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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/modules/html/code/TopologicalPharmacophoreAtomTripletsFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,754 @@ +<html> +<head> +<title>MayaChemTools:Code:Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints.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::TopologicalPharmacophoreAtomTripletsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints</span><span class="sc">;</span> + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: TopologicalPharmacophoreAtomTripletsFingerprints.pm,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> + 5 <span class="c"># $Revision: 1.30 $</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">'StringifyTopologicalPharmacophoreAtomTripletsFingerprints'</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">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomTripletsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 61 + 62 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> + 63 + 64 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 65 <span class="s">}</span> + 66 + 67 <span class="c"># Initialize object data...</span> + 68 <span class="c">#</span> +<a name="_InitializeTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 69 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span> + 70 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>->{<span class="w">Type</span>} = <span class="q">'TopologicalPharmacophoreAtomTriplets'</span><span class="sc">;</span> + 74 + 75 <span class="c"># Type of vector...</span> + 76 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> + 77 + 78 <span class="c"># AtomTripletsSetSizeToUse...</span> + 79 <span class="c">#</span> + 80 <span class="c"># ArbitrarySize - Corrresponds to atom triplets with non-zero count</span> + 81 <span class="c"># FixedSize - Corresponds to all atom triplets 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">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} = <span class="q">''</span><span class="sc">;</span> + 86 + 87 <span class="c">#</span> + 88 <span class="c"># OrderedNumericalValues - For ArbitrarySize value of AtomTripletsSetSizeToUse</span> + 89 <span class="c"># NumericalValues - For FixedSize value of AtomTripletsSetSizeToUse</span> + 90 <span class="c">#</span> + 91 <span class="c"># Possible values: OrderedNumericalValues or NumericalValues. Default: NumericalValues</span> + 92 <span class="c">#</span> + 93 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">''</span><span class="sc">;</span> + 94 + 95 <span class="c"># Minimum and maximum bond distance between pharmacophore atom pairs corresponding to</span> + 96 <span class="c"># atom triplets and distance bin size used for binning distances.</span> + 97 <span class="c">#</span> + 98 <span class="c"># In order to distribute distance bins of equal size, the last bin is allowed to go past the</span> + 99 <span class="c"># maximum distance specified by upto distance bin size.</span> + 100 <span class="c">#</span> + 101 <span class="c"># The default MinDistance and MaxDistance values of 1 and 10 with DistanceBinSize of</span> + 102 <span class="c"># 2 [ Ref 70 ] generates the following 5 distance bins: [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</span> + 103 <span class="c">#</span> + 104 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span> + 105 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> + 106 + 107 <span class="c"># Distance bin size used for binning distances...</span> + 108 <span class="c">#</span> + 109 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="n">2</span><span class="sc">;</span> + 110 + 111 <span class="c"># Determines whether to apply triangle inequality to distances triplets during basis set generation...</span> + 112 <span class="c">#</span> + 113 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="n">1</span><span class="sc">;</span> + 114 + 115 <span class="c"># Initialize pharmacophore atom types information...</span> + 116 <span class="i">$This</span><span class="i">->_InitializeToplogicalPharmacophoreAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 117 + 118 <span class="c"># Pharmacophore types assigned to each heavy atom...</span> + 119 <span class="c">#</span> + 120 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 121 + 122 <span class="c"># All pharmacophore atom triplets between minimum and maximum distance...</span> + 123 <span class="c">#</span> + 124 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 125 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 126 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 127 <span class="s">}</span> + 128 + 129 <span class="c"># Initialize class ...</span> +<a name="_InitializeClass-"></a> 130 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> + 131 <span class="c">#Class name...</span> + 132 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> + 133 <span class="s">}</span> + 134 + 135 <span class="c"># Initialize object properties....</span> +<a name="_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsProperties-"></a> 136 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsProperties</span> <span class="s">{</span> + 137 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 138 + 139 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 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> + 141 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> + 142 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 143 <span class="s">}</span> + 144 + 145 <span class="c"># Make sure molecule object was specified...</span> + 146 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> + 147 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> + 148 <span class="s">}</span> + 149 <span class="i">$This</span><span class="i">->_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 150 + 151 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 152 <span class="s">}</span> + 153 + 154 <span class="c"># Initialize fingerprints vector...