412 <span class="c"># Set fuzz factor values used for fuzzifying atom pairs count...</span> | |
| 426 413 <span class="c">#</span> | |
| 427 <a name="SetFuzzFactor-"></a> 414 <span class="k">sub </span><span class="m">SetFuzzFactor</span> <span class="s">{</span> | |
| 428 415 <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> | |
| 429 416 | |
| 430 417 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinning$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 431 418 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$Value</span> >=<span class="n">0</span> && <span class="i">$Value</span> <= <span class="n">1.0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 432 419 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzFactor: Specified fuzz factor value, $Value, must be >= 0 and <= 1..."</span><span class="sc">;</span> | |
| 433 420 <span class="s">}</span> | |
| 434 421 <span class="s">}</span> | |
| 435 422 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinSmoothing$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 436 423 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="i">$Value</span> >=<span class="n">0</span> && <span class="i">$Value</span> <= <span class="n">0.5</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 437 424 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzFactor: Specified fuzz factor value, $Value, must be >= 0 and <= 0.5..."</span><span class="sc">;</span> | |
| 438 425 <span class="s">}</span> | |
| 439 426 <span class="s">}</span> | |
| 440 427 <span class="k">else</span> <span class="s">{</span> | |
| 441 428 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzFactor: Fuzz factor value can't be changed: Uknown FuzzificationMethodology: $This->{FuzzificationMethodology}..."</span><span class="sc">;</span> | |
| 442 429 <span class="s">}</span> | |
| 443 430 | |
| 444 431 <span class="i">$This</span>->{<span class="w">FuzzFactor</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 445 432 | |
| 446 433 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 447 434 <span class="s">}</span> | |
| 448 435 | |
| 449 436 <span class="c"># Generate fingerprints description...</span> | |
| 450 437 <span class="c">#</span> | |
| 451 <a name="GetDescription-"></a> 438 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> | |
| 452 439 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 453 440 | |
| 454 441 <span class="c"># Is description explicity set?</span> | |
| 455 442 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> | |
| 456 443 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> | |
| 457 444 <span class="s">}</span> | |
| 458 445 | |
| 459 446 <span class="c"># Generate fingerprints description...</span> | |
| 460 447 | |
| 461 448 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomPairsSetSizeToUse}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"</span><span class="sc">;</span> | |
| 462 449 <span class="s">}</span> | |
| 463 450 | |
| 464 451 <span class="c"># Generate topological pharmacophore atom pairs [ Ref 60-62, Ref 65, Ref 68 ] fingerprints...</span> | |
| 465 452 <span class="c">#</span> | |
| 466 453 <span class="c"># Methodology:</span> | |
| 467 454 <span class="c"># . Generate a distance matrix.</span> | |
| 468 455 <span class="c"># . Assign pharmacophore atom types to all the atoms.</span> | |
| 469 456 <span class="c"># . Initialize pharmacophore atom pairs basis set for all unique pairs between</span> | |
| 470 457 <span class="c"># minimum and maximum distance.</span> | |
| 471 458 <span class="c"># . Using distance matrix and pharmacophore atom types, count occurance of</span> | |
| 472 459 <span class="c"># unique atom pairs between specified distance range - It corresponds to the</span> | |
| 473 460 <span class="c"># correlation-vector for the atom pairs.</span> | |
| 474 461 <span class="c"># . Weigh contribution of each atom type to atom pair interaction by its specified</span> | |
| 475 462 <span class="c"># weight during occurance count.</span> | |
| 476 463 <span class="c"># . Assign count to appropriate distance bin for a specific atom pair</span> | |
| 477 464 <span class="c">#</span> | |
| 478 465 <span class="c"># . Normalize occurance count of pharmacophore atom pairs by heavy atom count</span> | |
| 479 466 <span class="c"># or sum of AtomTypeCounts of each pharmacophore atom type in the atom pair</span> | |
| 480 467 <span class="c"># at a specific distance.</span> | |
| 481 468 <span class="c">#</span> | |
| 482 469 <span class="c"># . Fuzzify occurance count of pharmacophore atom pairs using FuzzyBinning or</span> | |
| 483 470 <span class="c"># FuzzySmothing methodology.</span> | |
| 484 471 <span class="c">#</span> | |
| 485 472 <span class="c"># Notes:</span> | |
| 486 473 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span> | |
| 487 474 <span class="c">#</span> | |
| 488 <a name="GenerateFingerprints-"></a> 475 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> | |
| 489 476 <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> | |
| 490 477 | |
| 491 478 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
| 492 479 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateTopologicalPharmacophoreAtomPairsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."</span><span class="sc">;</span> | |
| 493 480 <span class="s">}</span> | |
| 494 481 | |
| 495 482 <span class="c"># Cache appropriate molecule data...</span> | |
| 496 483 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 497 484 | |
| 498 485 <span class="c"># Generate distance matrix...</span> | |
| 499 486 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_SetupDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 500 487 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: Fingerprints generation didn't succeed: Couldn't generate distance matrix..."</span><span class="sc">;</span> | |
| 501 488 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 502 489 <span class="s">}</span> | |
