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<html> <head> <title>MayaChemTools:Code:Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> <a name="package-Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: TopologicalPharmacophoreAtomPairsFingerprints.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> 5 <span class="c"># $Revision: 1.34 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> 37 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> 39 40 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> 43 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> 45 46 <span class="c"># Setup class variables...</span> 47 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> 48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 49 50 <span class="c"># Overload Perl functions...</span> 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> 52 53 <span class="c"># Class constructor...</span> <a name="new-"></a> 54 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 55 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 56 57 <span class="c"># Initialize object...</span> 58 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 59 <span class="k">bless</span> <span class="i">$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> 60 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomPairsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 61 62 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 63 64 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 65 <span class="s">}</span> 66 67 <span class="c"># Initialize object data...</span> 68 <span class="c">#</span> <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprints-"></a> 69 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span> 70 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 71 72 <span class="c"># Type of fingerprint...</span> 73 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'TopologicalPharmacophoreAtomPairs'</span><span class="sc">;</span> 74 75 <span class="c"># Type of vector...</span> 76 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> 77 78 <span class="c"># AtomPairsSetSizeToUse...</span> 79 <span class="c">#</span> 80 <span class="c"># ArbitrarySize - Corrresponds to atom pairs with non-zero count</span> 81 <span class="c"># FixedSize - Corresponds to all atom pairs with zero and non-zero count</span> 82 <span class="c">#</span> 83 <span class="c"># Possible values: ArbitrarySize or FixedSize. Default: ArbitrarySize</span> 84 <span class="c">#</span> 85 <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="q">''</span><span class="sc">;</span> 86 87 <span class="c"># Type of FingerprintsVector...</span> 88 <span class="c">#</span> 89 <span class="c"># OrderedNumericalValues - For ArbitrarySize value of AtomPairsSetSizeToUse</span> 90 <span class="c"># NumericalValues - For FixedSize value of AtomPairsSetSizeToUse</span> 91 <span class="c">#</span> 92 <span class="c"># Possible values: OrderedNumericalValues or NumericalValues. Default: NumericalValues</span> 93 <span class="c">#</span> 94 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">''</span><span class="sc">;</span> 95 96 <span class="c"># Vector values precision for real values which might be generated after</span> 97 <span class="c"># normalization and fuzzification...</span> 98 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="n">2</span><span class="sc">;</span> 99 100 <span class="c"># Minimum and maximum bond distance between pharmacophore atom paris...</span> 101 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span> 102 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> 103 104 <span class="c"># Initialize atom types and weight information...</span> 105 <span class="i">$This</span><span class="i">->_InitializePharmacophoreAtomTypesAndWeightInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 106 107 <span class="c"># Normalization methodology to use for scaling the occurance count of pharmacophore atom</span> 108 <span class="c"># pairs at various distances.</span> 109 <span class="c">#</span> 110 <span class="c"># Possible values: None, ByHeavyAtomsCount, ByAtomTypesCount. Default: None</span> 111 <span class="c">#</span> 112 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="q">'None'</span><span class="sc">;</span> 113 114 <span class="c"># Initialize fuzzification parameters...</span> 115 <span class="c">#</span> 116 <span class="i">$This</span><span class="i">->_InitializeFuzzificationInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 117 118 <span class="c"># Pharmacophore types assigned to each heavy atom...</span> 119 <span class="c">#</span> 120 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 121 122 <span class="c"># Assigned Atom types count of each type in the molecule...</span> 123 <span class="c">#</span> 124 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 125 126 <span class="c"># All pharmacophore atom pairs between minimum and maximum distance...</span> 127 <span class="c">#</span> 128 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 129 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 130 <span class="s">}</span> 131 132 <span class="c"># Inialize pharmacophore atom types and weight information...</span> 133 <span class="c">#</span> <a name="_InitializePharmacophoreAtomTypesAndWeightInformation-"></a> 134 <span class="k">sub </span><span class="m">_InitializePharmacophoreAtomTypesAndWeightInformation</span> <span class="s">{</span> 135 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 136 137 <span class="c"># Default pharmacophore atom types to use for atom pairs fingerprint generation</span> 138 <span class="c"># are: HBD, HBA, PI, NI, H</span> 139 <span class="c">#</span> 140 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 141 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="k">sort</span> <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="s">)</span><span class="sc">;</span> 142 143 <span class="c"># Weight of the various pharmacophore atom types to use for their contribution to atom</span> 144 <span class="c"># pair interaction. It allows to increase the importance of specific pharmacophore atom</span> 145 <span class="c"># types in the generted fingerprints.</span> 146 <span class="c">#</span> 147 <span class="c"># A value of 0 eliminates the contribution by a particular pharmacophore atom</span> 148 <span class="c"># type and 2 doubles its contribution.</span> 149 <span class="c">#</span> 150 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span><span class="sc">;</span> 151 152 <span class="i">%AvailableAtomTypes</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 153 154 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 155 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span> <span class="s">{</span> 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> 157 <span class="s">}</span> 158 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 159 <span class="s">}</span> 160 161 <span class="c"># Initialize fuzzification information...</span> 162 <span class="c">#</span> <a name="_InitializeFuzzificationInformation-"></a> 163 <span class="k">sub </span><span class="m">_InitializeFuzzificationInformation</span> <span class="s">{</span> 164 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 165 166 <span class="c"># To fuzz or not to fuzz atom pairs count. Default: No fuzzication</span> 167 <span class="c">#</span> 168 <span class="i">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>} = <span class="n">0</span><span class="sc">;</span> 169 170 <span class="c"># When to fuzz atom pair count...