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comparison mayachemtools/docs/modules/html/code/TopologicalPharmacophoreAtomTripletsFingerprints.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: TopologicalPharmacophoreAtomTripletsFingerprints.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> | |
| 18 5 <span class="c"># $Revision: 1.30 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> | |
| 50 37 | |
| 51 38 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> | |
| 52 39 | |
| 53 40 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> | |
| 54 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 55 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 56 43 | |
| 57 44 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> | |
| 58 45 | |
| 59 46 <span class="c"># Setup class variables...</span> | |
| 60 47 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 61 48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 62 49 | |
| 63 50 <span class="c"># Overload Perl functions...</span> | |
| 64 51 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyTopologicalPharmacophoreAtomTripletsFingerprints'</span><span class="sc">;</span> | |
| 65 52 | |
| 66 53 <span class="c"># Class constructor...</span> | |
| 67 <a name="new-"></a> 54 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 68 55 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 69 56 | |
| 70 57 <span class="c"># Initialize object...</span> | |
| 71 58 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 72 59 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> | |
| 73 60 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 74 61 | |
| 75 62 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 76 63 | |
| 77 64 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 78 65 <span class="s">}</span> | |
| 79 66 | |
| 80 67 <span class="c"># Initialize object data...</span> | |
| 81 68 <span class="c">#</span> | |
| 82 <a name="_InitializeTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 69 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span> | |
| 83 70 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 84 71 | |
| 85 72 <span class="c"># Type of fingerprint...</span> | |
| 86 73 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'TopologicalPharmacophoreAtomTriplets'</span><span class="sc">;</span> | |
| 87 74 | |
| 88 75 <span class="c"># Type of vector...</span> | |
| 89 76 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> | |
| 90 77 | |
| 91 78 <span class="c"># AtomTripletsSetSizeToUse...</span> | |
| 92 79 <span class="c">#</span> | |
| 93 80 <span class="c"># ArbitrarySize - Corrresponds to atom triplets with non-zero count</span> | |
| 94 81 <span class="c"># FixedSize - Corresponds to all atom triplets with zero and non-zero count</span> | |
| 95 82 <span class="c">#</span> | |
| 96 83 <span class="c"># Possible values: ArbitrarySize or FixedSize. Default: ArbitrarySize</span> | |
| 97 84 <span class="c">#</span> | |
| 98 85 <span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 99 86 | |
| 100 87 <span class="c">#</span> | |
| 101 88 <span class="c"># OrderedNumericalValues - For ArbitrarySize value of AtomTripletsSetSizeToUse</span> | |
| 102 89 <span class="c"># NumericalValues - For FixedSize value of AtomTripletsSetSizeToUse</span> | |
| 103 90 <span class="c">#</span> | |
| 104 91 <span class="c"># Possible values: OrderedNumericalValues or NumericalValues. Default: NumericalValues</span> | |
| 105 92 <span class="c">#</span> | |
| 106 93 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 107 94 | |
| 108 95 <span class="c"># Minimum and maximum bond distance between pharmacophore atom pairs corresponding to</span> | |
| 109 96 <span class="c"># atom triplets and distance bin size used for binning distances.</span> | |
| 110 97 <span class="c">#</span> | |
| 111 98 <span class="c"># In order to distribute distance bins of equal size, the last bin is allowed to go past the</span> | |
| 112 99 <span class="c"># maximum distance specified by upto distance bin size.</span> | |
| 113 100 <span class="c">#</span> | |
| 114 101 <span class="c"># The default MinDistance and MaxDistance values of 1 and 10 with DistanceBinSize of</span> | |
| 115 102 <span class="c"># 2 [ Ref 70 ] generates the following 5 distance bins: [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</span> | |
| 116 103 <span class="c">#</span> | |
| 117 104 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 118 105 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> | |
| 119 106 | |
| 120 107 <span class="c"># Distance bin size used for binning distances...</span> | |
| 121 108 <span class="c">#</span> | |
| 122 109 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="n">2</span><span class="sc">;</span> | |
| 123 110 | |
| 124 111 <span class="c"># Determines whether to apply triangle inequality to distances triplets during basis set generation...</span> | |
| 125 112 <span class="c">#</span> | |
| 126 113 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 127 114 | |
| 128 115 <span class="c"># Initialize pharmacophore atom types information...</span> | |
| 129 116 <span class="i">$This</span><span class="i">->_InitializeToplogicalPharmacophoreAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 130 117 | |
| 131 118 <span class="c"># Pharmacophore types assigned to each heavy atom...</span> | |
| 132 119 <span class="c">#</span> | |
| 133 120 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 134 121 | |
| 135 122 <span class="c"># All pharmacophore atom triplets between minimum and maximum distance...</span> | |
| 136 123 <span class="c">#</span> | |
| 137 124 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 138 125 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 139 126 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 140 127 <span class="s">}</span> | |
| 141 128 | |
| 142 129 <span class="c"># Initialize class ...</span> | |
| 143 <a name="_InitializeClass-"></a> 130 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 144 131 <span class="c">#Class name...</span> | |
| 145 132 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 146 133 <span class="s">}</span> | |
| 147 134 | |
| 148 135 <span class="c"># Initialize object properties....</span> | |
| 149 <a name="_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsProperties-"></a> 136 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsProperties</span> <span class="s">{</span> | |
| 150 137 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 151 138 | |