</span> + 155 <span class="c">#</span> +<a name="_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsVector-"></a> 156 <span class="k">sub </span><span class="m">_InitializeTopologicalPharmacophoreAtomTripletsFingerprintsVector</span> <span class="s">{</span> + 157 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 158 + 159 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>}<span class="s">)</span> <span class="s">{</span> + 160 <span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} = <span class="q">'ArbitrarySize'</span><span class="sc">;</span> + 161 <span class="s">}</span> + 162 + 163 <span class="c"># Vector type and type of values...</span> + 164 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> + 165 + 166 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span> + 167 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'OrderedNumericalValues'</span><span class="sc">;</span> + 168 <span class="s">}</span> + 169 <span class="k">else</span> <span class="s">{</span> + 170 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> + 171 <span class="s">}</span> + 172 + 173 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 174 <span class="s">}</span> + 175 + 176 <span class="c"># Set atom parits set size to use...</span> + 177 <span class="c">#</span> +<a name="SetAtomTripletsSetSizeToUse-"></a> 178 <span class="k">sub </span><span class="m">SetAtomTripletsSetSizeToUse</span> <span class="s">{</span> + 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> + 180 + 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> + 182 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTripletsSetSizeToUse: Can't change size: It's already set..."</span><span class="sc">;</span> + 183 <span class="s">}</span> + 184 + 185 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ArbitrarySize|FixedSize)$/i</span><span class="s">)</span> <span class="s">{</span> + 186 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTripletsSetSizeToUse: Unknown AtomTripletsSetSizeToUse value: $Value; Supported values: ArbitrarySize or FixedSize"</span><span class="sc">;</span> + 187 <span class="s">}</span> + 188 + 189 <span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} = <span class="i">$Value</span><span class="sc">;</span> + 190 + 191 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 192 <span class="s">}</span> + 193 + 194 <span class="c"># Initialize topological atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> + 195 <span class="c"># class, to use for atom triplets fingerprint generation...</span> + 196 <span class="c">#</span> + 197 <span class="c"># Let:</span> + 198 <span class="c"># HBD: HydrogenBondDonor</span> + 199 <span class="c"># HBA: HydrogenBondAcceptor</span> + 200 <span class="c"># PI : PositivelyIonizable</span> + 201 <span class="c"># NI : NegativelyIonizable</span> + 202 <span class="c"># Ar : Aromatic</span> + 203 <span class="c"># Hal : Halogen</span> + 204 <span class="c"># H : Hydrophobic</span> + 205 <span class="c"># RA : RingAtom</span> + 206 <span class="c"># CA : ChainAtom</span> + 207 <span class="c">#</span> + 208 <span class="c"># Then:</span> + 209 <span class="c">#</span> + 210 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> + 211 <span class="c">#</span> + 212 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> + 213 <span class="c">#</span> + 214 <span class="c"># Default pharmacophore atom types [ Ref 71 ] to use for atom triplets fingerprint generation</span> + 215 <span class="c"># are: HBD, HBA, PI, NI, H, Ar</span> + 216 <span class="c">#</span> + 217 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> + 218 <span class="c">#</span> + 219 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> + 220 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> + 221 <span class="c"># PositivelyIonizable: +, NH2</span> + 222 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> + 223 <span class="c">#</span> +<a name="_InitializeToplogicalPharmacophoreAtomTypesInformation-"></a> 224 <span class="k">sub </span><span class="m">_InitializeToplogicalPharmacophoreAtomTypesInformation</span> <span class="s">{</span> + 225 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 226 + 227 <span class="c"># Default pharmacophore atom types to use for atom triplets fingerprint generation</span> + 228 <span class="c"># are: HBD, HBA, PI, NI, H, Ar</span> + 229 <span class="c">#</span> + 230 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 231 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="k">sort</span> <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="s">)</span><span class="sc">;</span> + 232 + 233 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 234 <span class="s">}</span> + 235 + 236 <span class="c"># Set atom types to use for atom triplets...</span> + 237 <span class="c">#</span> +<a name="SetAtomTypesToUse-"></a> 238 <span class="k">sub </span><span class="m">SetAtomTypesToUse</span> <span class="s">{</span> + 239 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 240 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 241 + 242 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> + 243 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomTypesToUse: No values specified..."</span><span class="sc">;</span> + 244 <span class="k">return</span><span class="sc">;</span> + 245 <span class="s">}</span> + 246 + 247 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> + 248 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> + 249 + 250 <span class="i">@SpecifiedAtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 251 <span class="i">@AtomTypesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 252 + 253 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> + 254 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> + 255 <span class="s">}</span> + 256 <span class="k">else</span> <span class="s">{</span> + 257 <span class="k">push</span> <span class="i">@SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> + 258 <span class="s">}</span> + 259 + 260 <span class="c"># Make sure specified AtomTypes are valid...