| 503 490 | |
| 504 491 <span class="c"># Assign pharmacohore atom types to all heavy atoms...</span> | |
| 505 492 <span class="i">$This</span><span class="i">->_AssignPharmacophoreAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 506 493 | |
| 507 494 <span class="c"># Initialize values of all possible pharmacohore atom pairs...</span> | |
| 508 495 <span class="i">$This</span><span class="i">->_InitializePharmacophoreAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 509 496 | |
| 510 497 <span class="c"># Count atom pairs...</span> | |
| 511 498 <span class="i">$This</span><span class="i">->_CountPharmacohoreAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 512 499 | |
| 513 500 <span class="c"># Fuzzify atom pairs count...</span> | |
| 514 501 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} =~ <span class="q">/^BeforeNormalization$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 515 502 <span class="i">$This</span><span class="i">->_FuzzifyPharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 516 503 <span class="s">}</span> | |
| 517 504 | |
| 518 505 <span class="c"># Normalize atom pairs count...</span> | |
| 519 506 <span class="i">$This</span><span class="i">->_NormalizePharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 520 507 | |
| 521 508 <span class="c"># Fuzzify atom pairs count...</span> | |
| 522 509 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} =~ <span class="q">/^AfterNormalization$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 523 510 <span class="i">$This</span><span class="i">->_FuzzifyPharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 524 511 <span class="s">}</span> | |
| 525 512 | |
| 526 513 <span class="c"># Set final fingerprints...</span> | |
| 527 514 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 528 515 | |
| 529 516 <span class="c"># Clear cached molecule data...</span> | |
| 530 517 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 531 518 | |
| 532 519 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 533 520 <span class="s">}</span> | |
| 534 521 | |
| 535 522 <span class="c"># Setup distance matrix...</span> | |
| 536 523 <span class="c">#</span> | |
| 537 <a name="_SetupDistanceMatrix-"></a> 524 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span> | |
| 538 525 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 539 526 | |
| 540 527 <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 541 528 | |
| 542 529 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span> | |
| 543 530 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 544 531 <span class="s">}</span> | |
| 545 532 | |
| 546 533 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 547 534 <span class="s">}</span> | |
| 548 535 | |
| 549 536 <span class="c"># Assign pharmacohore atom types to all heavy atoms and count each atom</span> | |
| 550 537 <span class="c"># types assigned...</span> | |
| 551 538 <span class="c">#</span> | |
| 552 <a name="_AssignPharmacophoreAtomTypes-"></a> 539 <span class="k">sub </span><span class="m">_AssignPharmacophoreAtomTypes</span> <span class="s">{</span> | |
| 553 540 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 554 541 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$AssignedAtomType</span><span class="cm">,</span> <span class="i">$FunctionalClassAtomTypes</span><span class="s">)</span><span class="sc">;</span> | |
| 555 542 | |
| 556 543 <span class="c"># Assign topological pharmacophore atom types...</span> | |
| 557 544 <span class="i">$FunctionalClassAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::FunctionalClassAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}<span class="s">)</span><span class="sc">;</span> | |
| 558 545 <span class="i">$FunctionalClassAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 559 546 | |
| 560 547 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 561 548 | |
| 562 549 <span class="c"># Initialize assigned atom types count...</span> | |
| 563 550 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 564 551 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 565 552 <span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 566 553 <span class="s">}</span> | |
| 567 554 | |
| 568 555 <span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 569 556 | |
| 570 557 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 571 558 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 572 559 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 573 560 <span class="s">}</span> | |
| 574 561 <span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 575 562 | |
| 576 563 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 577 564 | |
| 578 565 <span class="c"># Collect all possible pharmacophore atom types which could be assigned to atom...</span> | |
| 579 566 <span class="k">my</span><span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span><span class="sc">;</span> | |
| 580 567 | |
| 581 568 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 582 569 <span class="i">$AssignedAtomType</span> = <span class="i">$FunctionalClassAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 583 570 <span class="k">if</span> <span class="s">(</span><span class="i">$AssignedAtomType</span> && <span class="i">$AssignedAtomType</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 584 571 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AssignedAtomType</span><span class="sc">;</span> | |
| 585 572 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span> <span class="s">{</span> | |
| 586 573 <span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 587 574 <span class="s">}</span> | |
| 588 575 <span class="s">}</span> | |
| 589 576 | |
| 590 577 <span class="c"># Assign phramacophore types to atom...</span> | |
| 591 578 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 592 579 <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = \<span class="i">@AtomTypes</span><span class="sc">;</span> | |
