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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/TopologicalPharmacophoreAtomPairsFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,1050 @@ +<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>