</span> 171 <span class="c">#</span> 172 <span class="c"># Possible values: BeforeNormalization or AfterNormalization. Default: AfterNormalization</span> 173 <span class="c">#</span> 174 <span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} = <span class="q">'AfterNormalization'</span><span class="sc">;</span> 175 176 <span class="c"># How to fuzz atom pair count...</span> 177 <span class="c">#</span> 178 <span class="c"># Possible values: FuzzyBinning or FuzzyBinSmoothing. Default: FuzzyBinning</span> 179 <span class="c">#</span> 180 <span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} = <span class="q">'FuzzyBinning'</span><span class="sc">;</span> 181 182 <span class="c"># By how much to fuzz atom pairs count...</span> 183 <span class="c">#</span> 184 <span class="i">$This</span>->{<span class="w">FuzzFactor</span>} = <span class="n">0.15</span><span class="sc">;</span> 185 186 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 187 <span class="s">}</span> 188 189 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 190 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 191 <span class="c">#Class name...</span> 192 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 193 <span class="s">}</span> 194 195 <span class="c"># Initialize object properties....</span> <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties-"></a> 196 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprintsProperties</span> <span class="s">{</span> 197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 198 199 <span class="k">my</span><span class="s">(</span><span class="i">$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> 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> 201 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 202 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 203 <span class="s">}</span> 204 205 <span class="c"># Make sure molecule object was specified...</span> 206 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> 207 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> 208 <span class="s">}</span> 209 210 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 211 212 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 213 <span class="s">}</span> 214 215 <span class="c"># Initialize fingerprints vector...</span> 216 <span class="c">#</span> <a name="_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector-"></a> 217 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomPairsFingerprintsVector</span> <span class="s">{</span> 218 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 219 220 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span> 221 <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="q">'ArbitrarySize'</span><span class="sc">;</span> 222 <span class="s">}</span> 223 224 <span class="c"># Vector type and type of values...</span> 225 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> 226 227 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span> 228 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'OrderedNumericalValues'</span><span class="sc">;</span> 229 <span class="s">}</span> 230 <span class="k">else</span> <span class="s">{</span> 231 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> 232 <span class="s">}</span> 233 234 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 235 <span class="s">}</span> 236 237 <span class="c"># Set atom parits set size to use...</span> 238 <span class="c">#</span> <a name="SetAtomPairsSetSizeToUse-"></a> 239 <span class="k">sub </span><span class="m">SetAtomPairsSetSizeToUse</span> <span class="s">{</span> 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> 241 242 <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> 243 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomPairsSetSizeToUse: Can't change size: It's already set..."</span><span class="sc">;</span> 244 <span class="s">}</span> 245 246 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ArbitrarySize|FixedSize)$/i</span><span class="s">)</span> <span class="s">{</span> 247 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomPairsSetSizeToUse: Unknown AtomPairsSetSizeToUse value: $Value; Supported values: ArbitrarySize or FixedSize"</span><span class="sc">;</span> 248 <span class="s">}</span> 249 250 <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} = <span class="i">$Value</span><span class="sc">;</span> 251 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 253 <span class="s">}</span> 254 255 <span class="c"># Disable change of AvailableAtomTypes...</span> 256 <span class="c">#</span> <a name="SetAvailableAtomTypes-"></a> 257 <span class="k">sub </span><span class="m">SetAvailableAtomTypes</span> <span class="s">{</span> 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> 259 260 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAvailableAtomTypes: AvailableAtomTypes value can't be set..."</span><span class="sc">;</span> 261 262 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 263 <span class="s">}</span> 264 265 <span class="c"># Set atom types to use for atom pairs...</span> 266 <span class="c">#</span> <a name="SetAtomTypesToUse-"></a> 267 <span class="k">sub </span><span class="m">SetAtomTypesToUse</span> <span class="s">{</span> 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 269 <span class="k">my</span><span class="s">(</span><span class="i">$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> 270 271 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 272 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomTypesToUse: No values specified..."</span><span class="sc">;</span> 273 <span class="k">return</span><span class="sc">;</span> 274 <span class="s">}</span> 275 276 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 277 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 278 279 <span class="i">@SpecifiedAtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 280 <span class="i">@AtomTypesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 281 282 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 283 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> 284 <span class="s">}</span> 285 <span class="k">else</span> <span class="s">{</span> 286 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 287 <span class="s">}</span> 288 289 <span class="c"># Make sure specified AtomTypes are valid...</span> 290 <span class="k">for</span> <span class="i">$SpecifiedAtomType</span> <span class="s">(</span><span class="i">@SpecifiedAtomTypes</span><span class="s">)</span> <span class="s">{</span> 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> 292 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesToUse: Specified atom type, $SpecifiedAtomType, is not supported...\n "</span><span class="sc">;</span> 293 <span class="s">}</span> 294 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomType</span><span class="sc">;</span> 295 <span class="k">push</span> <span class="i">@AtomTypesToUse</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span> 296 <span class="s">}</span> 297 298 <span class="c"># Set atom types to use...</span> 299 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 300 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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> 301 302 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 303 <span class="s">}</span> 304 305 <span class="c"># Set vector values precision for real values which might be generated after</span> 306 <span class="c"># normalization and fuzzification...