| 593 580 <span class="s">}</span> | |
| 594 581 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 595 582 <span class="s">}</span> | |
| 596 583 | |
| 597 584 <span class="c"># Initialize values of all possible pharmacohore atom pairs...</span> | |
| 598 585 <span class="c">#</span> | |
| 599 586 <span class="c"># Let:</span> | |
| 600 587 <span class="c"># Dmin = Minimum distance correspoding to number of bonds between two atoms</span> | |
| 601 588 <span class="c"># Dmax = Maximum distance correspoding to number of bonds between two atoms</span> | |
| 602 589 <span class="c"># D = Distance correspoding to number of bonds between two atoms</span> | |
| 603 590 <span class="c">#</span> | |
| 604 591 <span class="c"># P = Number of pharmacophore atom types to consider</span> | |
| 605 592 <span class="c"># PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn</span> | |
| 606 593 <span class="c">#</span> | |
| 607 594 <span class="c"># PPT = Total number of possible pharmacophore atom pairs at all distances between Dmin and Dmax</span> | |
| 608 595 <span class="c">#</span> | |
| 609 596 <span class="c"># Then:</span> | |
| 610 597 <span class="c">#</span> | |
| 611 598 <span class="c"># PPD = (P * (P - 1))/2 + P</span> | |
| 612 599 <span class="c">#</span> | |
| 613 600 <span class="c"># PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P)</span> | |
| 614 601 <span class="c"># = ((Dmax - Dmin) + 1) * PPD</span> | |
| 615 602 <span class="c">#</span> | |
| 616 603 <span class="c">#</span> | |
| 617 604 <span class="c"># So for default values of Dmin = 1, Dmax = 10 and P = 5,</span> | |
| 618 605 <span class="c">#</span> | |
| 619 606 <span class="c"># PPD = (5 * (5 - 1))/2 + 5 = 15</span> | |
| 620 607 <span class="c"># PPT = ((10 - 1) + 1) * 15 = 150</span> | |
| 621 608 <span class="c">#</span> | |
| 622 609 <span class="c"># the pharmacophore atom pairs bais set includes 150 values.</span> | |
| 623 610 <span class="c">#</span> | |
| 624 <a name="_InitializePharmacophoreAtomPairs-"></a> 611 <span class="k">sub </span><span class="m">_InitializePharmacophoreAtomPairs</span> <span class="s">{</span> | |
| 625 612 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 626 613 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$Index1</span><span class="cm">,</span> <span class="i">$Index2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span><span class="sc">;</span> | |
| 627 614 | |
| 628 615 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 629 616 | |
| 630 617 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
| 631 618 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 632 619 | |
| 633 620 <span class="k">for</span> <span class="i">$Index1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 634 621 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span> | |
| 635 622 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 636 623 | |
| 637 624 <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="i">$Index1</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 638 625 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span> | |
| 639 626 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 640 627 <span class="s">}</span> | |
| 641 628 <span class="s">}</span> | |
| 642 629 <span class="s">}</span> | |
| 643 630 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 644 631 <span class="s">}</span> | |
| 645 632 | |
| 646 633 <span class="c"># Count pharmacophore atom pairs between mininum and maximum distance at each</span> | |
| 647 634 <span class="c"># distance using distance matrix and pharmacophore atom types assiged to each heavy</span> | |
| 648 635 <span class="c"># atom.</span> | |
| 649 636 <span class="c">#</span> | |
| 650 637 <span class="c"># Let:</span> | |
| 651 638 <span class="c"># Px = Pharmacophore atom type x</span> | |
| 652 639 <span class="c"># Py = Pharmacophore atom type y</span> | |
| 653 640 <span class="c"># Dn = Distance between Px and Py in specified distance range</span> | |
| 654 641 <span class="c">#</span> | |
| 655 642 <span class="c"># Then:</span> | |
| 656 643 <span class="c"># Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn</span> | |
| 657 644 <span class="c">#</span> | |
| 658 645 <span class="c"># For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on</span> | |
| 659 646 <span class="c">#</span> | |
| 660 647 <span class="c"># Notes:</span> | |
| 661 648 <span class="c"># . The row and column indices of distance matrix correspond to atom indices.</span> | |
| 662 649 <span class="c"># . Distance value of BigNumber implies the atom is not connected to any other atom.</span> | |
| 663 650 <span class="c"># . Due to symmetric nature of distance matrix, only upper or lower triangular matrix</span> | |
| 664 651 <span class="c"># needs to be processed during identification and count of pharmacophore atom pairs.</span> | |
| 665 652 <span class="c">#</span> | |
| 666 <a name="_CountPharmacohoreAtomPairs-"></a> 653 <span class="k">sub </span><span class="m">_CountPharmacohoreAtomPairs</span> <span class="s">{</span> | |
| 667 654 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 668 655 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="cm">,</span> <span class="i">$CountIncrement</span><span class="s">)</span><span class="sc">;</span> | |
| 669 656 | |
| 670 657 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span> | |
| 671 658 <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 672 659 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span> | |
| 673 660 | |
| 674 661 <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 675 662 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span> | |
| 676 663 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span> && <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 677 664 <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span> | |
