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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/TopologicalAtomTripletsFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,826 @@ +<html> +<head> +<title>MayaChemTools:Code:Fingerprints::TopologicalAtomTripletsFingerprints.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::TopologicalAtomTripletsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalAtomTripletsFingerprints</span><span class="sc">;</span> + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: TopologicalAtomTripletsFingerprints.pm,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> + 5 <span class="c"># $Revision: 1.15 $</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">Molecule</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span> + 38 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> + 39 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span> + 40 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span> + 41 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span> + 42 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span> + 43 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span> + 44 + 45 <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> + 46 + 47 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> + 48 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> + 49 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> + 50 + 51 <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> + 52 + 53 <span class="c"># Setup class variables...</span> + 54 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> + 55 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 56 + 57 <span class="c"># Overload Perl functions...</span> + 58 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyTopologicalAtomTripletsFingerprints'</span><span class="sc">;</span> + 59 + 60 <span class="c"># Class constructor...</span> +<a name="new-"></a> 61 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> + 62 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 63 + 64 <span class="c"># Initialize object...</span> + 65 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 66 <span class="k">bless</span> <span class="i">$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> + 67 <span class="i">$This</span><span class="i">->_InitializeTopologicalAtomTripletsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 68 + 69 <span class="i">$This</span><span class="i">->_InitializeTopologicalAtomTripletsFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> + 70 + 71 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 72 <span class="s">}</span> + 73 + 74 <span class="c"># Initialize object data...</span> + 75 <span class="c">#</span> +<a name="_InitializeTopologicalAtomTripletsFingerprints-"></a> 76 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomTripletsFingerprints</span> <span class="s">{</span> + 77 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 78 + 79 <span class="c"># Type of fingerprint...</span> + 80 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'TopologicalAtomTriplets'</span><span class="sc">;</span> + 81 + 82 <span class="c"># Type of vector...</span> + 83 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> + 84 + 85 <span class="c"># Type of FingerprintsVector...</span> + 86 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> + 87 + 88 <span class="c"># Minimum and maximum bond distance between atom paris...</span> + 89 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span> + 90 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> + 91 + 92 <span class="c"># Determines whether to apply triangle inequality to distance triplets...</span> + 93 <span class="c">#</span> + 94 <span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} = <span class="n">0</span><span class="sc">;</span> + 95 + 96 <span class="c"># Atom identifier type to use for atom IDs in atom triplets...</span> + 97 <span class="c">#</span> + 98 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span> + 99 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span> + 100 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> + 101 <span class="c">#</span> + 102 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> + 103 + 104 <span class="c"># Atom types assigned to each heavy atom...</span> + 105 <span class="c">#</span> + 106 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 107 + 108 <span class="c"># All atom triplets between minimum and maximum distance...</span> + 109 <span class="c">#</span> + 110 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTripletsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 111 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTripletsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 112 <span class="s">}</span> + 113 + 114 <span class="c"># Initialize class ...</span> +<a name="_InitializeClass-"></a> 115 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> + 116 <span class="c">#Class name...</span> + 117 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> + 118 <span class="s">}</span> + 119 + 120 <span class="c"># Initialize object properties....</span> +<a name="_InitializeTopologicalAtomTripletsFingerprintsProperties-"></a> 121 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomTripletsFingerprintsProperties</span> <span class="s">{</span> + 122 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 123 + 124 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> + 125 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> + 126 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> + 127 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 128 <span class="s">}</span> + 129 + 130 <span class="c"># Make sure molecule object was specified...</span> + 131 <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> + 132 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> + 133 <span class="s">}</span> + 134 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> + 135 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."