</span> 307 <span class="c">#</span> <a name="SetValuesPrecision-"></a> 308 <span class="k">sub </span><span class="m">SetValuesPrecision</span> <span class="s">{</span> 309 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 310 311 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 312 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetValuesPrecision: ValuesPrecision value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> 313 <span class="s">}</span> 314 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="i">$Value</span><span class="sc">;</span> 315 316 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 317 <span class="s">}</span> 318 319 <span class="c"># Set minimum distance for pharmacophore atom pairs...</span> 320 <span class="c">#</span> <a name="SetMinDistance-"></a> 321 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span> 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> 323 324 <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> 325 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> 326 <span class="s">}</span> 327 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> 328 329 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 330 <span class="s">}</span> 331 332 <span class="c"># Set maximum distance for pharmacophore atom pairs...</span> 333 <span class="c">#</span> <a name="SetMaxDistance-"></a> 334 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span> 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> 336 337 <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> 338 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> 339 <span class="s">}</span> 340 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> 341 342 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 343 <span class="s">}</span> 344 345 <span class="c"># Set normalization methodology to use for scaling the occurance count of pharmacophore atom</span> 346 <span class="c"># pairs over distance range beween minimum and maximum distance.</span> 347 <span class="c">#</span> <a name="SetNormalizationMethodology-"></a> 348 <span class="k">sub </span><span class="m">SetNormalizationMethodology</span> <span class="s">{</span> 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> 350 351 <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> 352 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNormalizationMethodology: NormalizationMethodology value, $Value, is not valid. Supported values: None, ByHeavyAtomsCount or ByAtomTypesCount..."</span><span class="sc">;</span> 353 <span class="s">}</span> 354 355 <span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span> 356 357 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 358 <span class="s">}</span> 359 360 <span class="c"># Set weight of the various pharmacophore atom types to use for their contribution to atom</span> 361 <span class="c"># pair interaction using atom types label and value hash.</span> 362 <span class="c">#</span> 363 <span class="c"># It allows to increase the importance of specific pharmacophore atom</span> 364 <span class="c"># types in the generted fingerprints.</span> 365 <span class="c">#</span> 366 <span class="c"># A value of 0 eliminates the contribution by a particular pharmacophore atom</span> 367 <span class="c"># type and 2 doubles its contribution.</span> 368 <span class="c">#</span> <a name="SetAtomTypesWeight-"></a> 369 <span class="k">sub </span><span class="m">SetAtomTypesWeight</span> <span class="s">{</span> 370 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%AtomTypesWeight</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 371 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span><span class="sc">;</span> 372 373 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%AtomTypesWeight</span><span class="s">)</span> <span class="s">{</span> 374 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> <span class="s">{</span> 375 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesWeight: AtomTypeWeight for $AtomType couldn't be set: Unknown atom type..."</span><span class="sc">;</span> 376 <span class="s">}</span> 377 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$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> 378 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesWeight: Specified weight value, $Weight, for AtomType, $AtomType, muts be >= 0..."</span><span class="sc">;</span> 379 <span class="s">}</span> 380 <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType</span>} = <span class="i">$Weight</span><span class="sc">;</span> 381 <span class="s">}</span> 382 <span class="s">}</span> 383 384 <span class="c"># Set fuzzification methodology to use for fuzzifying atom pairs count...</span> 385 <span class="c">#</span> <a name="SetFuzzificationMethodology-"></a> 386 <span class="k">sub </span><span class="m">SetFuzzificationMethodology</span> <span class="s">{</span> 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> 388 389 <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> 390 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzificationMethodology: FuzzificationMethodology value, $Value, is not valid. Supported values: FuzzyBinning or FuzzyBinSmoothing..."</span><span class="sc">;</span> 391 <span class="s">}</span> 392 393 <span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} = <span class="i">$Value</span><span class="sc">;</span> 394 395 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 396 <span class="s">}</span> 397 398 <span class="c"># Set fuzzification mode for fuzzifying atom pairs count...</span> 399 <span class="c">#</span> <a name="SetFuzzificationMode-"></a> 400 <span class="k">sub </span><span class="m">SetFuzzificationMode</span> <span class="s">{</span> 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> 402 403 <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> 404 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzificationMode: FuzzificationMode value, $Value, is not valid. Supported values: BeforeNormalization or AfterNormalization..."</span><span class="sc">;</span> 405 <span class="s">}</span> 406 407 <span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} = <span class="i">$Value</span><span class="sc">;</span> 408 409 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 410 <span class="s">}</span> 411 412 <span class="c"># Set fuzz factor values used for fuzzifying atom pairs count...</span> 413 <span class="c">#</span> <a name="SetFuzzFactor-"></a> 414 <span class="k">sub </span><span class="m">SetFuzzFactor</span> <span class="s">{</span> 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> 416 417 <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> 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> 419 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzFactor: Specified fuzz factor value, $Value, must be >= 0 and <= 1..."</span><span class="sc">;</span> 420 <span class="s">}</span> 421 <span class="s">}</span> 422 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMethodology</span>} =~ <span class="q">/^FuzzyBinSmoothing$/i</span><span class="s">)</span> <span class="s">{</span> 423 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">TextUtil::IsFloat</span><span class="s">(</span><span class="i">$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> 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> 425 <span class="s">}</span> 426 <span class="s">}</span> 427 <span class="k">else</span> <span class="s">{</span> 428 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFuzzFactor: Fuzz factor value can't be changed: Uknown FuzzificationMethodology: $This->{FuzzificationMethodology}..."