| 152 139 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 153 140 <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> | |
| 154 141 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 155 142 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 156 143 <span class="s">}</span> | |
| 157 144 | |
| 158 145 <span class="c"># Make sure molecule object was specified...</span> | |
| 159 146 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
| 160 147 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> | |
| 161 148 <span class="s">}</span> | |
| 162 149 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 163 150 | |
| 164 151 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 165 152 <span class="s">}</span> | |
| 166 153 | |
| 167 154 <span class="c"># Initialize fingerprints vector...</span> | |
| 168 155 <span class="c">#</span> | |
| 169 <a name="_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsVector-"></a> 156 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsVector</span> <span class="s">{</span> | |
| 170 157 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 171 158 | |
| 172 159 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span> | |
| 173 160 <span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} = <span class="q">'ArbitrarySize'</span><span class="sc">;</span> | |
| 174 161 <span class="s">}</span> | |
| 175 162 | |
| 176 163 <span class="c"># Vector type and type of values...</span> | |
| 177 164 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> | |
| 178 165 | |
| 179 166 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 180 167 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'OrderedNumericalValues'</span><span class="sc">;</span> | |
| 181 168 <span class="s">}</span> | |
| 182 169 <span class="k">else</span> <span class="s">{</span> | |
| 183 170 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> | |
| 184 171 <span class="s">}</span> | |
| 185 172 | |
| 186 173 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 187 174 <span class="s">}</span> | |
| 188 175 | |
| 189 176 <span class="c"># Set atom parits set size to use...</span> | |
| 190 177 <span class="c">#</span> | |
| 191 <a name="SetAtomTripletsSetSizeToUse-"></a> 178 <span class="k">sub </span><span class="m">SetAtomTripletsSetSizeToUse</span> <span class="s">{</span> | |
| 192 179 <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> | |
| 193 180 | |
| 194 181 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span> | |
| 195 182 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTripletsSetSizeToUse: Can't change size: It's already set..."</span><span class="sc">;</span> | |
| 196 183 <span class="s">}</span> | |
| 197 184 | |
| 198 185 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ArbitrarySize|FixedSize)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 199 186 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTripletsSetSizeToUse: Unknown AtomTripletsSetSizeToUse value: $Value; Supported values: ArbitrarySize or FixedSize"</span><span class="sc">;</span> | |
| 200 187 <span class="s">}</span> | |
| 201 188 | |
| 202 189 <span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 203 190 | |
| 204 191 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 205 192 <span class="s">}</span> | |
| 206 193 | |
| 207 194 <span class="c"># Initialize topological atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> | |
| 208 195 <span class="c"># class, to use for atom triplets fingerprint generation...</span> | |
| 209 196 <span class="c">#</span> | |
| 210 197 <span class="c"># Let:</span> | |
| 211 198 <span class="c"># HBD: HydrogenBondDonor</span> | |
| 212 199 <span class="c"># HBA: HydrogenBondAcceptor</span> | |
| 213 200 <span class="c"># PI : PositivelyIonizable</span> | |
| 214 201 <span class="c"># NI : NegativelyIonizable</span> | |
| 215 202 <span class="c"># Ar : Aromatic</span> | |
| 216 203 <span class="c"># Hal : Halogen</span> | |
| 217 204 <span class="c"># H : Hydrophobic</span> | |
| 218 205 <span class="c"># RA : RingAtom</span> | |
| 219 206 <span class="c"># CA : ChainAtom</span> | |
| 220 207 <span class="c">#</span> | |
| 221 208 <span class="c"># Then:</span> | |
| 222 209 <span class="c">#</span> | |
| 223 210 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> | |
| 224 211 <span class="c">#</span> | |
| 225 212 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> | |
| 226 213 <span class="c">#</span> | |
| 227 214 <span class="c"># Default pharmacophore atom types [ Ref 71 ] to use for atom triplets fingerprint generation</span> | |
| 228 215 <span class="c"># are: HBD, HBA, PI, NI, H, Ar</span> | |
| 229 216 <span class="c">#</span> | |
| 230 217 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> | |
| 231 218 <span class="c">#</span> | |
| 232 219 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> | |
| 233 220 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> | |
| 234 221 <span class="c"># PositivelyIonizable: +, NH2</span> | |
| 235 222 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> | |
| 236 223 <span class="c">#</span> | |
| 237 <a name="_InitializeToplogicalPharmacophoreAtomTypesInformation-"></a> 224 <span class="k">sub </span><span class="m">_InitializeToplogicalPharmacophoreAtomTypesInformation</span> <span class="s">{</span> | |
| 238 225 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 239 226 | |
| 240 227 <span class="c"># Default pharmacophore atom types to use for atom triplets fingerprint generation</span> | |
| 241 228 <span class="c"># are: HBD, HBA, PI, NI, H, Ar</span> | |
| 242 229 <span class="c">#</span> | |
| 243 230 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 244 231 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="k">sort</span> <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="s">)</span><span class="sc">;</span> | |
| 245 232 | |
| 246 233 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 247 234 <span class="s">}</span> | |
| 248 235 | |
| 249 236 <span class="c"># Set atom types to use for atom triplets...</span> | |
| 250 237 <span class="c">#</span> | |
| 251 <a name="SetAtomTypesToUse-"></a> 238 <span class="k">sub </span><span class="m">SetAtomTypesToUse</span> <span class="s">{</span> | |
| 252 239 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 253 240 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 254 241 | |
| 255 242 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
| 256 243 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomTypesToUse: No values specified..."</span><span class="sc">;</span> | |
| 257 244 <span class="k">return</span><span class="sc">;</span> | |