</span><span class="sc">;</span> + 136 <span class="s">}</span> + 137 + 138 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 139 + 140 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 141 <span class="s">}</span> + 142 + 143 <span class="c"># Set minimum distance for atom triplets...</span> + 144 <span class="c">#</span> +<a name="SetMinDistance-"></a> 145 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span> + 146 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 147 + 148 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 149 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 150 <span class="s">}</span> + 151 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> + 152 + 153 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 154 <span class="s">}</span> + 155 + 156 <span class="c"># Set maximum distance for atom triplets...</span> + 157 <span class="c">#</span> +<a name="SetMaxDistance-"></a> 158 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span> + 159 <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> + 160 + 161 <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> + 162 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> + 163 <span class="s">}</span> + 164 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> + 165 + 166 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 167 <span class="s">}</span> + 168 + 169 <span class="c"># Set atom identifier type..</span> + 170 <span class="c">#</span> +<a name="SetAtomIdentifierType-"></a> 171 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> + 172 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IdentifierType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 173 + 174 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> + 175 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes."</span><span class="sc">;</span> + 176 <span class="s">}</span> + 177 + 178 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> + 179 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SeAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span> + 180 <span class="s">}</span> + 181 + 182 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> + 183 + 184 <span class="c"># Initialize atom identifier type information...</span> + 185 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 186 + 187 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 188 <span class="s">}</span> + 189 + 190 <span class="c"># Generate fingerprints description...</span> + 191 <span class="c">#</span> +<a name="GetDescription-"></a> 192 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> + 193 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 194 + 195 <span class="c"># Is description explicity set?</span> + 196 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> + 197 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> + 198 <span class="s">}</span> + 199 + 200 <span class="c"># Generate fingerprints description...</span> + 201 + 202 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomIdentifierType}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"</span><span class="sc">;</span> + 203 <span class="s">}</span> + 204 + 205 <span class="c"># Generate topological atom triplets fingerprints...</span> + 206 <span class="c">#</span> + 207 <span class="c"># Let:</span> + 208 <span class="c">#</span> + 209 <span class="c"># AT = Any of the supported atom types</span> + 210 <span class="c">#</span> + 211 <span class="c"># ATx = Atom type for atom x</span> + 212 <span class="c"># ATy = Atom type for atom y</span> + 213 <span class="c"># ATz = Atom type for atom z</span> + 214 <span class="c">#</span> + 215 <span class="c"># Dxy = Distance between Px and Py</span> + 216 <span class="c"># Dxz = Distance between Px and Pz</span> + 217 <span class="c"># Dyz = Distance between Py and Pz</span> + 218 <span class="c">#</span> + 219 <span class="c"># Then:</span> + 220 <span class="c">#</span> + 221 <span class="c"># ATx-Dyz-ATy-Dxz-ATz-Dxy = Atom triplet ID for atom types ATx, ATy and Atz</span> + 222 <span class="c">#</span> + 223 <span class="c"># Methodology:</span> + 224 <span class="c"># . Generate a distance matrix.</span> + 225 <span class="c"># . Assign atom types to all the atoms.</span> + 226 <span class="c"># . Using distance matrix and atom types, count occurrence of unique atom triplets</span> + 227 <span class="c"># within specified distance range along with optional trinagle inequality</span> + 228 <span class="c">#</span> + 229 <span class="c"># Notes:</span> + 230 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span> + 231 <span class="c"># . For a molecule containing N atoms with all different atom type, the total number of</span> + 232 <span class="c"># possible unique atom triplets without applying triangle inquality check corresponds to:</span> + 233 <span class="c">#</span> + 234 <span class="c"># Factorial( N ) / ( Factorial( N - 3 ) * Factorial (3) )</span> + 235 <span class="c">#</span> + 236 <span class="c"># However, due to similar atom types assigned to atoms in a molecule for a specific atom</span> + 237 <span class="c"># typing methodology and specified distance range used during fingerprints generation, the</span> + 238 <span class="c"># actual number of unique triplets is usually smaller than the theoretical limit.</span> + 239 <span class="c">#</span> +<a name="GenerateFingerprints-"></a> 240 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> + 241 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 242 + 243 <span class="k">if</span> <span class="s">(</span><span class="i">$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> + 244 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateTopologicalAtomTripletsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."</span><span class="sc">;</span> + 245 <span class="s">}</span> + 246 + 247 <span class="c"># Cache appropriate molecule data...</span> + 248 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 249 + 250 <span class="c"># Generate distance matrix...