| 678 665 <span class="s">}</span> | |
| 679 666 | |
| 680 667 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="i">$RowIndex</span> .. <span class="s">(</span><span class="i">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 681 668 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$ColIndex</span>}<span class="sc">;</span> | |
| 682 669 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span> && <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 683 670 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> | |
| 684 671 <span class="s">}</span> | |
| 685 672 | |
| 686 673 <span class="i">$Distance</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 687 674 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance</span> < <span class="i">$This</span>->{<span class="w">MinDistance</span>} || <span class="i">$Distance</span> > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
| 688 675 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> | |
| 689 676 <span class="s">}</span> | |
| 690 677 | |
| 691 678 <span class="j">ATOMTYPE1:</span> <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 692 679 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType1</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 693 680 <span class="k">next</span> <span class="j">ATOMTYPE1</span><span class="sc">;</span> | |
| 694 681 <span class="s">}</span> | |
| 695 682 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 696 683 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType2</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 697 684 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span> | |
| 698 685 <span class="s">}</span> | |
| 699 686 <span class="i">$CountIncrement</span> = <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType1</span>} * <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span> | |
| 700 687 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType1</span> <span class="k">le</span> <span class="i">$AtomType2</span><span class="s">)</span> <span class="s">{</span> | |
| 701 688 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="i">$CountIncrement</span><span class="sc">;</span> | |
| 702 689 <span class="s">}</span> | |
| 703 690 <span class="k">else</span> <span class="s">{</span> | |
| 704 691 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType2</span>}{<span class="i">$AtomType1</span>} += <span class="i">$CountIncrement</span><span class="sc">;</span> | |
| 705 692 <span class="s">}</span> | |
| 706 693 <span class="s">}</span> | |
| 707 694 <span class="s">}</span> | |
| 708 695 <span class="s">}</span> | |
| 709 696 <span class="s">}</span> | |
| 710 697 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 711 698 <span class="s">}</span> | |
| 712 699 | |
| 713 700 <span class="c"># Normalize the occurance count of pharmacophore atom pairs over the specified distance</span> | |
| 714 701 <span class="c"># range...</span> | |
| 715 702 <span class="c">#</span> | |
| 716 <a name="_NormalizePharmacohoreAtomPairsCount-"></a> 703 <span class="k">sub </span><span class="m">_NormalizePharmacohoreAtomPairsCount</span> <span class="s">{</span> | |
| 717 704 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 718 705 | |
| 719 706 <span class="j">METHODOLOGY:</span> <span class="s">{</span> | |
| 720 707 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 721 708 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span> | |
| 722 709 <span class="s">}</span> | |
| 723 710 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByHeavyAtomsCount$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 724 711 <span class="i">$This</span><span class="i">->_NormalizeAtomPairsCountByHeavyAtomsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 725 712 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span> | |
| 726 713 <span class="s">}</span> | |
| 727 714 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByAtomTypesCount$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 728 715 <span class="i">$This</span><span class="i">->_NormalizeAtomPairsCountByAtomTypesCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 729 716 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span> | |
| 730 717 <span class="s">}</span> | |
| 731 718 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_NormalizePharmacohoreAtomPairsCount: Unknown NormalizationMethodology: $This->{NormalizationMethodology}..."</span><span class="sc">;</span> | |
| 732 719 <span class="s">}</span> | |
| 733 720 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 734 721 <span class="s">}</span> | |
| 735 722 | |
| 736 723 | |
| 737 724 <span class="c"># Normalize the occurance count of pharmacophore atom pairs at various distances by</span> | |
| 738 725 <span class="c"># heavy atom count...</span> | |
| 739 726 <span class="c">#</span> | |
| 740 <a name="_NormalizeAtomPairsCountByHeavyAtomsCount-"></a> 727 <span class="k">sub </span><span class="m">_NormalizeAtomPairsCountByHeavyAtomsCount</span> <span class="s">{</span> | |
| 741 728 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 742 729 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span><span class="sc">;</span> | |
| 743 730 | |
| 744 731 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 745 732 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 746 733 <span class="s">}</span> | |
| 747 734 | |
| 748 735 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} <span class="s">)</span> <span class="s">{</span> | |
| 749 736 <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} <span class="s">)</span> <span class="s">{</span> | |
| 750 737 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span> | |
| 751 738 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 752 739 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span> | |
| 753 740 <span class="s">}</span> | |