| 258 245 <span class="s">}</span> | |
| 259 246 | |
| 260 247 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 261 248 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
| 262 249 | |
| 263 250 <span class="i">@SpecifiedAtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 264 251 <span class="i">@AtomTypesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 265 252 | |
| 266 253 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
| 267 254 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
| 268 255 <span class="s">}</span> | |
| 269 256 <span class="k">else</span> <span class="s">{</span> | |
| 270 257 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
| 271 258 <span class="s">}</span> | |
| 272 259 | |
| 273 260 <span class="c"># Make sure specified AtomTypes are valid...</span> | |
| 274 261 <span class="k">for</span> <span class="i">$SpecifiedAtomType</span> <span class="s">(</span><span class="i">@SpecifiedAtomTypes</span><span class="s">)</span> <span class="s">{</span> | |
| 275 262 <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> | |
| 276 263 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesToUse: Specified atom type, $SpecifiedAtomType, is not supported...\n "</span><span class="sc">;</span> | |
| 277 264 <span class="s">}</span> | |
| 278 265 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomType</span><span class="sc">;</span> | |
| 279 266 <span class="k">push</span> <span class="i">@AtomTypesToUse</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span> | |
| 280 267 <span class="s">}</span> | |
| 281 268 | |
| 282 269 <span class="c"># Set atom types to use...</span> | |
| 283 270 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 284 271 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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> | |
| 285 272 | |
| 286 273 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 287 274 <span class="s">}</span> | |
| 288 275 | |
| 289 276 <span class="c"># Set minimum distance for pharmacophore atom pairs in atom triplets...</span> | |
| 290 277 <span class="c">#</span> | |
| 291 <a name="SetMinDistance-"></a> 278 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span> | |
| 292 279 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 293 280 | |
| 294 281 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 295 282 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 296 283 <span class="s">}</span> | |
| 297 284 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 298 285 | |
| 299 286 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 300 287 <span class="s">}</span> | |
| 301 288 | |
| 302 289 <span class="c"># Set maximum distance for pharmacophore atom pairs in atom triplets...</span> | |
| 303 290 <span class="c">#</span> | |
| 304 <a name="SetMaxDistance-"></a> 291 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span> | |
| 305 292 <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> | |
| 306 293 | |
| 307 294 <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> | |
| 308 295 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 309 296 <span class="s">}</span> | |
| 310 297 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 311 298 | |
| 312 299 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 313 300 <span class="s">}</span> | |
| 314 301 | |
| 315 302 <span class="c"># Set distance bin size for binning pharmacophore atom pair distances in atom triplets...</span> | |
| 316 303 <span class="c">#</span> | |
| 317 <a name="SetDistanceBinSize-"></a> 304 <span class="k">sub </span><span class="m">SetDistanceBinSize</span> <span class="s">{</span> | |
| 318 305 <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> | |
| 319 306 | |
| 320 307 <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> | |
| 321 308 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDistanceBinSize: DistanceBinSize value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> | |
| 322 309 <span class="s">}</span> | |
| 323 310 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 324 311 | |
| 325 312 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 326 313 <span class="s">}</span> | |
| 327 314 | |
| 328 315 <span class="c"># Generate fingerprints description...</span> | |
| 329 316 <span class="c">#</span> | |
| 330 <a name="GetDescription-"></a> 317 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> | |
| 331 318 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 332 319 | |
| 333 320 <span class="c"># Is description explicity set?</span> | |
| 334 321 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> | |
| 335 322 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> | |
| 336 323 <span class="s">}</span> | |
| 337 324 | |
| 338 325 <span class="c"># Generate fingerprints description...</span> | |
| 339 326 | |
| 340 327 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomTripletsSetSizeToUse}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"</span><span class="sc">;</span> | |
| 341 328 <span class="s">}</span> | |
| 342 329 | |
| 343 330 <span class="c"># Generate topological pharmacophore atom triplets [ Ref 66, Ref 68-71 ] fingerprints...</span> | |
| 344 331 <span class="c">#</span> | |
| 345 332 <span class="c"># Let:</span> | |
| 346 333 <span class="c">#</span> | |
| 347 334 <span class="c"># P = Any of the supported pharmacophore atom types</span> | |
| 348 335 <span class="c">#</span> | |
| 349 336 <span class="c"># Px = Pharmacophore atom x</span> | |
| 350 337 <span class="c"># Py = Pharmacophore atom y</span> | |
| 351 338 <span class="c"># Pz = Pharmacophore atom z</span> | |
| 352 339 <span class="c">#</span> | |
| 353 340 <span class="c"># Dxy = Distance or lower bound of binned distance between Px and Py</span> | |
| 354 341 <span class="c"># Dxz = Distance or lower bound of binned distance between Px and Pz</span> | |
| 355 342 <span class="c"># Dyz = Distance or lower bound of binned distance between Py and Pz</span> | |
| 356 343 <span class="c">#</span> | |
| 357 344 <span class="c"># Then:</span> | |
| 358 345 <span class="c"># PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet ID for atoms Px, Py and Pz</span> | |
| 359 346 <span class="c">#</span> | |
| 360 347 <span class="c"># For example: H1-H1-H1, H2-HBA-H2 and so on</span> | |
| 361 348 <span class="c">#</span> | |
| 362 349 <span class="c"># Methodology:</span> | |
| 363 350 <span class="c"># . Generate a distance matrix.</span> | |
| 364 351 <span class="c"># . Using specified minimum, maximum and distance bin size, generate a binned distance</span> | |