</span> + 251 <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> + 252 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't generate distance matrix..."</span><span class="sc">;</span> + 253 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 254 <span class="s">}</span> + 255 + 256 <span class="c"># Assign atom types to all heavy atoms...</span> + 257 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 258 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."</span><span class="sc">;</span> + 259 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 260 <span class="s">}</span> + 261 + 262 <span class="c"># Intialize values of toplogical atom triplets...</span> + 263 <span class="i">$This</span><span class="i">->_InitializeToplogicalAtomTriplets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 264 + 265 <span class="c"># Count atom triplets...</span> + 266 <span class="i">$This</span><span class="i">->_GenerateAndCountAtomTriplets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 267 + 268 <span class="c"># Set final fingerprints...</span> + 269 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 270 + 271 <span class="c"># Clear cached molecule data...</span> + 272 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 273 + 274 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 275 <span class="s">}</span> + 276 + 277 <span class="c"># Setup distance matrix...</span> + 278 <span class="c">#</span> +<a name="_SetupDistanceMatrix-"></a> 279 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span> + 280 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 281 + 282 <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> + 283 + 284 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span> + 285 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 286 <span class="s">}</span> + 287 + 288 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 289 <span class="s">}</span> + 290 + 291 <span class="c"># Assign appropriate atom types to all heavy atoms...</span> + 292 <span class="c">#</span> +<a name="_AssignAtomTypes-"></a> 293 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span> + 294 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 295 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 296 + 297 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 298 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span> + 299 + 300 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span> + 301 + 302 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> + 303 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 304 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::AtomicInvariantsAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">'AtomicInvariantsToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}<span class="s">)</span><span class="sc">;</span> + 305 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 306 <span class="s">}</span> + 307 + 308 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^DREIDINGAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 309 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::DREIDINGAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 310 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 311 <span class="s">}</span> + 312 + 313 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 314 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::EStateAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 315 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 316 <span class="s">}</span> + 317 + 318 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 319 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::FunctionalClassAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}<span class="s">)</span><span class="sc">;</span> + 320 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 321 <span class="s">}</span> + 322 + 323 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^MMFF94AtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 324 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::MMFF94AtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 325 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 326 <span class="s">}</span> + 327 + 328 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 329 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SLogPAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 330 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 331 <span class="s">}</span> + 332 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SYBYLAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 333 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SYBYLAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 334 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 335 <span class="s">}</span> + 336 + 337 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 338 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">0</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> + 339 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 340 <span class="s">}</span> + 341 + 342 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 343 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::UFFAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 344 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 345 <span class="s">}</span> + 346 + 347 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_AssignAtomTypes: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> + 348 <span class="s">}</span> + 349 + 350 <span class="c"># Assign atom types...</span> + 351 <span class="i">$SpecifiedAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 352 + 353 <span class="c"># Make sure atom types assignment is successful...</span> + 354 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 355 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 356 <span class="s">}</span> + 357 + 358 <span class="c"># Collect assigned atom types...