</span> + 261 <span class="k">for</span> <span class="i">$SpecifiedAtomType</span> <span class="s">(</span><span class="i">@SpecifiedAtomTypes</span><span class="s">)</span> <span class="s">{</span> + 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> + 263 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomTypesToUse: Specified atom type, $SpecifiedAtomType, is not supported...\n "</span><span class="sc">;</span> + 264 <span class="s">}</span> + 265 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomType</span><span class="sc">;</span> + 266 <span class="k">push</span> <span class="i">@AtomTypesToUse</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span> + 267 <span class="s">}</span> + 268 + 269 <span class="c"># Set atom types to use...</span> + 270 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTypesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 271 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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> + 272 + 273 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 274 <span class="s">}</span> + 275 + 276 <span class="c"># Set minimum distance for pharmacophore atom pairs in atom triplets...</span> + 277 <span class="c">#</span> +<a name="SetMinDistance-"></a> 278 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span> + 279 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 280 + 281 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 282 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 283 <span class="s">}</span> + 284 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> + 285 + 286 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 287 <span class="s">}</span> + 288 + 289 <span class="c"># Set maximum distance for pharmacophore atom pairs in atom triplets...</span> + 290 <span class="c">#</span> +<a name="SetMaxDistance-"></a> 291 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span> + 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> + 293 + 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> + 295 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 296 <span class="s">}</span> + 297 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> + 298 + 299 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 300 <span class="s">}</span> + 301 + 302 <span class="c"># Set distance bin size for binning pharmacophore atom pair distances in atom triplets...</span> + 303 <span class="c">#</span> +<a name="SetDistanceBinSize-"></a> 304 <span class="k">sub </span><span class="m">SetDistanceBinSize</span> <span class="s">{</span> + 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> + 306 + 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> + 308 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDistanceBinSize: DistanceBinSize value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 309 <span class="s">}</span> + 310 <span class="i">$This</span>->{<span class="w">DistanceBinSize</span>} = <span class="i">$Value</span><span class="sc">;</span> + 311 + 312 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 313 <span class="s">}</span> + 314 + 315 <span class="c"># Generate fingerprints description...</span> + 316 <span class="c">#</span> +<a name="GetDescription-"></a> 317 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> + 318 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 319 + 320 <span class="c"># Is description explicity set?</span> + 321 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> + 322 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> + 323 <span class="s">}</span> + 324 + 325 <span class="c"># Generate fingerprints description...</span> + 326 + 327 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomTripletsSetSizeToUse}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"</span><span class="sc">;</span> + 328 <span class="s">}</span> + 329 + 330 <span class="c"># Generate topological pharmacophore atom triplets [ Ref 66, Ref 68-71 ] fingerprints...</span> + 331 <span class="c">#</span> + 332 <span class="c"># Let:</span> + 333 <span class="c">#</span> + 334 <span class="c"># P = Any of the supported pharmacophore atom types</span> + 335 <span class="c">#</span> + 336 <span class="c"># Px = Pharmacophore atom x</span> + 337 <span class="c"># Py = Pharmacophore atom y</span> + 338 <span class="c"># Pz = Pharmacophore atom z</span> + 339 <span class="c">#</span> + 340 <span class="c"># Dxy = Distance or lower bound of binned distance between Px and Py</span> + 341 <span class="c"># Dxz = Distance or lower bound of binned distance between Px and Pz</span> + 342 <span class="c"># Dyz = Distance or lower bound of binned distance between Py and Pz</span> + 343 <span class="c">#</span> + 344 <span class="c"># Then:</span> + 345 <span class="c"># PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet ID for atoms Px, Py and Pz</span> + 346 <span class="c">#</span> + 347 <span class="c"># For example: H1-H1-H1, H2-HBA-H2 and so on</span> + 348 <span class="c">#</span> + 349 <span class="c"># Methodology:</span> + 350 <span class="c"># . Generate a distance matrix.</span> + 351 <span class="c"># . Using specified minimum, maximum and distance bin size, generate a binned distance</span> + 352 <span class="c"># matrix from distance matrix. The lower distance bound on the distance bin is used</span> + 353 <span class="c"># in the binned distance matrix and atom triplet IDs.</span> + 354 <span class="c"># . Assign pharmacophore atom types to all the atoms.</span> + 355 <span class="c"># . Initialize pharmacophore atom triplets basis set for all unique triplets constituting</span> + 356 <span class="c"># atom pairs binned distances between minimum and maximum distance.