</span><span class="sc">;</span> 429 <span class="s">}</span> 430 431 <span class="i">$This</span>->{<span class="w">FuzzFactor</span>} = <span class="i">$Value</span><span class="sc">;</span> 432 433 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 434 <span class="s">}</span> 435 436 <span class="c"># Generate fingerprints description...</span> 437 <span class="c">#</span> <a name="GetDescription-"></a> 438 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> 439 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 440 441 <span class="c"># Is description explicity set?</span> 442 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> 443 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> 444 <span class="s">}</span> 445 446 <span class="c"># Generate fingerprints description...</span> 447 448 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomPairsSetSizeToUse}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"</span><span class="sc">;</span> 449 <span class="s">}</span> 450 451 <span class="c"># Generate topological pharmacophore atom pairs [ Ref 60-62, Ref 65, Ref 68 ] fingerprints...</span> 452 <span class="c">#</span> 453 <span class="c"># Methodology:</span> 454 <span class="c"># . Generate a distance matrix.</span> 455 <span class="c"># . Assign pharmacophore atom types to all the atoms.</span> 456 <span class="c"># . Initialize pharmacophore atom pairs basis set for all unique pairs between</span> 457 <span class="c"># minimum and maximum distance.</span> 458 <span class="c"># . Using distance matrix and pharmacophore atom types, count occurance of</span> 459 <span class="c"># unique atom pairs between specified distance range - It corresponds to the</span> 460 <span class="c"># correlation-vector for the atom pairs.</span> 461 <span class="c"># . Weigh contribution of each atom type to atom pair interaction by its specified</span> 462 <span class="c"># weight during occurance count.</span> 463 <span class="c"># . Assign count to appropriate distance bin for a specific atom pair</span> 464 <span class="c">#</span> 465 <span class="c"># . Normalize occurance count of pharmacophore atom pairs by heavy atom count</span> 466 <span class="c"># or sum of AtomTypeCounts of each pharmacophore atom type in the atom pair</span> 467 <span class="c"># at a specific distance.</span> 468 <span class="c">#</span> 469 <span class="c"># . Fuzzify occurance count of pharmacophore atom pairs using FuzzyBinning or</span> 470 <span class="c"># FuzzySmothing methodology.</span> 471 <span class="c">#</span> 472 <span class="c"># Notes:</span> 473 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span> 474 <span class="c">#</span> <a name="GenerateFingerprints-"></a> 475 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> 476 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 477 478 <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> 479 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateTopologicalPharmacophoreAtomPairsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."</span><span class="sc">;</span> 480 <span class="s">}</span> 481 482 <span class="c"># Cache appropriate molecule data...</span> 483 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 484 485 <span class="c"># Generate distance matrix...</span> 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> 487 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: Fingerprints generation didn't succeed: Couldn't generate distance matrix..."</span><span class="sc">;</span> 488 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 489 <span class="s">}</span> 490 491 <span class="c"># Assign pharmacohore atom types to all heavy atoms...</span> 492 <span class="i">$This</span><span class="i">->_AssignPharmacophoreAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 493 494 <span class="c"># Initialize values of all possible pharmacohore atom pairs...</span> 495 <span class="i">$This</span><span class="i">->_InitializePharmacophoreAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 496 497 <span class="c"># Count atom pairs...</span> 498 <span class="i">$This</span><span class="i">->_CountPharmacohoreAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 499 500 <span class="c"># Fuzzify atom pairs count...</span> 501 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} =~ <span class="q">/^BeforeNormalization$/i</span><span class="s">)</span> <span class="s">{</span> 502 <span class="i">$This</span><span class="i">->_FuzzifyPharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 503 <span class="s">}</span> 504 505 <span class="c"># Normalize atom pairs count...</span> 506 <span class="i">$This</span><span class="i">->_NormalizePharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 507 508 <span class="c"># Fuzzify atom pairs count...</span> 509 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FuzzificationMode</span>} =~ <span class="q">/^AfterNormalization$/i</span><span class="s">)</span> <span class="s">{</span> 510 <span class="i">$This</span><span class="i">->_FuzzifyPharmacohoreAtomPairsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 511 <span class="s">}</span> 512 513 <span class="c"># Set final fingerprints...</span> 514 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 515 516 <span class="c"># Clear cached molecule data...</span> 517 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 518 519 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 520 <span class="s">}</span> 521 522 <span class="c"># Setup distance matrix...</span> 523 <span class="c">#</span> <a name="_SetupDistanceMatrix-"></a> 524 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span> 525 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 526 527 <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> 528 529 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span> 530 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 531 <span class="s">}</span> 532 533 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 534 <span class="s">}</span> 535 536 <span class="c"># Assign pharmacohore atom types to all heavy atoms and count each atom</span> 537 <span class="c"># types assigned...</span> 538 <span class="c">#</span> <a name="_AssignPharmacophoreAtomTypes-"></a> 539 <span class="k">sub </span><span class="m">_AssignPharmacophoreAtomTypes</span> <span class="s">{</span> 540 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 541 <span class="k">my</span><span class="s">(</span><span class="i">$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> 542 543 <span class="c"># Assign topological pharmacophore atom types...</span> 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">$This</span>->{<span class="w">AtomTypesToUse</span>}<span class="s">)</span><span class="sc">;</span> 545 <span class="i">$FunctionalClassAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 546 547 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 548 549 <span class="c"># Initialize assigned atom types count...