| 365 352 <span class="c"># matrix from distance matrix. The lower distance bound on the distance bin is used</span> | |
| 366 353 <span class="c"># in the binned distance matrix and atom triplet IDs.</span> | |
| 367 354 <span class="c"># . Assign pharmacophore atom types to all the atoms.</span> | |
| 368 355 <span class="c"># . Initialize pharmacophore atom triplets basis set for all unique triplets constituting</span> | |
| 369 356 <span class="c"># atom pairs binned distances between minimum and maximum distance.</span> | |
| 370 357 <span class="c"># . Optionally, trinagle inequality is also implied which means:</span> | |
| 371 358 <span class="c"># . Distance or binned distance between any two pairs in a triplet must be less than the</span> | |
| 372 359 <span class="c"># sum of distances or binned distances between other two pairs and greater than the</span> | |
| 373 360 <span class="c"># difference of distances between other pairs.</span> | |
| 374 361 <span class="c"># . Using binned distance matrix and pharmacophore atom types, count occurance of</span> | |
| 375 362 <span class="c"># unique atom triplets.</span> | |
| 376 363 <span class="c">#</span> | |
| 377 364 <span class="c"># Notes:</span> | |
| 378 365 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span> | |
| 379 366 <span class="c">#</span> | |
| 380 <a name="GenerateFingerprints-"></a> 367 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> | |
| 381 368 <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> | |
| 382 369 | |
| 383 370 <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> | |
| 384 371 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateTopologicalPharmacophoreAtomTripletsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."</span><span class="sc">;</span> | |
| 385 372 <span class="s">}</span> | |
| 386 373 | |
| 387 374 <span class="c"># Cache appropriate molecule data...</span> | |
| 388 375 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 389 376 | |
| 390 377 <span class="c"># Generate distance matrix...</span> | |
| 391 378 <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> | |
| 392 379 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: Fingerprints generation didn't succeed: Couldn't generate distance matrix..."</span><span class="sc">;</span> | |
| 393 380 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 394 381 <span class="s">}</span> | |
| 395 382 | |
| 396 383 <span class="c"># Generate binned distance matrix...</span> | |
| 397 384 <span class="i">$This</span><span class="i">->_GenerateBinnedDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 398 385 | |
| 399 386 <span class="c"># Assign pharmacohore atom types to all heavy atoms...</span> | |
| 400 387 <span class="i">$This</span><span class="i">->_AssignPharmacophoreAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 401 388 | |
| 402 389 <span class="c"># Initialize values of all possible pharmacohore atom triplets...</span> | |
| 403 390 <span class="i">$This</span><span class="i">->_InitializePharmacophoreAtomTriplets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 404 391 | |
| 405 392 <span class="c"># Count atom triplets...</span> | |
| 406 393 <span class="i">$This</span><span class="i">->_CountPharmacohoreAtomTriplets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 407 394 | |
| 408 395 <span class="c"># Set final fingerprints...</span> | |
| 409 396 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 410 397 | |
| 411 398 <span class="c"># Clear cached molecule data...</span> | |
| 412 399 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 413 400 | |
| 414 401 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 415 402 <span class="s">}</span> | |
| 416 403 | |
| 417 404 <span class="c"># Setup distance matrix...</span> | |
| 418 405 <span class="c">#</span> | |
| 419 <a name="_SetupDistanceMatrix-"></a> 406 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span> | |
| 420 407 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 421 408 | |
| 422 409 <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> | |
| 423 410 | |
| 424 411 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span> | |
| 425 412 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 426 413 <span class="s">}</span> | |
| 427 414 | |
| 428 415 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 429 416 <span class="s">}</span> | |
| 430 417 | |
| 431 418 <span class="c"># Generate binned distance matrix for distances with in the specified distance ranges...</span> | |
| 432 419 <span class="c">#</span> | |
| 433 <a name="_GenerateBinnedDistanceMatrix-"></a> 420 <span class="k">sub </span><span class="m">_GenerateBinnedDistanceMatrix</span> <span class="s">{</span> | |
| 434 421 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 435 422 <span class="k">my</span><span class="s">(</span><span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$BinnedDistanceMatrix</span><span class="cm">,</span> <span class="i">$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">$ColIndex</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 436 423 | |
| 437 424 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span> | |
| 438 425 <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">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 439 426 | |
| 440 427 <span class="c"># Initialize binned distance matrix...</span> | |
| 441 428 <span class="i">$BinnedDistanceMatrix</span> = <span class="i">new</span> <span class="i">Matrix</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span><span class="sc">;</span> | |
| 442 429 | |
| 443 430 <span class="c"># Setup distance to binned distance map...</span> | |
| 444 431 <span class="k">my</span><span class="s">(</span><span class="i">$BinnedDistance</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">%DistanceToBinnedDistance</span><span class="s">)</span><span class="sc">;</span> | |
| 445 432 <span class="i">%DistanceToBinnedDistance</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 446 433 <span class="k">for</span> <span class="s">(</span><span class="i">$BinnedDistance</span> = <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance</span> <= <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance</span> += <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="s">)</span> <span class="s">{</span> | |
| 447 434 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$BinnedDistance</span> .. <span class="s">(</span><span class="i">$BinnedDistance</span> + <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 448 435 <span class="i">$DistanceToBinnedDistance</span>{<span class="i">$Distance</span>} = <span class="i">$BinnedDistance</span><span class="sc">;</span> | |