</span> + 359 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> + 360 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 361 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> + 362 <span class="s">}</span> + 363 <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> + 364 <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$SpecifiedAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> + 365 <span class="s">}</span> + 366 + 367 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 368 <span class="s">}</span> + 369 + 370 <span class="c"># Initialize topological atom triplets between specified distance range...</span> + 371 <span class="c">#</span> +<a name="_InitializeToplogicalAtomTriplets-"></a> 372 <span class="k">sub </span><span class="m">_InitializeToplogicalAtomTriplets</span> <span class="s">{</span> + 373 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 374 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="s">)</span><span class="sc">;</span> + 375 + 376 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTripletsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 377 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTripletsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 378 + 379 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 380 <span class="s">}</span> + 381 + 382 <span class="c"># Count atom triplets between mininum and maximum distance at each</span> + 383 <span class="c"># distance using distance matrix and atom types assiged to each heavy</span> + 384 <span class="c"># atom.</span> + 385 <span class="c">#</span> +<a name="_GenerateAndCountAtomTriplets-"></a> 386 <span class="k">sub </span><span class="m">_GenerateAndCountAtomTriplets</span> <span class="s">{</span> + 387 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 388 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomType3</span><span class="cm">,</span> <span class="i">$Distance12</span><span class="cm">,</span> <span class="i">$Distance13</span><span class="cm">,</span> <span class="i">$Distance23</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="cm">,</span> <span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$AtomTripletID</span><span class="s">)</span><span class="sc">;</span> + 389 + 390 <span class="i">$NumOfAtoms</span> = <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span> + 391 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span> + 392 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span> + 393 + 394 <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> + 395 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex1</span>}<span class="sc">;</span> + 396 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 397 <span class="k">next</span> <span class="j">ATOMINDEX1</span><span class="sc">;</span> + 398 <span class="s">}</span> + 399 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="sc">;</span> + 400 + 401 <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">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 402 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex2</span>}<span class="sc">;</span> + 403 <span class="k">if</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="s">)</span> <span class="s">{</span> + 404 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span> + 405 <span class="s">}</span> + 406 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="sc">;</span> + 407 + 408 <span class="i">$Distance12</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$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> + 409 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance12</span> < <span class="i">$This</span>->{<span class="w">MinDistance</span>} || <span class="i">$Distance12</span> > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> + 410 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span> + 411 <span class="s">}</span> + 412 + 413 <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">$NumOfAtoms</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 414 <span class="i">$AtomID3</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$AtomIndex3</span>}<span class="sc">;</span> + 415 <span class="k">if</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="s">)</span> <span class="s">{</span> + 416 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span> + 417 <span class="s">}</span> + 418 <span class="i">$AtomType3</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID3</span>}<span class="sc">;</span> + 419 + 420 <span class="i">$Distance13</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$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> + 421 <span class="i">$Distance23</span> = <span class="i">$DistanceMatrix</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">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> + 422 + 423 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance13</span> < <span class="i">$This</span>->{<span class="w">MinDistance</span>} || <span class="i">$Distance13</span> > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> + 424 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span> + 425 <span class="s">}</span> + 426 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance23</span> < <span class="i">$This</span>->{<span class="w">MinDistance</span>} || <span class="i">$Distance23</span> > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> + 427 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span> + 428 <span class="s">}</span> + 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseTriangleInequality</span>} && !