| 754 741 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} /= <span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>}<span class="sc">;</span> | |
| 755 742 <span class="s">}</span> | |
| 756 743 <span class="s">}</span> | |
| 757 744 <span class="s">}</span> | |
| 758 745 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 759 746 <span class="s">}</span> | |
| 760 747 | |
| 761 748 <span class="c"># Normalize the occurance count of pharmacophore atom pairs at various distances by</span> | |
| 762 749 <span class="c"># dividing it using sum of the count of each pharmacophore atom type present in the</span> | |
| 763 750 <span class="c"># molecule for the corresponding atom pair.</span> | |
| 764 751 <span class="c">#</span> | |
| 765 <a name="_NormalizeAtomPairsCountByAtomTypesCount-"></a> 752 <span class="k">sub </span><span class="m">_NormalizeAtomPairsCountByAtomTypesCount</span> <span class="s">{</span> | |
| 766 753 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 767 754 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$AtomType1Count</span><span class="cm">,</span> <span class="i">$AtomType2Count</span><span class="cm">,</span> <span class="i">$NormalizationFactor</span><span class="s">)</span><span class="sc">;</span> | |
| 768 755 | |
| 769 756 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} <span class="s">)</span> <span class="s">{</span> | |
| 770 757 <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} <span class="s">)</span> <span class="s">{</span> | |
| 771 758 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span> | |
| 772 759 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 773 760 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span> | |
| 774 761 <span class="s">}</span> | |
| 775 762 <span class="i">$NormalizationFactor</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType1</span>} + <span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span> | |
| 776 763 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} /= <span class="i">$NormalizationFactor</span><span class="sc">;</span> | |
| 777 764 <span class="s">}</span> | |
| 778 765 <span class="s">}</span> | |
| 779 766 <span class="s">}</span> | |
| 780 767 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 781 768 <span class="s">}</span> | |
| 782 769 | |
| 783 770 <span class="c"># Fuzzify pharmacophore atom pairs count...</span> | |
| 784 771 <span class="c">#</span> | |
| 785 772 <span class="c"># Let:</span> | |
| 786 773 <span class="c"># Px = Pharmacophore atom type x</span> | |
| 787 774 <span class="c"># Py = Pharmacophore atom type y</span> | |
| 788 775 <span class="c">#</span> | |
| 789 776 <span class="c"># PPxy = Pharmacophore atom pair between atom type Px and Py</span> | |
| 790 777 <span class="c">#</span> | |
| 791 778 <span class="c"># PPxyDn = Pharmacophore atom pairs count between atom type Px and Py at distance Dn</span> | |
| 792 779 <span class="c"># PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py at distance Dn - 1</span> | |
| 793 780 <span class="c"># PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py at distance Dn + 1</span> | |
| 794 781 <span class="c">#</span> | |
| 795 782 <span class="c"># FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing</span> | |
| 796 783 <span class="c">#</span> | |
| 797 784 <span class="c"># Then:</span> | |
| 798 785 <span class="c">#</span> | |
| 799 786 <span class="c"># For FuzzyBinning:</span> | |
| 800 787 <span class="c">#</span> | |
| 801 788 <span class="c"># PPxyDn = PPxyDn (Unchanged)</span> | |
| 802 789 <span class="c">#</span> | |
| 803 790 <span class="c"># PPxyDn-1 = PPxyDn-1 + PPxyDn * FF</span> | |
| 804 791 <span class="c"># PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</span> | |
| 805 792 <span class="c">#</span> | |
| 806 793 <span class="c"># For FuzzyBinSmoothing:</span> | |
| 807 794 <span class="c">#</span> | |
| 808 795 <span class="c"># PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin < Dn < Dmax</span> | |
| 809 796 <span class="c"># PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax</span> | |
| 810 797 <span class="c">#</span> | |
| 811 798 <span class="c"># PPxyDn-1 = PPxyDn-1 + PPxyDn * FF</span> | |
| 812 799 <span class="c"># PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</span> | |
| 813 800 <span class="c">#</span> | |
| 814 801 <span class="c"># In both fuzzification schemes, a value of 0 for FF implies no fuzzification of occurance counts.</span> | |
| 815 802 <span class="c"># A value of 1 during FuzzyBinning corresponds to maximum fuzzification of occurance counts;</span> | |
| 816 803 <span class="c"># however, a value of 1 during FuzzyBinSmoothing ends up completely distributing the value over</span> | |
| 817 804 <span class="c"># the previous and next distance bins.</span> | |
| 818 805 <span class="c">#</span> | |
| 819 806 <span class="c"># So for default value of FuzzFactor (FF) 0.15, the occurance count of pharmacohore atom pairs</span> | |
| 820 807 <span class="c"># at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn -1 and Dn + 1</span> | |
| 821 808 <span class="c"># are incremened by PPxyDn * 0.15.</span> | |
| 822 809 <span class="c">#</span> | |
| 823 810 <span class="c"># And during FuzzyBinSmoothing the occurance counts at Distance Dn is scaled back using multiplicate</span> | |
| 824 811 <span class="c"># factor of (1 - 2*0.15) and the occurance counts at distances Dn -1 and Dn + 1 are incremened by</span> | |
| 825 812 <span class="c"># PPxyDn * 0.15. In otherwords, occurance bin count is smoothed out by distributing it over the</span> | |
| 826 813 <span class="c"># previous and next distance value.</span> | |
| 827 814 <span class="c">#</span> | |
| 828 <a name="_FuzzifyPharmacohoreAtomPairsCount-"></a> 815 <span class="k">sub </span><span class="m">_FuzzifyPharmacohoreAtomPairsCount</span> <span class="s">{</span> | |