</span> + 357 <span class="c"># . Optionally, trinagle inequality is also implied which means:</span> + 358 <span class="c"># . Distance or binned distance between any two pairs in a triplet must be less than the</span> + 359 <span class="c"># sum of distances or binned distances between other two pairs and greater than the</span> + 360 <span class="c"># difference of distances between other pairs.</span> + 361 <span class="c"># . Using binned distance matrix and pharmacophore atom types, count occurance of</span> + 362 <span class="c"># unique atom triplets.</span> + 363 <span class="c">#</span> + 364 <span class="c"># Notes:</span> + 365 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span> + 366 <span class="c">#</span> +<a name="GenerateFingerprints-"></a> 367 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> + 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> + 369 + 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> + 371 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateTopologicalPharmacophoreAtomTripletsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."</span><span class="sc">;</span> + 372 <span class="s">}</span> + 373 + 374 <span class="c"># Cache appropriate molecule data...</span> + 375 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 376 + 377 <span class="c"># Generate distance matrix...</span> + 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> + 379 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: Fingerprints generation didn't succeed: Couldn't generate distance matrix..."</span><span class="sc">;</span> + 380 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 381 <span class="s">}</span> + 382 + 383 <span class="c"># Generate binned distance matrix...</span> + 384 <span class="i">$This</span><span class="i">->_GenerateBinnedDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 385 + 386 <span class="c"># Assign pharmacohore atom types to all heavy atoms...</span> + 387 <span class="i">$This</span><span class="i">->_AssignPharmacophoreAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 388 + 389 <span class="c"># Initialize values of all possible pharmacohore atom triplets...</span> + 390 <span class="i">$This</span><span class="i">->_InitializePharmacophoreAtomTriplets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 391 + 392 <span class="c"># Count atom triplets...</span> + 393 <span class="i">$This</span><span class="i">->_CountPharmacohoreAtomTriplets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 394 + 395 <span class="c"># Set final fingerprints...</span> + 396 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 397 + 398 <span class="c"># Clear cached molecule data...</span> + 399 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 400 + 401 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 402 <span class="s">}</span> + 403 + 404 <span class="c"># Setup distance matrix...</span> + 405 <span class="c">#</span> +<a name="_SetupDistanceMatrix-"></a> 406 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span> + 407 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 408 + 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> + 410 + 411 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span> + 412 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 413 <span class="s">}</span> + 414 + 415 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 416 <span class="s">}</span> + 417 + 418 <span class="c"># Generate binned distance matrix for distances with in the specified distance ranges...</span> + 419 <span class="c">#</span> +<a name="_GenerateBinnedDistanceMatrix-"></a> 420 <span class="k">sub </span><span class="m">_GenerateBinnedDistanceMatrix</span> <span class="s">{</span> + 421 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 422 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 423 + 424 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span> + 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">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 426 + 427 <span class="c"># Initialize binned distance matrix...</span> + 428 <span class="i">$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> + 429 + 430 <span class="c"># Setup distance to binned distance map...</span> + 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> + 432 <span class="i">%DistanceToBinnedDistance</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 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> + 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> + 435 <span class="i">$DistanceToBinnedDistance</span>{<span class="i">$Distance</span>} = <span class="i">$BinnedDistance</span><span class="sc">;</span> + 436 <span class="s">}</span> + 437 <span class="s">}</span> + 438 + 439 <span class="c"># Generate binned distance matrix...</span> + 440 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span> + 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> + 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">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> + 443 <span class="i">$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> + 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> + 445 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> + 446 <span class="s">}</span> + 447 <span class="i">$BinnedDistance</span> = <span class="i">$DistanceToBinnedDistance</span>{<span class="i">$Distance</span>}<span class="sc">;</span> + 448 <span class="i">$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> + 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">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> + 450 <span class="s">}</span> + 451 <span class="s">}</span> + 452 + 453 <span class="i">$This</span>->{<span class="w">BinnedDistanceMatrix</span>} = <span class="i">$BinnedDistanceMatrix</span><span class="sc">;</span> + 454 + 455 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 456 <span class="s">}</span> + 457 + 458 <span class="c"># Assign pharmacohore atom types to all heavy atoms...