| 449 436 <span class="s">}</span> | |
| 450 437 <span class="s">}</span> | |
| 451 438 | |
| 452 439 <span class="c"># Generate binned distance matrix...</span> | |
| 453 440 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span> | |
| 454 441 <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> | |
| 455 442 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="s">(</span><span class="i">$RowIndex</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 456 443 <span class="i">$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> | |
| 457 444 <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> | |
| 458 445 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> | |
| 459 446 <span class="s">}</span> | |
| 460 447 <span class="i">$BinnedDistance</span> = <span class="i">$DistanceToBinnedDistance</span>{<span class="i">$Distance</span>}<span class="sc">;</span> | |
| 461 448 <span class="i">$BinnedDistanceMatrix</span><span class="i">->SetValue</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">$BinnedDistance</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 462 449 <span class="i">$BinnedDistanceMatrix</span><span class="i">->SetValue</span><span class="s">(</span><span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$BinnedDistance</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 463 450 <span class="s">}</span> | |
| 464 451 <span class="s">}</span> | |
| 465 452 | |
| 466 453 <span class="i">$This</span>->{<span class="w">BinnedDistanceMatrix</span>} = <span class="i">$BinnedDistanceMatrix</span><span class="sc">;</span> | |
| 467 454 | |
| 468 455 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 469 456 <span class="s">}</span> | |
| 470 457 | |
| 471 458 <span class="c"># Assign pharmacohore atom types to all heavy atoms...</span> | |
| 472 459 <span class="c">#</span> | |
| 473 <a name="_AssignPharmacophoreAtomTypes-"></a> 460 <span class="k">sub </span><span class="m">_AssignPharmacophoreAtomTypes</span> <span class="s">{</span> | |
| 474 461 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 475 462 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FunctionalClassAtomTypes</span><span class="s">)</span><span class="sc">;</span> | |
| 476 463 | |
| 477 464 <span class="c"># Assign topological pharmacophore atom types...</span> | |
| 478 465 <span class="i">$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> | |
| 479 466 <span class="i">$FunctionalClassAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 480 467 | |
| 481 468 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 482 469 | |
| 483 470 <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> | |
| 484 471 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 485 472 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 486 473 <span class="s">}</span> | |
| 487 474 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 488 475 | |
| 489 476 <span class="k">my</span><span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span><span class="sc">;</span> | |
| 490 477 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 491 478 | |
| 492 479 <span class="i">$AtomType</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> | |
| 493 480 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> && <span class="i">$AtomType</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 494 481 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span> | |
| 495 482 <span class="s">}</span> | |
| 496 483 <span class="c"># Assign phramacophore types list to atom...</span> | |
| 497 484 <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = \<span class="i">@AtomTypes</span><span class="sc">;</span> | |
| 498 485 <span class="s">}</span> | |
| 499 486 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 500 487 <span class="s">}</span> | |
| 501 488 | |
| 502 489 <span class="c"># Initialize pharmacophore atom triplets basis set for all unique triplets constituting atom pairs</span> | |
| 503 490 <span class="c"># binned distances between minimum and maximum distance and optionally applying triangle</span> | |
| 504 491 <span class="c"># inequality. The DistanceBinSize determines the size of the distance bins. The lower distance</span> | |
| 505 492 <span class="c"># bound, along with specified pharmacophore types, is used during generation of atom triplet</span> | |
| 506 493 <span class="c"># IDs.</span> | |
| 507 494 <span class="c">#</span> | |
| 508 495 <span class="c">#</span> | |
| 509 <a name="_InitializePharmacophoreAtomTriplets-"></a> 496 <span class="k">sub </span><span class="m">_InitializePharmacophoreAtomTriplets</span> <span class="s">{</span> | |
| 510 497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 511 498 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$AtomType3</span><span class="cm">,</span> <span class="i">$BinnedDistance12</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="cm">,</span> <span class="i">$AtomTripletID</span><span class="s">)</span><span class="sc">;</span> | |
| 512 499 | |
| 513 500 <span class="c"># Initialize atom triplets information...</span> | |
| 514 501 <span class="k">for</span> <span class="s">(</span><span class="i">$BinnedDistance12</span> = <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance12</span> <= <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance12</span> += <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="s">)</span> <span class="s">{</span> | |
| 515 502 <span class="k">for</span> <span class="s">(</span><span class="i">$BinnedDistance13</span> = <span class="i">$This</span>->{<span class="w">MinDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance13</span> <= <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance13</span> += <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="s">)</span> <span class="s">{</span> | |
| 516 503 <span class="j">DISTANCE23:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$BinnedDistance23</span> = <span class="i">$BinnedDistance12</span><span class="sc">;</span> <span class="i">$BinnedDistance23</span> <= <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="sc">;</span> <span class="i">$BinnedDistance23</span> += <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="s">)</span> <span class="s">{</span> | |
| 517 504 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} && !<span class="i">$This</span><span class="i">->_DoDistancesSatisfyTriangleInequality</span><span class="s">(</span><span class="i">$BinnedDistance12</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 518 505 <span class="k">next</span> <span class="j">DISTANCE23</span><span class="sc">;</span> | |