| 829 816 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 830 817 <span class="k">my</span><span class="s">(</span><span class="i">$Index1</span><span class="cm">,</span> <span class="i">$Index2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$CurrentDistance</span><span class="cm">,</span> <span class="i">$CurrentCount</span><span class="cm">,</span> <span class="i">$NextDistance</span><span class="cm">,</span> <span class="i">$NextCount</span><span class="cm">,</span> <span class="i">$PreviousDistance</span><span class="cm">,</span> <span class="i">$ModifyCurrentCount</span><span class="cm">,</span> <span class="i">$ChangeInCountValue</span><span class="s">)</span><span class="sc">;</span> | |
| 831 818 | |
| 832 819 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>} && <span class="i">$This</span>->{<span class="w">FuzzFactor</span>} > <span class="n">0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 833 820 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 834 821 <span class="s">}</span> | |
| 835 822 | |
| 836 823 <span class="i">$ModifyCurrentCount</span> = <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinSmoothing$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 837 824 | |
| 838 825 <span class="k">for</span> <span class="i">$Index1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 839 826 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span> | |
| 840 827 <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="i">$Index1</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 841 828 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span> | |
| 842 829 | |
| 843 830 <span class="i">$CurrentCount</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$NextCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 844 831 | |
| 845 832 <span class="i">$NextDistance</span> = <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="sc">;</span> | |
| 846 833 <span class="i">$NextCount</span> = <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$NextDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span> | |
| 847 834 | |
| 848 835 <span class="j">DISTANCE:</span> <span class="k">for</span> <span class="i">$CurrentDistance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
| 849 836 <span class="i">$NextDistance</span> = <span class="i">$CurrentDistance</span> + <span class="n">1</span><span class="sc">;</span> | |
| 850 837 <span class="i">$PreviousDistance</span> = <span class="i">$CurrentDistance</span> - <span class="n">1</span><span class="sc">;</span> | |
| 851 838 | |
| 852 839 <span class="i">$CurrentCount</span> = <span class="i">$NextCount</span><span class="sc">;</span> | |
| 853 840 <span class="i">$NextCount</span> = <span class="s">(</span><span class="i">$CurrentDistance</span> < <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> ? <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$NextDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 854 841 | |
| 855 842 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentCount</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 856 843 <span class="c"># No contribution to fuzzy binning from this distance...</span> | |
| 857 844 <span class="k">next</span> <span class="j">DISTANCE</span><span class="sc">;</span> | |
| 858 845 <span class="s">}</span> | |
| 859 846 | |
| 860 847 <span class="i">$ChangeInCountValue</span> = <span class="i">$CurrentCount</span> * <span class="i">$This</span>->{<span class="w">FuzzFactor</span>}<span class="sc">;</span> | |
| 861 848 | |
| 862 849 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentDistance</span> > <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
| 863 850 <span class="c"># Increment count at previous distance...</span> | |
| 864 851 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$PreviousDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="i">$ChangeInCountValue</span><span class="sc">;</span> | |
| 865 852 <span class="s">}</span> | |
| 866 853 | |
| 867 854 <span class="k">if</span> <span class="s">(</span><span class="i">$ModifyCurrentCount</span><span class="s">)</span> <span class="s">{</span> | |
| 868 855 <span class="c"># Decrement count at current distance for FuzzyBinSmoothing...</span> | |
| 869 856 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentDistance</span> > <span class="i">$This</span>->{<span class="w">MinDistance</span>} && <span class="i">$CurrentDistance</span> < <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
| 870 857 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$CurrentDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} -= <span class="n">2</span> * <span class="i">$ChangeInCountValue</span><span class="sc">;</span> | |
| 871 858 <span class="s">}</span> | |
| 872 859 <span class="k">else</span> <span class="s">{</span> | |
| 873 860 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$CurrentDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} -= <span class="i">$ChangeInCountValue</span><span class="sc">;</span> | |
| 874 861 <span class="s">}</span> | |
| 875 862 <span class="s">}</span> | |
| 876 863 | |
| 877 864 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentDistance</span> < <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
| 878 865 <span class="c"># Increment count at next distance...</span> | |
| 879 866 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$NextDistance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="i">$ChangeInCountValue</span><span class="sc">;</span> | |
| 880 867 <span class="s">}</span> | |
| 881 868 <span class="s">}</span> | |
| 882 869 <span class="s">}</span> | |
| 883 870 <span class="s">}</span> | |
| 884 871 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 885 872 <span class="s">}</span> | |
| 886 873 | |
| 887 874 <span class="c"># Set final fingerpritns vector...</span> | |
| 888 875 <span class="c">#</span> | |
| 889 <a name="_SetFinalFingerprints-"></a> 876 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> | |