</span> 550 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 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> 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> 553 <span class="s">}</span> 554 555 <span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>} = <span class="n">0</span><span class="sc">;</span> 556 557 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> 558 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 559 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 560 <span class="s">}</span> 561 <span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>} += <span class="n">1</span><span class="sc">;</span> 562 563 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 564 565 <span class="c"># Collect all possible pharmacophore atom types which could be assigned to atom...</span> 566 <span class="k">my</span><span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span><span class="sc">;</span> 567 568 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 569 <span class="i">$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> 570 <span class="k">if</span> <span class="s">(</span><span class="i">$AssignedAtomType</span> && <span class="i">$AssignedAtomType</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> 571 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AssignedAtomType</span><span class="sc">;</span> 572 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span> <span class="s">{</span> 573 <span class="i">$This</span>->{<span class="w">AssignedAtomTypesCount</span>}{<span class="i">$AtomType</span>} += <span class="n">1</span><span class="sc">;</span> 574 <span class="s">}</span> 575 <span class="s">}</span> 576 577 <span class="c"># Assign phramacophore types to atom...</span> 578 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 579 <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = \<span class="i">@AtomTypes</span><span class="sc">;</span> 580 <span class="s">}</span> 581 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 582 <span class="s">}</span> 583 584 <span class="c"># Initialize values of all possible pharmacohore atom pairs...</span> 585 <span class="c">#</span> 586 <span class="c"># Let:</span> 587 <span class="c"># Dmin = Minimum distance correspoding to number of bonds between two atoms</span> 588 <span class="c"># Dmax = Maximum distance correspoding to number of bonds between two atoms</span> 589 <span class="c"># D = Distance correspoding to number of bonds between two atoms</span> 590 <span class="c">#</span> 591 <span class="c"># P = Number of pharmacophore atom types to consider</span> 592 <span class="c"># PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn</span> 593 <span class="c">#</span> 594 <span class="c"># PPT = Total number of possible pharmacophore atom pairs at all distances between Dmin and Dmax</span> 595 <span class="c">#</span> 596 <span class="c"># Then:</span> 597 <span class="c">#</span> 598 <span class="c"># PPD = (P * (P - 1))/2 + P</span> 599 <span class="c">#</span> 600 <span class="c"># PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P)</span> 601 <span class="c"># = ((Dmax - Dmin) + 1) * PPD</span> 602 <span class="c">#</span> 603 <span class="c">#</span> 604 <span class="c"># So for default values of Dmin = 1, Dmax = 10 and P = 5,</span> 605 <span class="c">#</span> 606 <span class="c"># PPD = (5 * (5 - 1))/2 + 5 = 15</span> 607 <span class="c"># PPT = ((10 - 1) + 1) * 15 = 150</span> 608 <span class="c">#</span> 609 <span class="c"># the pharmacophore atom pairs bais set includes 150 values.</span> 610 <span class="c">#</span> <a name="_InitializePharmacophoreAtomPairs-"></a> 611 <span class="k">sub </span><span class="m">_InitializePharmacophoreAtomPairs</span> <span class="s">{</span> 612 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 613 <span class="k">my</span><span class="s">(</span><span class="i">$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> 614 615 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 616 617 <span class="k">for</span> <span class="i">$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> 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> 619 620 <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">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> 621 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span> 622 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 623 624 <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="i">$Index1</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> 625 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span> 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> 627 <span class="s">}</span> 628 <span class="s">}</span> 629 <span class="s">}</span> 630 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 631 <span class="s">}</span> 632 633 <span class="c"># Count pharmacophore atom pairs between mininum and maximum distance at each</span> 634 <span class="c"># distance using distance matrix and pharmacophore atom types assiged to each heavy</span> 635 <span class="c"># atom.</span> 636 <span class="c">#</span> 637 <span class="c"># Let:</span> 638 <span class="c"># Px = Pharmacophore atom type x</span> 639 <span class="c"># Py = Pharmacophore atom type y</span> 640 <span class="c"># Dn = Distance between Px and Py in specified distance range</span> 641 <span class="c">#</span> 642 <span class="c"># Then:</span> 643 <span class="c"># Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn</span> 644 <span class="c">#</span> 645 <span class="c"># For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on</span> 646 <span class="c">#</span> 647 <span class="c"># Notes:</span> 648 <span class="c"># . The row and column indices of distance matrix correspond to atom indices.</span> 649 <span class="c"># . Distance value of BigNumber implies the atom is not connected to any other atom.</span> 650 <span class="c"># . Due to symmetric nature of distance matrix, only upper or lower triangular matrix</span> 651 <span class="c"># needs to be processed during identification and count of pharmacophore atom pairs.</span> 652 <span class="c">#</span> <a name="_CountPharmacohoreAtomPairs-"></a> 653 <span class="k">sub </span><span class="m">_CountPharmacohoreAtomPairs</span> <span class="s">{</span> 654 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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> 656 657 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span> 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">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 659 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span> 660 661 <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> 662 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span> 663 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$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">$AtomID1</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> 664 <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span> 665 <span class="s">}</span> 666 667 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$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> 668 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$ColIndex</span>}<span class="sc">;</span> 669 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$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">$AtomID2</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> 670 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> 671 <span class="s">}</span> 672 673 <span class="i">$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> 