| 519 506 <span class="s">}</span> | |
| 520 507 <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">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 521 508 <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">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 522 509 <span class="j">ATOMTYPE3:</span> <span class="k">for</span> <span class="i">$AtomType3</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 523 510 <span class="i">$AtomTripletID</span> = <span class="i">$This</span><span class="i">->_GetAtomTripletID</span><span class="s">(</span><span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$AtomType3</span><span class="cm">,</span> <span class="i">$BinnedDistance12</span><span class="s">)</span><span class="sc">;</span> | |
| 524 511 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}{<span class="i">$AtomTripletID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 525 512 <span class="k">next</span> <span class="j">ATOMTYPE3</span><span class="sc">;</span> | |
| 526 513 <span class="s">}</span> | |
| 527 514 <span class="c"># Unique atom triplets information...</span> | |
| 528 515 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$AtomTripletID</span><span class="sc">;</span> | |
| 529 516 <span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}{<span class="i">$AtomTripletID</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 530 517 <span class="s">}</span> | |
| 531 518 <span class="s">}</span> | |
| 532 519 <span class="s">}</span> | |
| 533 520 <span class="s">}</span> | |
| 534 521 <span class="s">}</span> | |
| 535 522 <span class="s">}</span> | |
| 536 523 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 537 524 <span class="s">}</span> | |
| 538 525 | |
| 539 526 <span class="c"># Check triangle inequality...</span> | |
| 540 527 <span class="c">#</span> | |
| 541 <a name="_DoDistancesSatisfyTriangleInequality-"></a> 528 <span class="k">sub </span><span class="m">_DoDistancesSatisfyTriangleInequality</span> <span class="s">{</span> | |
| 542 529 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Distance1</span><span class="cm">,</span> <span class="i">$Distance2</span><span class="cm">,</span> <span class="i">$Distance3</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 543 530 | |
| 544 531 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$Distance1</span> > <span class="k">abs</span><span class="s">(</span><span class="i">$Distance2</span> - <span class="i">$Distance3</span><span class="s">)</span> && <span class="i">$Distance1</span> < <span class="s">(</span><span class="i">$Distance2</span> + <span class="i">$Distance3</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 545 532 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 546 533 <span class="s">}</span> | |
| 547 534 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$Distance2</span> > <span class="k">abs</span><span class="s">(</span><span class="i">$Distance1</span> - <span class="i">$Distance3</span><span class="s">)</span> && <span class="i">$Distance2</span> < <span class="s">(</span><span class="i">$Distance1</span> + <span class="i">$Distance3</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 548 535 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 549 536 <span class="s">}</span> | |
| 550 537 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$Distance3</span> > <span class="k">abs</span><span class="s">(</span><span class="i">$Distance1</span> - <span class="i">$Distance2</span><span class="s">)</span> && <span class="i">$Distance3</span> < <span class="s">(</span><span class="i">$Distance1</span> + <span class="i">$Distance2</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 551 538 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 552 539 <span class="s">}</span> | |
| 553 540 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 554 541 <span class="s">}</span> | |
| 555 542 | |
| 556 543 <span class="c"># Count pharmacophore atom triplets...</span> | |
| 557 544 <span class="c">#</span> | |
| 558 <a name="_CountPharmacohoreAtomTriplets-"></a> 545 <span class="k">sub </span><span class="m">_CountPharmacohoreAtomTriplets</span> <span class="s">{</span> | |
| 559 546 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 560 547 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfAtoms</span><span class="cm">,</span> <span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$AtomIndex3</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">$AtomID3</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$AtomType3</span><span class="cm">,</span> <span class="i">$BinnedDistance12</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="cm">,</span> <span class="i">$BinnedDistanceMatrix</span><span class="cm">,</span> <span class="i">$AtomTripletID</span><span class="s">)</span><span class="sc">;</span> | |
| 561 548 | |
| 562 549 <span class="i">$NumOfAtoms</span> = <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span> | |
| 563 550 <span class="i">$BinnedDistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">BinnedDistanceMatrix</span>}<span class="sc">;</span> | |
| 564 551 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span> | |
| 565 552 | |
| 566 553 <span class="j">ATOMINDEX1:</span> <span class="k">for</span> <span class="i">$AtomIndex1</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 567 554 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex1</span>}<span class="sc">;</span> | |
| 568 555 <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> | |
| 569 556 <span class="k">next</span> <span class="j">ATOMINDEX1</span><span class="sc">;</span> | |
| 570 557 <span class="s">}</span> | |
| 571 558 | |
| 572 559 <span class="j">ATOMINDEX2:</span> <span class="k">for</span> <span class="i">$AtomIndex2</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomIndex1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 573 560 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex2</span>}<span class="sc">;</span> | |
| 574 561 <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> | |
| 575 562 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span> | |
| 576 563 <span class="s">}</span> | |
| 577 564 <span class="i">$BinnedDistance12</span> = <span class="i">$BinnedDistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 578 565 <span class="k">if</span> <span class="s">(</span><span class="i">$BinnedDistance12</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 579 566 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span> | |