| 890 877 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 891 878 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$Index1</span><span class="cm">,</span> <span class="i">$Index2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$RoundOffValues</span><span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="cm">,</span> <span class="i">$UseArbitrarySetSize</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> | |
| 892 879 | |
| 893 880 <span class="c"># Mark successful generation of fingerprints...</span> | |
| 894 881 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 895 882 | |
| 896 883 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 897 884 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 898 885 | |
| 899 886 <span class="c"># Do values need to be rounded off?</span> | |
| 900 887 <span class="i">$RoundOffValues</span> = <span class="s">(</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} !~ <span class="q">/^None$/i</span><span class="s">)</span> || <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzifyAtomPairsCount</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> | |
| 901 888 <span class="i">$ValuesPrecision</span> = <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>}<span class="sc">;</span> | |
| 902 889 | |
| 903 890 <span class="c"># Is it an ArbitraySize atom pairs set size?</span> | |
| 904 891 <span class="i">$UseArbitrarySetSize</span> = <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 905 892 | |
| 906 893 <span class="c"># Collect all atom paris count values...</span> | |
| 907 894 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> | |
| 908 895 <span class="k">for</span> <span class="i">$Index1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 909 896 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span> | |
| 910 897 <span class="j">INDEX2:</span> <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="i">$Index1</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 911 898 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span> | |
| 912 899 | |
| 913 900 <span class="c"># Atom pair count...</span> | |
| 914 901 <span class="i">$Value</span> = <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span> | |
| 915 902 <span class="k">if</span> <span class="s">(</span><span class="i">$RoundOffValues</span><span class="s">)</span> <span class="s">{</span> | |
| 916 903 <span class="i">$Value</span> = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$Value</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>}<span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> | |
| 917 904 <span class="s">}</span> | |
| 918 905 | |
| 919 906 <span class="c"># Ignore or not to ignore...</span> | |
| 920 907 <span class="k">if</span> <span class="s">(</span><span class="i">$UseArbitrarySetSize</span> && <span class="i">$Value</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 921 908 <span class="k">next</span> <span class="j">INDEX2</span><span class="sc">;</span> | |
| 922 909 <span class="s">}</span> | |
| 923 910 | |
| 924 911 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="cm">,</span> <span class="q">"${AtomType1}-D${Distance}-${AtomType2}"</span><span class="sc">;</span> | |
| 925 912 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span> | |
| 926 913 <span class="s">}</span> | |
| 927 914 <span class="s">}</span> | |
| 928 915 <span class="s">}</span> | |
| 929 916 | |
| 930 917 <span class="c"># Add AtomPairsIDs and count values to fingerprint vector...</span> | |
| 931 918 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="s">)</span><span class="sc">;</span> | |
| 932 919 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> | |
| 933 920 | |
| 934 921 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 935 922 <span class="s">}</span> | |
| 936 923 | |
| 937 924 <span class="c"># Get pharmacophore atom pair IDs corresponding to atom pairs count values in</span> | |
| 938 925 <span class="c"># fingerprint vector as an array or reference to an array...</span> | |
| 939 926 <span class="c">#</span> | |
| 940 927 <span class="c"># AtomPairIDs list is generated during finalization of fingerprints and the fingerprint</span> | |
| 941 928 <span class="c"># vector containing count values matches the atom pairs array.</span> | |
| 942 929 <span class="c">#</span> | |
| 943 930 <span class="c">#</span> | |
| 944 <a name="GetAtomPairIDs-"></a> 931 <span class="k">sub </span><span class="m">GetAtomPairIDs</span> <span class="s">{</span> | |
| 945 932 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 946 933 | |
| 947 934 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="sc">;</span> | |
| 948 935 <span class="s">}</span> | |
| 949 936 | |
| 950 937 <span class="c"># Cache appropriate molecule data...</span> | |
| 951 938 <span class="c">#</span> | |
| 952 <a name="_SetupMoleculeDataCache-"></a> 939 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> | |
| 953 940 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 954 941 | |
| 955 942 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span> | |
| 956 943 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span> | |
| 957 944 <span class="c">#</span> | |
| 958 945 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 959 946 | |
| 960 947 <span class="c"># Get all atom IDs...</span> | |
| 961 948 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 962 949 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 963 950 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span> | |
| 964 951 | |
| 965 952 <span class="c"># Set AtomIndex to AtomID hash...</span> | |
| 966 953 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 967 954 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> } = <span class="i">@AtomIDs</span><span class="sc">;</span> | |
| 968 955 | |
| 969 956 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 970 957 <span class="s">}</span> | |
| 971 958 | |