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> 675 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> 676 <span class="s">}</span> 677 678 <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">$AtomID1</span>}}<span class="s">)</span> <span class="s">{</span> 679 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$AtomType1</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 680 <span class="k">next</span> <span class="j">ATOMTYPE1</span><span class="sc">;</span> 681 <span class="s">}</span> 682 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$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> 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> 684 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span> 685 <span class="s">}</span> 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">$AtomType2</span>}<span class="sc">;</span> 687 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType1</span> <span class="k">le</span> <span class="i">$AtomType2</span><span class="s">)</span> <span class="s">{</span> 688 <span class="i">$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> 689 <span class="s">}</span> 690 <span class="k">else</span> <span class="s">{</span> 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">$CountIncrement</span><span class="sc">;</span> 692 <span class="s">}</span> 693 <span class="s">}</span> 694 <span class="s">}</span> 695 <span class="s">}</span> 696 <span class="s">}</span> 697 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 698 <span class="s">}</span> 699 700 <span class="c"># Normalize the occurance count of pharmacophore atom pairs over the specified distance</span> 701 <span class="c"># range...</span> 702 <span class="c">#</span> <a name="_NormalizePharmacohoreAtomPairsCount-"></a> 703 <span class="k">sub </span><span class="m">_NormalizePharmacohoreAtomPairsCount</span> <span class="s">{</span> 704 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 705 706 <span class="j">METHODOLOGY:</span> <span class="s">{</span> 707 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> 708 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span> 709 <span class="s">}</span> 710 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NormalizationMethodology</span>} =~ <span class="q">/^ByHeavyAtomsCount$/i</span><span class="s">)</span> <span class="s">{</span> 711 <span class="i">$This</span><span class="i">->_NormalizeAtomPairsCountByHeavyAtomsCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 712 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span> 713 <span class="s">}</span> 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> 715 <span class="i">$This</span><span class="i">->_NormalizeAtomPairsCountByAtomTypesCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 716 <span class="k">last</span> <span class="j">METHODOLOGY</span><span class="sc">;</span> 717 <span class="s">}</span> 718 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_NormalizePharmacohoreAtomPairsCount: Unknown NormalizationMethodology: $This->{NormalizationMethodology}..."</span><span class="sc">;</span> 719 <span class="s">}</span> 720 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 721 <span class="s">}</span> 722 723 724 <span class="c"># Normalize the occurance count of pharmacophore atom pairs at various distances by</span> 725 <span class="c"># heavy atom count...</span> 726 <span class="c">#</span> <a name="_NormalizeAtomPairsCountByHeavyAtomsCount-"></a> 727 <span class="k">sub </span><span class="m">_NormalizeAtomPairsCountByHeavyAtomsCount</span> <span class="s">{</span> 728 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 729 <span class="k">my</span><span class="s">(</span><span class="i">$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> 730 731 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">HeavyAtomCount</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 732 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 733 <span class="s">}</span> 734 735 <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> 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">$Distance</span>}} <span class="s">)</span> <span class="s">{</span> 737 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$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">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span> 738 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 739 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span> 740 <span class="s">}</span> 741 <span class="i">$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> 742 <span class="s">}</span> 743 <span class="s">}</span> 744 <span class="s">}</span> 745 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 746 <span class="s">}</span> 747 748 <span class="c"># Normalize the occurance count of pharmacophore atom pairs at various distances by</span> 749 <span class="c"># dividing it using sum of the count of each pharmacophore atom type present in the</span> 750 <span class="c"># molecule for the corresponding atom pair.</span> 751 <span class="c">#</span> <a name="_NormalizeAtomPairsCountByAtomTypesCount-"></a> 752 <span class="k">sub </span><span class="m">_NormalizeAtomPairsCountByAtomTypesCount</span> <span class="s">{</span> 753 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 754 <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> 755 756 <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> 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">$Distance</span>}} <span class="s">)</span> <span class="s">{</span> 758 <span class="j">ATOMTYPE2:</span> <span class="k">for</span> <span class="i">$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">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span> 759 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 760 <span class="k">next</span> <span class="j">ATOMTYPE2</span><span class="sc">;</span> 761 <span class="s">}</span> 762 <span class="i">$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> 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">$NormalizationFactor</span><span class="sc">;</span> 764 <span class="s">}</span> 765 <span class="s">}</span> 766 <span class="s">}</span> 767 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 768 <span class="s">}</span> 769 770 <span class="c"># Fuzzify pharmacophore atom pairs count...</span> 771 <span class="c">#</span> 772 <span class="c"># Let:</span> 773 <span class="c"># Px = Pharmacophore atom type x</span> 774 <span class="c"># Py = Pharmacophore atom type y</span> 775 <span class="c">#</span> 776 <span class="c"># PPxy = Pharmacophore atom pair between atom type Px and Py</span> 777 <span class="c">#</span> 778 <span class="c"># PPxyDn = Pharmacophore atom pairs count between atom type Px and Py at distance Dn</span> 779 <span class="c"># PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py at distance Dn - 1</span> 780 <span class="c"># PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py at distance Dn + 1</span> 781 <span class="c">#</span> 782 <span class="c"># FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing</span> 783 <span class="c">#</span> 784 <span class="c"># Then:</span> 785 <span class="c">#</span> 786 <span class="c"># For FuzzyBinning:</span> 787 <span class="c">#</span> 788 <span class="c"># PPxyDn = PPxyDn (Unchanged)</span> 789 <span class="c">#</span> 790 <span class="c"># PPxyDn-1 = PPxyDn-1 + PPxyDn * FF</span> 791 <span class="c"># PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</span> 792 <span class="c">#</span> 793 <span class="c"># For FuzzyBinSmoothing:</span> 794 <span class="c">#</span> 795 <span class="c"># PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin < Dn < Dmax</span> 796 <span class="c"># PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax</span> 797 <span class="c">#</span> 798 <span class="c"># PPxyDn-1 = PPxyDn-1 + PPxyDn * FF</span> 799 <span class="c"># PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</span> 800 <span class="c">#</span> 801 <span class="c"># In both fuzzification schemes, a value of 0 for FF implies no fuzzification of occurance counts.