</span> + 459 <span class="c">#</span> +<a name="_AssignPharmacophoreAtomTypes-"></a> 460 <span class="k">sub </span><span class="m">_AssignPharmacophoreAtomTypes</span> <span class="s">{</span> + 461 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 462 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FunctionalClassAtomTypes</span><span class="s">)</span><span class="sc">;</span> + 463 + 464 <span class="c"># Assign topological pharmacophore atom types...</span> + 465 <span class="i">$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> + 466 <span class="i">$FunctionalClassAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 467 + 468 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 469 + 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> + 471 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 472 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> + 473 <span class="s">}</span> + 474 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 475 + 476 <span class="k">my</span><span class="s">(</span><span class="i">@AtomTypes</span><span class="s">)</span><span class="sc">;</span> + 477 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 478 + 479 <span class="i">$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> + 480 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> && <span class="i">$AtomType</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> + 481 <span class="k">push</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="sc">;</span> + 482 <span class="s">}</span> + 483 <span class="c"># Assign phramacophore types list to atom...</span> + 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> + 485 <span class="s">}</span> + 486 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 487 <span class="s">}</span> + 488 + 489 <span class="c"># Initialize pharmacophore atom triplets basis set for all unique triplets constituting atom pairs</span> + 490 <span class="c"># binned distances between minimum and maximum distance and optionally applying triangle</span> + 491 <span class="c"># inequality. The DistanceBinSize determines the size of the distance bins. The lower distance</span> + 492 <span class="c"># bound, along with specified pharmacophore types, is used during generation of atom triplet</span> + 493 <span class="c"># IDs.</span> + 494 <span class="c">#</span> + 495 <span class="c">#</span> +<a name="_InitializePharmacophoreAtomTriplets-"></a> 496 <span class="k">sub </span><span class="m">_InitializePharmacophoreAtomTriplets</span> <span class="s">{</span> + 497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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">$AtomTripletID</span><span class="s">)</span><span class="sc">;</span> + 499 + 500 <span class="c"># Initialize atom triplets information...</span> + 501 <span class="k">for</span> <span class="s">(</span><span class="i">$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">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="s">)</span> <span class="s">{</span> + 502 <span class="k">for</span> <span class="s">(</span><span class="i">$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">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="s">)</span> <span class="s">{</span> + 503 <span class="j">DISTANCE23:</span> <span class="k">for</span> <span class="s">(</span><span class="i">$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">$This</span>->{<span class="w">DistanceBinSize</span>}<span class="s">)</span> <span class="s">{</span> + 504 <span class="k">if</span> <span class="s">(</span><span class="i">$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> + 505 <span class="k">next</span> <span class="j">DISTANCE23</span><span class="sc">;</span> + 506 <span class="s">}</span> + 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> + 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> + 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> + 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> + 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> + 512 <span class="k">next</span> <span class="j">ATOMTYPE3</span><span class="sc">;</span> + 513 <span class="s">}</span> + 514 <span class="c"># Unique atom triplets information...</span> + 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> + 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> + 517 <span class="s">}</span> + 518 <span class="s">}</span> + 519 <span class="s">}</span> + 520 <span class="s">}</span> + 521 <span class="s">}</span> + 522 <span class="s">}</span> + 523 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 524 <span class="s">}</span> + 525 + 526 <span class="c"># Check triangle inequality...</span> + 527 <span class="c">#</span> +<a name="_DoDistancesSatisfyTriangleInequality-"></a> 528 <span class="k">sub </span><span class="m">_DoDistancesSatisfyTriangleInequality</span> <span class="s">{</span> + 529 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Distance3</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 530 + 531 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$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">$Distance3</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> + 532 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 533 <span class="s">}</span> + 534 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$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">$Distance3</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> + 535 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 536 <span class="s">}</span> + 537 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$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">$Distance2</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> + 538 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 539 <span class="s">}</span> + 540 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> + 541 <span class="s">}</span> + 542 + 543 <span class="c"># Count pharmacophore atom triplets...