<span class="i">$This</span><span class="i">->_DoDistancesSatisfyTriangleInequality</span><span class="s">(</span><span class="i">$Distance12</span><span class="cm">,</span> <span class="i">$Distance13</span><span class="cm">,</span> <span class="i">$Distance23</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 430 <span class="k">next</span> <span class="j">ATOMINDEX3</span><span class="sc">;</span> + 431 <span class="s">}</span> + 432 + 433 <span class="i">$AtomTripletID</span> = <span class="i">$This</span><span class="i">->_GetAtomTripletID</span><span class="s">(</span><span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$Distance23</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$Distance13</span><span class="cm">,</span> <span class="i">$AtomType3</span><span class="cm">,</span> <span class="i">$Distance12</span><span class="s">)</span><span class="sc">;</span> + 434 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomTripletsCount</span>}{<span class="i">$AtomTripletID</span>}<span class="s">)</span> <span class="s">{</span> + 435 <span class="i">$This</span>->{<span class="w">AtomTripletsCount</span>}{<span class="i">$AtomTripletID</span>} = <span class="n">0</span><span class="sc">;</span> + 436 <span class="s">}</span> + 437 <span class="i">$This</span>->{<span class="w">AtomTripletsCount</span>}{<span class="i">$AtomTripletID</span>} += <span class="n">1</span><span class="sc">;</span> + 438 <span class="s">}</span> + 439 <span class="s">}</span> + 440 <span class="s">}</span> + 441 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 442 <span class="s">}</span> + 443 + 444 <span class="c"># Check triangle inequality...</span> + 445 <span class="c">#</span> +<a name="_DoDistancesSatisfyTriangleInequality-"></a> 446 <span class="k">sub </span><span class="m">_DoDistancesSatisfyTriangleInequality</span> <span class="s">{</span> + 447 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Distance3</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 448 + 449 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$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">$Distance3</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> + 450 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 451 <span class="s">}</span> + 452 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$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">$Distance3</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> + 453 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 454 <span class="s">}</span> + 455 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="i">$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">$Distance2</span><span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> + 456 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 457 <span class="s">}</span> + 458 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> + 459 <span class="s">}</span> + 460 + 461 <span class="c"># Get atom triplet ID corresponding to atom types and distances corresponding to atom triplet...</span> + 462 <span class="c">#</span> +<a name="_GetAtomTripletID-"></a> 463 <span class="k">sub </span><span class="m">_GetAtomTripletID</span> <span class="s">{</span> + 464 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ATx</span><span class="cm">,</span> <span class="i">$Dyz</span><span class="cm">,</span> <span class="i">$ATy</span><span class="cm">,</span> <span class="i">$Dxz</span><span class="cm">,</span> <span class="i">$ATz</span><span class="cm">,</span> <span class="i">$Dxy</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 465 <span class="k">my</span><span class="s">(</span><span class="i">$AtomTripletID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> + 466 + 467 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 468 + 469 <span class="i">@AtomIDs</span> = <span class="k">sort</span><span class="s">(</span><span class="q">"${ATx}-D${Dyz}"</span><span class="cm">,</span> <span class="q">"${ATy}-D${Dxz}"</span><span class="cm">,</span> <span class="q">"${ATz}-D${Dxy}"</span><span class="s">)</span><span class="sc">;</span> + 470 <span class="i">$AtomTripletID</span> = <span class="k">join</span> <span class="q">"-"</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="sc">;</span> + 471 + 472 <span class="k">return</span> <span class="i">$AtomTripletID</span><span class="sc">;</span> + 473 <span class="s">}</span> + 474 + 475 <span class="c"># Set final fingerpritns vector...</span> + 476 <span class="c">#</span> +<a name="_SetFinalFingerprints-"></a> 477 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> + 478 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 479 <span class="k">my</span><span class="s">(</span><span class="i">$AtomTripletID</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> + 480 + 481 <span class="c"># Mark successful generation of fingerprints...</span> + 482 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> + 483 + 484 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 485 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTripletsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 486 + 487 <span class="k">for</span> <span class="i">$AtomTripletID</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTripletsCount</span>}}<span class="s">)</span> <span class="s">{</span> + 488 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTripletsIDs</span>}}<span class="cm">,</span> <span class="i">$AtomTripletID</span><span class="sc">;</span> + 489 <span class="i">$Value</span> = <span class="i">$This</span>->{<span class="w">AtomTripletsCount</span>}{<span class="i">$AtomTripletID</span>}<span class="sc">;</span> + 490 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span> + 491 <span class="s">}</span> + 492 + 493 <span class="c"># Add AtomTripletsIDs and values to fingerprint vector...</span> + 494 <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">AtomTripletsIDs</span>}}<span class="s">)</span><span class="sc">;</span> + 495 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> + 496 + 497 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 498 <span class="s">}</span> + 499 + 500 <span class="c"># Get atom triplet IDs corresponding to atom triplets count values in fingerprint</span> + 501 <span class="c"># vector as an array or reference to an array...</span> + 502 <span class="c">#</span> + 503 <span class="c"># AtomTripletIDs list differes in molecules and is generated during finalization</span> + 504 <span class="c"># of fingerprints to make sure the fingerprint vector containing count values</span> + 505 <span class="c"># matches the atom triplets array.