</span> 802 <span class="c"># A value of 1 during FuzzyBinning corresponds to maximum fuzzification of occurance counts;</span> 803 <span class="c"># however, a value of 1 during FuzzyBinSmoothing ends up completely distributing the value over</span> 804 <span class="c"># the previous and next distance bins.</span> 805 <span class="c">#</span> 806 <span class="c"># So for default value of FuzzFactor (FF) 0.15, the occurance count of pharmacohore atom pairs</span> 807 <span class="c"># at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn -1 and Dn + 1</span> 808 <span class="c"># are incremened by PPxyDn * 0.15.</span> 809 <span class="c">#</span> 810 <span class="c"># And during FuzzyBinSmoothing the occurance counts at Distance Dn is scaled back using multiplicate</span> 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> 812 <span class="c"># PPxyDn * 0.15. In otherwords, occurance bin count is smoothed out by distributing it over the</span> 813 <span class="c"># previous and next distance value.</span> 814 <span class="c">#</span> <a name="_FuzzifyPharmacohoreAtomPairsCount-"></a> 815 <span class="k">sub </span><span class="m">_FuzzifyPharmacohoreAtomPairsCount</span> <span class="s">{</span> 816 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 817 <span class="k">my</span><span class="s">(</span><span class="i">$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> 818 819 <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> 820 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 821 <span class="s">}</span> 822 823 <span class="i">$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> 824 825 <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">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> 826 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span> 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> 828 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span> 829 830 <span class="i">$CurrentCount</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$NextCount</span> = <span class="n">0</span><span class="sc">;</span> 831 832 <span class="i">$NextDistance</span> = <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="sc">;</span> 833 <span class="i">$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> 834 835 <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">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> 836 <span class="i">$NextDistance</span> = <span class="i">$CurrentDistance</span> + <span class="n">1</span><span class="sc">;</span> 837 <span class="i">$PreviousDistance</span> = <span class="i">$CurrentDistance</span> - <span class="n">1</span><span class="sc">;</span> 838 839 <span class="i">$CurrentCount</span> = <span class="i">$NextCount</span><span class="sc">;</span> 840 <span class="i">$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> 841 842 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentCount</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 843 <span class="c"># No contribution to fuzzy binning from this distance...</span> 844 <span class="k">next</span> <span class="j">DISTANCE</span><span class="sc">;</span> 845 <span class="s">}</span> 846 847 <span class="i">$ChangeInCountValue</span> = <span class="i">$CurrentCount</span> * <span class="i">$This</span>->{<span class="w">FuzzFactor</span>}<span class="sc">;</span> 848 849 <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> 850 <span class="c"># Increment count at previous distance...</span> 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">$ChangeInCountValue</span><span class="sc">;</span> 852 <span class="s">}</span> 853 854 <span class="k">if</span> <span class="s">(</span><span class="i">$ModifyCurrentCount</span><span class="s">)</span> <span class="s">{</span> 855 <span class="c"># Decrement count at current distance for FuzzyBinSmoothing...</span> 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> 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">$ChangeInCountValue</span><span class="sc">;</span> 858 <span class="s">}</span> 859 <span class="k">else</span> <span class="s">{</span> 860 <span class="i">$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> 861 <span class="s">}</span> 862 <span class="s">}</span> 863 864 <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> 865 <span class="c"># Increment count at next distance...</span> 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">$ChangeInCountValue</span><span class="sc">;</span> 867 <span class="s">}</span> 868 <span class="s">}</span> 869 <span class="s">}</span> 870 <span class="s">}</span> 871 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 872 <span class="s">}</span> 873 874 <span class="c"># Set final fingerpritns vector...</span> 875 <span class="c">#</span> <a name="_SetFinalFingerprints-"></a> 876 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> 877 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 878 <span class="k">my</span><span class="s">(</span><span class="i">$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> 879 880 <span class="c"># Mark successful generation of fingerprints...</span> 881 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> 882 883 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 884 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 885 886 <span class="c"># Do values need to be rounded off?</span> 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> 888 <span class="i">$ValuesPrecision</span> = <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>}<span class="sc">;</span> 889 890 <span class="c"># Is it an ArbitraySize atom pairs set size?</span> 891 <span class="i">$UseArbitrarySetSize</span> = <span class="i">$This</span>->{<span class="w">AtomPairsSetSizeToUse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 892 893 <span class="c"># Collect all atom paris count values...</span> 894 <span class="k">for</span> <span class="i">$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> 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">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> 896 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index1</span>]<span class="sc">;</span> 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> 898 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}[<span class="i">$Index2</span>]<span class="sc">;</span> 899 900 <span class="c"># Atom pair count...</span> 901 <span class="i">$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> 902 <span class="k">if</span> <span class="s">(</span><span class="i">$RoundOffValues</span><span class="s">)</span> <span class="s">{</span> 903 <span class="i">$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> 904 <span class="s">}</span> 905 906 <span class="c"># Ignore or not to ignore...