</span> + 544 <span class="c">#</span> +<a name="_CountPharmacohoreAtomTriplets-"></a> 545 <span class="k">sub </span><span class="m">_CountPharmacohoreAtomTriplets</span> <span class="s">{</span> + 546 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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> + 548 + 549 <span class="i">$NumOfAtoms</span> = <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span> + 550 <span class="i">$BinnedDistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">BinnedDistanceMatrix</span>}<span class="sc">;</span> + 551 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span> + 552 + 553 <span class="j">ATOMINDEX1:</span> <span class="k">for</span> <span class="i">$AtomIndex1</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 554 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex1</span>}<span class="sc">;</span> + 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> + 556 <span class="k">next</span> <span class="j">ATOMINDEX1</span><span class="sc">;</span> + 557 <span class="s">}</span> + 558 + 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">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 560 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex2</span>}<span class="sc">;</span> + 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> + 562 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span> + 563 <span class="s">}</span> + 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">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> + 565 <span class="k">if</span> <span class="s">(</span><span class="i">$BinnedDistance12</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> + 566 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span> + 567 <span class="s">}</span> + 568 + 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">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 570 <span class="i">$AtomID3</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex3</span>}<span class="sc">;</span> + 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> + 572 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span> + 573 <span class="s">}</span> + 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">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> + 575 <span class="i">$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> + 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> + 577 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span> + 578 <span class="s">}</span> + 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">$BinnedDistance23</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 580 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span> + 581 <span class="s">}</span> + 582 + 583 <span class="c"># Go over possible pharmacohore triplets for the three pharmacophore atoms using the</span> + 584 <span class="c"># binned distances...</span> + 585 <span class="k">for</span> <span class="i">$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> + 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">$AtomID2</span>}}<span class="s">)</span> <span class="s">{</span> + 587 <span class="k">for</span> <span class="i">$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> + 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> + 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> + 590 <span class="s">}</span> + 591 <span class="s">}</span> + 592 <span class="s">}</span> + 593 <span class="s">}</span> + 594 <span class="s">}</span> + 595 <span class="s">}</span> + 596 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 597 <span class="s">}</span> + 598 + 599 <span class="c"># Set final fingerpritns vector...</span> + 600 <span class="c">#</span> +<a name="_SetFinalFingerprints-"></a> 601 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> + 602 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 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">$Value</span><span class="cm">,</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> + 604 + 605 <span class="c"># Mark successful generation of fingerprints...</span> + 606 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> + 607 + 608 <span class="c"># Is it an ArbitraySize atom triplets set size?</span> + 609 <span class="i">$UseArbitrarySetSize</span> = <span class="i">$This</span>->{<span class="w">AtomTripletsSetSizeToUse</span>} =~ <span class="q">/^ArbitrarySize$/i</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 610 + 611 <span class="c"># Set atom triplet count values...</span> + 612 <span class="i">@IDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 613 + 614 <span class="k">if</span> <span class="s">(</span><span class="i">$UseArbitrarySetSize</span><span class="s">)</span> <span class="s">{</span> + 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> + 616 <span class="i">$Value</span> = <span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">Count</span>}{<span class="i">$ID</span>}<span class="sc">;</span> + 617 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> + 618 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span> + 619 <span class="s">}</span> + 620 <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span> + 621 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span> + 622 <span class="s">}</span> + 623 <span class="s">}</span> + 624 <span class="k">else</span> <span class="s">{</span> + 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">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="sc">;</span> + 626 <span class="s">}</span> + 627 + 628 <span class="c"># Set atom triplet IDs for fingerprint vector...