| 972 959 <span class="c"># Clear cached molecule data...</span> | |
| 973 960 <span class="c">#</span> | |
| 974 <a name="_ClearMoleculeDataCache-"></a> 961 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> | |
| 975 962 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 976 963 | |
| 977 964 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 978 965 | |
| 979 966 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 980 967 <span class="s">}</span> | |
| 981 968 | |
| 982 969 | |
| 983 970 <span class="c"># Return a string containg data for TopologicalPharmacophoreAtomPairsFingerprints object...</span> | |
| 984 <a name="StringifyTopologicalPharmacophoreAtomPairsFingerprints-"></a> 971 <span class="k">sub </span><span class="m">StringifyTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span> | |
| 985 972 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 986 973 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span> | |
| 987 974 | |
| 988 975 <span class="c"># Type of fingerprint...</span> | |
| 989 976 <span class="i">$FingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomPairsSetSizeToUse: $This->{AtomPairsSetSizeToUse}"</span><span class="sc">;</span> | |
| 990 977 | |
| 991 978 <span class="c"># Min and max distance...</span> | |
| 992 979 <span class="i">$FingerprintsString</span> .= <span class="q">"; MinDistance: $This->{MinDistance}; MaxDistance: $This->{MaxDistance}"</span><span class="sc">;</span> | |
| 993 980 | |
| 994 981 <span class="c"># Pharmacophore type labels and description...</span> | |
| 995 982 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span><span class="sc">;</span> | |
| 996 983 | |
| 997 984 <span class="i">@AtomTypesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 998 985 <span class="i">%AvailableAtomTypes</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 999 986 | |
| 1000 987 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1001 988 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypesOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 1002 989 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="q">"$AtomType: $AvailableAtomTypes{$AtomType}"</span><span class="sc">;</span> | |
| 1003 990 <span class="s">}</span> | |
| 1004 991 | |
| 1005 992 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</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> | |
| 1006 993 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
| 1007 994 <span class="i">$FingerprintsString</span> .= <span class="q">"; AvailableAtomTypes: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypes</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> | |
| 1008 995 | |
| 1009 996 <span class="c"># Normalization method...</span> | |
| 1010 997 <span class="i">$FingerprintsString</span> .= <span class="q">"; NormalizationMethodology: $This->{NormalizationMethodology}"</span><span class="sc">;</span> | |
| 1011 998 | |
| 1012 999 <span class="c"># Weights...</span> | |
| 1013 1000 <span class="k">my</span><span class="s">(</span><span class="i">$FirstLabel</span><span class="cm">,</span> <span class="i">$Label</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span><span class="sc">;</span> | |
| 1014 1001 | |
| 1015 1002 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesWeight <Labels: Weight>: <"</span><span class="sc">;</span> | |
| 1016 1003 <span class="i">$FirstLabel</span> = <span class="n">1</span><span class="sc">;</span> | |
| 1017 1004 <span class="k">for</span> <span class="i">$Label</span> <span class="s">(</span><span class="k">sort</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 1018 1005 <span class="i">$Weight</span> = <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$Label</span>}<span class="sc">;</span> | |
| 1019 1006 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstLabel</span><span class="s">)</span> <span class="s">{</span> | |
| 1020 1007 <span class="i">$FirstLabel</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1021 1008 <span class="i">$FingerprintsString</span> .= <span class="q">" ${Label}: ${Weight}"</span><span class="sc">;</span> | |
| 1022 1009 <span class="s">}</span> | |
| 1023 1010 <span class="k">else</span> <span class="s">{</span> | |
| 1024 1011 <span class="i">$FingerprintsString</span> .= <span class="q">"; ${Label}: ${Weight}"</span><span class="sc">;</span> | |
| 1025 1012 <span class="s">}</span> | |
| 1026 1013 <span class="s">}</span> | |
| 1027 1014 <span class="i">$FingerprintsString</span> .= <span class="q">">"</span><span class="sc">;</span> | |
| 1028 1015 | |
| 1029 1016 <span class="c"># Fuzzification of count...</span> | |
| 1030 1017 <span class="k">my</span><span class="s">(</span><span class="i">$FuzzifyFlag</span><span class="s">)</span><span class="sc">;</span> | |
| 1031 1018 <span class="i">$FuzzifyFlag</span> = <span class="i">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span> | |
| 1032 1019 <span class="i">$FingerprintsString</span> .= <span class="q">"; FuzzifyAtomPairsCount: $FuzzifyFlag; FuzzificationMode: $This->{FuzzificationMode}; FuzzificationMethodology: $This->{FuzzificationMethodology}; FuzzFactor: $This->{FuzzFactor}"</span><span class="sc">;</span> | |
| 1033 1020 | |
| 1034 1021 <span class="c"># Total number of pharmacophore atom pairs...</span> | |
| 1035 1022 <span class="i">$FingerprintsString</span> .= <span class="q">"; NumOfAtomPairs: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1036 1023 | |
| 1037 1024 <span class="c"># FingerprintsVector...</span> | |
| 1038 1025 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> | |
| 1039 1026 | |
| 1040 1027 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span> | |
| 1041 1028 <span class="s">}</span> | |
| 1042 1029 | |
| 1043 <a name="EOF-"></a></pre> | |
| 1044 <p> </p> | |
| 1045 <br /> | |
| 1046 <center> | |
| 1047 <img src="../../../images/h2o2.png"> | |
| 1048 </center> | |
| 1049 </body> | |
| 1050 </html> |