</span> 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> 908 <span class="k">next</span> <span class="j">INDEX2</span><span class="sc">;</span> 909 <span class="s">}</span> 910 911 <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> 912 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span> 913 <span class="s">}</span> 914 <span class="s">}</span> 915 <span class="s">}</span> 916 917 <span class="c"># Add AtomPairsIDs and count values to fingerprint vector...</span> 918 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="s">)</span><span class="sc">;</span> 919 <span class="i">$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> 920 921 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 922 <span class="s">}</span> 923 924 <span class="c"># Get pharmacophore atom pair IDs corresponding to atom pairs count values in</span> 925 <span class="c"># fingerprint vector as an array or reference to an array...</span> 926 <span class="c">#</span> 927 <span class="c"># AtomPairIDs list is generated during finalization of fingerprints and the fingerprint</span> 928 <span class="c"># vector containing count values matches the atom pairs array.</span> 929 <span class="c">#</span> 930 <span class="c">#</span> <a name="GetAtomPairIDs-"></a> 931 <span class="k">sub </span><span class="m">GetAtomPairIDs</span> <span class="s">{</span> 932 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 933 934 <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> 935 <span class="s">}</span> 936 937 <span class="c"># Cache appropriate molecule data...</span> 938 <span class="c">#</span> <a name="_SetupMoleculeDataCache-"></a> 939 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> 940 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 941 942 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span> 943 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span> 944 <span class="c">#</span> 945 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 946 947 <span class="c"># Get all atom IDs...</span> 948 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 949 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 950 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</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">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span> 951 952 <span class="c"># Set AtomIndex to AtomID hash...</span> 953 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 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> 955 956 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 957 <span class="s">}</span> 958 959 <span class="c"># Clear cached molecule data...</span> 960 <span class="c">#</span> <a name="_ClearMoleculeDataCache-"></a> 961 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> 962 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 963 964 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 965 966 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 967 <span class="s">}</span> 968 969 970 <span class="c"># Return a string containg data for TopologicalPharmacophoreAtomPairsFingerprints object...</span> <a name="StringifyTopologicalPharmacophoreAtomPairsFingerprints-"></a> 971 <span class="k">sub </span><span class="m">StringifyTopologicalPharmacophoreAtomPairsFingerprints</span> <span class="s">{</span> 972 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 973 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span> 974 975 <span class="c"># Type of fingerprint...</span> 976 <span class="i">$FingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomPairsSetSizeToUse: $This->{AtomPairsSetSizeToUse}"</span><span class="sc">;</span> 977 978 <span class="c"># Min and max distance...</span> 979 <span class="i">$FingerprintsString</span> .= <span class="q">"; MinDistance: $This->{MinDistance}; MaxDistance: $This->{MaxDistance}"</span><span class="sc">;</span> 980 981 <span class="c"># Pharmacophore type labels and description...</span> 982 <span class="k">my</span><span class="s">(</span><span class="i">$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> 983 984 <span class="i">@AtomTypesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 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> 986 987 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 988 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypesOrder</span><span class="s">)</span> <span class="s">{</span> 989 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="q">"$AtomType: $AvailableAtomTypes{$AtomType}"</span><span class="sc">;</span> 990 <span class="s">}</span> 991 992 <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> 993 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 994 <span class="i">$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> 995 996 <span class="c"># Normalization method...</span> 997 <span class="i">$FingerprintsString</span> .= <span class="q">"; NormalizationMethodology: $This->{NormalizationMethodology}"</span><span class="sc">;</span> 998 999 <span class="c"># Weights...</span> 1000 <span class="k">my</span><span class="s">(</span><span class="i">$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> 1001 1002 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesWeight <Labels: Weight>: <"</span><span class="sc">;</span> 1003 <span class="i">$FirstLabel</span> = <span class="n">1</span><span class="sc">;</span> 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> 1005 <span class="i">$Weight</span> = <span class="i">$This</span>->{<span class="w">AtomTypesWeight</span>}{<span class="i">$Label</span>}<span class="sc">;</span> 1006 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstLabel</span><span class="s">)</span> <span class="s">{</span> 1007 <span class="i">$FirstLabel</span> = <span class="n">0</span><span class="sc">;</span> 1008 <span class="i">$FingerprintsString</span> .= <span class="q">" ${Label}: ${Weight}"</span><span class="sc">;</span> 1009 <span class="s">}</span> 1010 <span class="k">else</span> <span class="s">{</span> 1011 <span class="i">$FingerprintsString</span> .= <span class="q">"; ${Label}: ${Weight}"</span><span class="sc">;</span> 1012 <span class="s">}</span> 1013 <span class="s">}</span> 1014 <span class="i">$FingerprintsString</span> .= <span class="q">">"</span><span class="sc">;</span> 1015 1016 <span class="c"># Fuzzification of count...</span> 1017 <span class="k">my</span><span class="s">(</span><span class="i">$FuzzifyFlag</span><span class="s">)</span><span class="sc">;</span> 1018 <span class="i">$FuzzifyFlag</span> = <span class="i">$This</span>->{<span class="w">FuzzifyAtomPairsCount</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="sc">;</span> 1019 <span class="i">$FingerprintsString</span> .= <span class="q">"; FuzzifyAtomPairsCount: $FuzzifyFlag; FuzzificationMode: $This->{FuzzificationMode}; FuzzificationMethodology: $This->{FuzzificationMethodology}; FuzzFactor: $This->{FuzzFactor}"</span><span class="sc">;</span> 1020 1021 <span class="c"># Total number of pharmacophore atom pairs...</span> 1022 <span class="i">$FingerprintsString</span> .= <span class="q">"; NumOfAtomPairs: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1023 1024 <span class="c"># FingerprintsVector...</span> 1025 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> 1026 1027 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span> 1028 <span class="s">}</span> 1029 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>