</span> + 506 <span class="c">#</span> +<a name="GetAtomTripletIDs-"></a> 507 <span class="k">sub </span><span class="m">GetAtomTripletIDs</span> <span class="s">{</span> + 508 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 509 + 510 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTripletsIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomTripletsIDs</span>}}<span class="sc">;</span> + 511 <span class="s">}</span> + 512 + 513 <span class="c"># Cache appropriate molecule data...</span> + 514 <span class="c">#</span> +<a name="_SetupMoleculeDataCache-"></a> 515 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> + 516 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 517 + 518 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span> + 519 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span> + 520 <span class="c">#</span> + 521 <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> + 522 + 523 <span class="c"># Get all atom IDs...</span> + 524 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> + 525 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 526 <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> + 527 + 528 <span class="c"># Set AtomIndex to AtomID hash...</span> + 529 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 530 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> } = <span class="i">@AtomIDs</span><span class="sc">;</span> + 531 + 532 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 533 <span class="s">}</span> + 534 + 535 <span class="c"># Set atomic invariants to use for atom identifiers...</span> + 536 <span class="c">#</span> +<a name="SetAtomicInvariantsToUse-"></a> 537 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> + 538 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 539 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$SpecifiedAtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomicInvariantValue</span><span class="cm">,</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span> + 540 + 541 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> + 542 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> + 543 <span class="k">return</span><span class="sc">;</span> + 544 <span class="s">}</span> + 545 + 546 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> + 547 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> + 548 + 549 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 550 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 551 + 552 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> + 553 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> + 554 <span class="s">}</span> + 555 <span class="k">else</span> <span class="s">{</span> + 556 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> + 557 <span class="s">}</span> + 558 + 559 <span class="c"># Make sure specified AtomicInvariants are valid...</span> + 560 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> + 561 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 562 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> + 563 <span class="s">}</span> + 564 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> + 565 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> + 566 <span class="s">}</span> + 567 + 568 <span class="c"># Set atomic invariants to use...</span> + 569 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 570 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> + 571 + 572 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 573 <span class="s">}</span> + 574 + 575 <span class="c"># Set functional classes to use for atom identifiers...</span> + 576 <span class="c">#</span> +<a name="SetFunctionalClassesToUse-"></a> 577 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> + 578 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 579 <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">$FunctionalClass</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="cm">,</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span> + 580 + 581 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> + 582 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> + 583 <span class="k">return</span><span class="sc">;</span> + 584 <span class="s">}</span> + 585 + 586 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 587 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> + 588 <span class="k">return</span><span class="sc">;</span> + 589 <span class="s">}</span> + 590 + 591 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> + 592 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> + 593 + 594 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 595 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 596 + 597 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> + 598 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> + 599 <span class="s">}</span> + 600 <span class="k">else</span> <span class="s">{</span> + 601 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> + 602 <span class="s">}</span> + 603 + 604 <span class="c"># Make sure specified FunctionalClasses are valid...</span> + 605 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> + 606 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedFunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 607 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> + 608 <span class="s">}</span> + 609 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> + 610 <span class="s">}</span> + 611 + 612 <span class="c"># Set functional classes to use...</span> + 613 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 614 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> + 615 + 616 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 617 <span class="s">}</span> + 618 + 619 <span class="c"># Initialize atom indentifier type information...