| 580 567 <span class="s">}</span> | |
| 581 568 | |
| 582 569 <span class="j">ATOMINDEX3:</span> <span class="k">for</span> <span class="i">$AtomIndex3</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomIndex2</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 583 570 <span class="i">$AtomID3</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex3</span>}<span class="sc">;</span> | |
| 584 571 <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">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID3</span>}<span class="s">)</span> && <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID3</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 585 572 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span> | |
| 586 573 <span class="s">}</span> | |
| 587 574 <span class="i">$BinnedDistance13</span> = <span class="i">$BinnedDistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomIndex3</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 588 575 <span class="i">$BinnedDistance23</span> = <span class="i">$BinnedDistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$AtomIndex3</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 589 576 <span class="k">if</span> <span class="s">(</span><span class="i">$BinnedDistance13</span> == <span class="n">0</span> || <span class="i">$BinnedDistance23</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 590 577 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span> | |
| 591 578 <span class="s">}</span> | |
| 592 579 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} && !<span class="i">$This</span><span class="i">->_DoDistancesSatisfyTriangleInequality</span><span class="s">(</span><span class="i">$BinnedDistance12</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 593 580 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span> | |
| 594 581 <span class="s">}</span> | |
| 595 582 | |
| 596 583 <span class="c"># Go over possible pharmacohore triplets for the three pharmacophore atoms using the</span> | |
| 597 584 <span class="c"># binned distances...</span> | |
| 598 585 <span class="k">for</span> <span class="i">$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> | |
| 599 586 <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">$AtomID2</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 600 587 <span class="k">for</span> <span class="i">$AtomType3</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID3</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 601 588 <span class="i">$AtomTripletID</span> = <span class="i">$This</span><span class="i">->_GetAtomTripletID</span><span class="s">(</span><span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$BinnedDistance23</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$BinnedDistance13</span><span class="cm">,</span> <span class="i">$AtomType3</span><span class="cm">,</span> <span class="i">$BinnedDistance12</span><span class="s">)</span><span class="sc">;</span> | |
| 602 589 <span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}{<span class="i">$AtomTripletID</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 603 590 <span class="s">}</span> | |
| 604 591 <span class="s">}</span> | |
| 605 592 <span class="s">}</span> | |
| 606 593 <span class="s">}</span> | |
| 607 594 <span class="s">}</span> | |
| 608 595 <span class="s">}</span> | |
| 609 596 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 610 597 <span class="s">}</span> | |
| 611 598 | |
| 612 599 <span class="c"># Set final fingerpritns vector...</span> | |
| 613 600 <span class="c">#</span> | |
| 614 <a name="_SetFinalFingerprints-"></a> 601 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> | |
| 615 602 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 616 603 <span class="k">my</span><span class="s">(</span><span class="i">$UseArbitrarySetSize</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> | |
| 617 604 | |
| 618 605 <span class="c"># Mark successful generation of fingerprints...</span> | |
| 619 606 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 620 607 | |
| 621 608 <span class="c"># Is it an ArbitraySize atom triplets set size?</span> | |
| 622 609 <span class="i">$UseArbitrarySetSize</span> = <span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 623 610 | |
| 624 611 <span class="c"># Set atom triplet count values...</span> | |
| 625 612 <span class="i">@IDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 626 613 | |
| 627 614 <span class="k">if</span> <span class="s">(</span><span class="i">$UseArbitrarySetSize</span><span class="s">)</span> <span class="s">{</span> | |
| 628 615 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 629 616 <span class="i">$Value</span> = <span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}{<span class="i">$ID</span>}<span class="sc">;</span> | |
| 630 617 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 631 618 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span> | |
| 632 619 <span class="s">}</span> | |
| 633 620 <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span> | |
| 634 621 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span> | |
| 635 622 <span class="s">}</span> | |
| 636 623 <span class="s">}</span> | |
| 637 624 <span class="k">else</span> <span class="s">{</span> | |
| 638 625 <span class="i">@Values</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}{<span class="i">$_</span>} <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="sc">;</span> | |
| 639 626 <span class="s">}</span> | |
| 640 627 | |
| 641 628 <span class="c"># Set atom triplet IDs for fingerprint vector...</span> | |
| 642 629 <span class="k">if</span> <span class="s">(</span><span class="i">$UseArbitrarySetSize</span><span class="s">)</span> <span class="s">{</span> | |
| 643 630 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span> | |
| 644 631 <span class="s">}</span> | |
| 645 632 <span class="k">else</span> <span class="s">{</span> | |
| 646 633 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="s">)</span><span class="sc">;</span> | |
| 647 634 <span class="s">}</span> | |
| 648 635 | |
| 649 636 <span class="c"># Set atom triplets count values for fingerprint vector...</span> | |
| 650 637 <span class="i">$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> | |
| 651 638 | |
| 652 639 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 653 640 <span class="s">}</span> | |
| 654 641 | |
| 655 642 <span class="c"># Return an array or reference to an array containing atom triplet IDs...</span> | |