</span> + 629 <span class="k">if</span> <span class="s">(</span><span class="i">$UseArbitrarySetSize</span><span class="s">)</span> <span class="s">{</span> + 630 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span> + 631 <span class="s">}</span> + 632 <span class="k">else</span> <span class="s">{</span> + 633 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTriplets</span>}{<span class="w">IDs</span>}}<span class="s">)</span><span class="sc">;</span> + 634 <span class="s">}</span> + 635 + 636 <span class="c"># Set atom triplets count values for fingerprint vector...</span> + 637 <span class="i">$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> + 638 + 639 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 640 <span class="s">}</span> + 641 + 642 <span class="c"># Return an array or reference to an array containing atom triplet IDs...</span> + 643 <span class="c">#</span> +<a name="GetAtomTripletIDs-"></a> 644 <span class="k">sub </span><span class="m">GetAtomTripletIDs</span> <span class="s">{</span> + 645 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 646 + 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> + 648 <span class="s">}</span> + 649 + 650 <span class="c"># Get pharmacophore atom triplet ID corresponding to atom types and distances</span> + 651 <span class="c"># corresponding to atom triplet...</span> + 652 <span class="c">#</span> +<a name="_GetAtomTripletID-"></a> 653 <span class="k">sub </span><span class="m">_GetAtomTripletID</span> <span class="s">{</span> + 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">$Dxy</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 655 <span class="k">my</span><span class="s">(</span><span class="i">$AtomTripletID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> + 656 + 657 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 658 + 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> + 660 <span class="i">$AtomTripletID</span> = <span class="k">join</span> <span class="q">"-"</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="sc">;</span> + 661 + 662 <span class="k">return</span> <span class="i">$AtomTripletID</span><span class="sc">;</span> + 663 <span class="s">}</span> + 664 + 665 <span class="c"># Cache appropriate molecule data...</span> + 666 <span class="c">#</span> +<a name="_SetupMoleculeDataCache-"></a> 667 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> + 668 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 669 + 670 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span> + 671 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span> + 672 <span class="c">#</span> + 673 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 674 + 675 <span class="c"># Get all atom IDs...</span> + 676 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> + 677 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 678 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</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">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span> + 679 + 680 <span class="c"># Set AtomIndex to AtomID hash...</span> + 681 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 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> + 683 + 684 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 685 <span class="s">}</span> + 686 + 687 <span class="c"># Clear cached molecule data...</span> + 688 <span class="c">#</span> +<a name="_ClearMoleculeDataCache-"></a> 689 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> + 690 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 691 + 692 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 693 + 694 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 695 <span class="s">}</span> + 696 + 697 + 698 <span class="c"># Return a string containg data for TopologicalPharmacophoreAtomTripletsFingerprints object...</span> + 699 <span class="c">#</span> +<a name="StringifyTopologicalPharmacophoreAtomTripletsFingerprints-"></a> 700 <span class="k">sub </span><span class="m">StringifyTopologicalPharmacophoreAtomTripletsFingerprints</span> <span class="s">{</span> + 701 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 702 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="cm">,</span> <span class="i">$UseTriangleInequality</span><span class="s">)</span><span class="sc">;</span> + 703 + 704 <span class="c"># Type of fingerprint...</span> + 705 <span class="i">$FingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomTripletsSetSizeToUse: $This->{AtomTripletsSetSizeToUse}"</span><span class="sc">;</span> + 706 + 707 <span class="c"># Distances information...</span> + 708 <span class="i">$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> + 709 + 710 <span class="c"># Pharmacophore atom type labels and description...</span> + 711 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">@AtomTypes</span><span class="cm">,</span> <span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomTypes</span><span class="s">)</span><span class="sc">;</span> + 712 + 713 <span class="i">@AtomTypesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 714 <span class="i">%AvailableAtomTypes</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 715 + 716 <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 717 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@AtomTypesOrder</span><span class="s">)</span> <span class="s">{</span> + 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> + 719 <span class="s">}</span> + 720 + 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> + 722 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomTypesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomTypesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> + 723 <span class="i">$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> + 724 + 725 <span class="c"># Total number of pharmacophore atom triplets...</span> + 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> + 727 + 728 <span class="c"># FingerprintsVector...</span> + 729 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> + 730 + 731 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span> + 732 <span class="s">}</span> + 733 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>