| 656 643 <span class="c">#</span> | |
| 657 <a name="GetAtomTripletIDs-"></a> 644 <span class="k">sub </span><span class="m">GetAtomTripletIDs</span> <span class="s">{</span> | |
| 658 645 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 659 646 | |
| 660 647 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="sc">;</span> | |
| 661 648 <span class="s">}</span> | |
| 662 649 | |
| 663 650 <span class="c"># Get pharmacophore atom triplet ID corresponding to atom types and distances</span> | |
| 664 651 <span class="c"># corresponding to atom triplet...</span> | |
| 665 652 <span class="c">#</span> | |
| 666 <a name="_GetAtomTripletID-"></a> 653 <span class="k">sub </span><span class="m">_GetAtomTripletID</span> <span class="s">{</span> | |
| 667 654 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Px</span><span class="cm">,</span> <span class="i">$Dyz</span><span class="cm">,</span> <span class="i">$Py</span><span class="cm">,</span> <span class="i">$Dxz</span><span class="cm">,</span> <span class="i">$Pz</span><span class="cm">,</span> <span class="i">$Dxy</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 668 655 <span class="k">my</span><span class="s">(</span><span class="i">$AtomTripletID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 669 656 | |
| 670 657 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 671 658 | |
| 672 659 <span class="i">@AtomIDs</span> = <span class="k">sort</span><span class="s">(</span><span class="q">"${Px}${Dyz}"</span><span class="cm">,</span> <span class="q">"${Py}${Dxz}"</span><span class="cm">,</span> <span class="q">"${Pz}${Dxy}"</span><span class="s">)</span><span class="sc">;</span> | |
| 673 660 <span class="i">$AtomTripletID</span> = <span class="k">join</span> <span class="q">"-"</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="sc">;</span> | |
| 674 661 | |
| 675 662 <span class="k">return</span> <span class="i">$AtomTripletID</span><span class="sc">;</span> | |
| 676 663 <span class="s">}</span> | |
| 677 664 | |
| 678 665 <span class="c"># Cache appropriate molecule data...</span> | |
| 679 666 <span class="c">#</span> | |
| 680 <a name="_SetupMoleculeDataCache-"></a> 667 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> | |
| 681 668 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 682 669 | |
| 683 670 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span> | |
| 684 671 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span> | |
| 685 672 <span class="c">#</span> | |
| 686 673 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 687 674 | |
| 688 675 <span class="c"># Get all atom IDs...</span> | |
| 689 676 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 690 677 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 691 678 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</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">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span> | |
| 692 679 | |
| 693 680 <span class="c"># Set AtomIndex to AtomID hash...</span> | |
| 694 681 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 695 682 <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> | |
| 696 683 | |
| 697 684 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 698 685 <span class="s">}</span> | |
| 699 686 | |
| 700 687 <span class="c"># Clear cached molecule data...</span> | |
| 701 688 <span class="c">#</span> | |
| 702 <a name="_ClearMoleculeDataCache-"></a> 689 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> | |
| 703 690 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 704 691 | |
| 705 692 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 706 693 | |
| 707 694 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 708 695 <span class="s">}</span> | |
| 709 696 | |
| 710 697 | |
| 711 698 <span class="c"># Return a string containg data for TopologicalPharmacophoreAtomTripletsFingerprints object...</span> | |
| 712 699 <span class="c">#</span> | |
| 713 <a name="StringifyTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 700 <span class="k">sub </span><span class="m">StringifyTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span> | |
| 714 701 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 715 702 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="cm">,</span> <span class="i">$UseTriangleInequality</span><span class="s">)</span><span class="sc">;</span> | |
| 716 703 | |
| 717 704 <span class="c"># Type of fingerprint...</span> | |
| 718 705 <span class="i">$FingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomTripletsSetSizeToUse: $This->{AtomTripletsSetSizeToUse}"</span><span class="sc">;</span> | |
| 719 706 | |
| 720 707 <span class="c"># Distances information...</span> | |
| 721 708 <span class="i">$FingerprintsString</span> .= <span class="q">"; MinDistance: $This->{MinDistance}; MaxDistance: $This->{MaxDistance}; DistanceBinSize: $This->{DistanceBinSize}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> | |
| 722 709 | |
| 723 710 <span class="c"># Pharmacophore atom type labels and description...</span> | |
| 724 711 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span><span class="sc">;</span> | |
| 725 712 | |
| 726 713 <span class="i">@AtomTypesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 727 714 <span class="i">%AvailableAtomTypes</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 728 715 | |
| 729 716 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 730 717 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypesOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 731 718 <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> | |
| 732 719 <span class="s">}</span> | |
| 733 720 | |
| 734 721 <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> | |
| 735 722 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
| 736 723 <span class="i">$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> | |
| 737 724 | |
| 738 725 <span class="c"># Total number of pharmacophore atom triplets...</span> | |
| 739 726 <span class="i">$FingerprintsString</span> .= <span class="q">"; NumOfAtomTriplets: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 740 727 | |
| 741 728 <span class="c"># FingerprintsVector...</span> | |
| 742 729 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> | |
| 743 730 | |
| 744 731 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span> | |
| 745 732 <span class="s">}</span> | |
| 746 733 | |
| 747 <a name="EOF-"></a></pre> | |
| 748 <p> </p> | |
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| 752 </center> | |
| 753 </body> | |
| 754 </html> |