</span> + 620 <span class="c">#</span> + 621 <span class="c"># Current supported values:</span> + 622 <span class="c">#</span> + 623 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span> + 624 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> + 625 <span class="c">#</span> +<a name="_InitializeAtomIdentifierTypeInformation-"></a> 626 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> + 627 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 628 + 629 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 630 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 631 <span class="s">}</span> + 632 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 633 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 634 <span class="s">}</span> + 635 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> + 636 <span class="c"># Nothing to do for now...</span> + 637 <span class="s">}</span> + 638 <span class="k">else</span> <span class="s">{</span> + 639 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> + 640 <span class="s">}</span> + 641 + 642 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 643 <span class="s">}</span> + 644 + 645 <span class="c"># Initialize atomic invariants atom types to use for generating atom IDs in atom triplets...</span> + 646 <span class="c">#</span> + 647 <span class="c"># Let:</span> + 648 <span class="c"># AS = Atom symbol corresponding to element symbol</span> + 649 <span class="c">#</span> + 650 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 651 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 652 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 653 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 654 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 655 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 656 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> + 657 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> + 658 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> + 659 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> + 660 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> + 661 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> + 662 <span class="c">#</span> + 663 <span class="c"># ATx = Atomic invariants atom type for atom x</span> + 664 <span class="c"># ATy = Atomic invariants atom type for atom y</span> + 665 <span class="c"># ATz = Atomic invariants atom type for atom z</span> + 666 <span class="c">#</span> + 667 <span class="c"># Dxy = Distance between Px and Py</span> + 668 <span class="c"># Dxz = Distance between Px and Pz</span> + 669 <span class="c"># Dyz = Distance between Py and Pz</span> + 670 <span class="c">#</span> + 671 <span class="c"># Then:</span> + 672 <span class="c">#</span> + 673 <span class="c"># Atom triplet AtomID generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> + 674 <span class="c">#</span> + 675 <span class="c"># AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></span> + 676 <span class="c">#</span> + 677 <span class="c"># Toplogical atom triplet ID between atom IDs ATx, ATy and ATz corresponds to:</span> + 678 <span class="c">#</span> + 679 <span class="c"># ATx-Dyz-ATy-Dxz-ATz-Dxy</span> + 680 <span class="c">#</span> + 681 <span class="c"># Except for AS which is a required atomic invariant in atom triplet AtomIDs, all other atomic invariants are</span> + 682 <span class="c"># optional. Default atomic invariants used for AtomID are: AS, X<n>, BO<n>, H<n>, FC<+n/-n>.</span> + 683 <span class="c"># AtomID specification doesn't include atomic invariants with zero or undefined values.</span> + 684 <span class="c">#</span> + 685 <span class="c"># Examples of atom triplet AtomIDs:</span> + 686 <span class="c">#</span> + 687 <span class="c"># O.X1.BO1.H1 - Hydroxyl oxygen in carboxylate with attached hydrogen and no explicit charge</span> + 688 <span class="c"># O.X1.BO1.FC-1 - Hydroxyl ozygen in carboxylate with explicit negative charge</span> + 689 <span class="c"># O.X1.BO2 - Carbonyl oxygen in carboxylate with double bond to carbon</span> + 690 <span class="c"># O.X2.BO2 - Hydroxyl ozygen in carboxylate attached to carbonyl carbon and another heavy atom</span> + 691 <span class="c">#</span> + 692 <span class="c"># C.X2.BO3.H1.Ar - Aromatic carbon</span> + 693 <span class="c">#</span> +<a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 694 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> + 695 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 696 + 697 <span class="c"># Default atomic invariants to use for generating atom triplet atom IDs: AS, X, BO, H, FC</span> + 698 <span class="c">#</span> + 699 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 700 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span> + 701 + 702 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 703 <span class="s">}</span> + 704 + 705 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> + 706 <span class="c"># class, to use for generating atom identifiers...</span> + 707 <span class="c">#</span> + 708 <span class="c"># Let:</span> + 709 <span class="c"># HBD: HydrogenBondDonor</span> + 710 <span class="c"># HBA: HydrogenBondAcceptor</span> + 711 <span class="c"># PI : PositivelyIonizable</span> + 712 <span class="c"># NI : NegativelyIonizable</span> + 713 <span class="c"># Ar : Aromatic</span> + 714 <span class="c"># Hal : Halogen</span> + 715 <span class="c"># H : Hydrophobic</span> + 716 <span class="c"># RA : RingAtom</span> + 717 <span class="c"># CA : ChainAtom</span> + 718 <span class="c">#</span> + 719 <span class="c"># Then:</span> + 720 <span class="c">#</span> + 721 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> + 722 <span class="c">#</span> + 723 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> + 724 <span class="c">#</span> + 725 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> + 726 <span class="c">#</span> + 727 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> + 728 <span class="c">#</span> + 729 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> + 730 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> + 731 <span class="c"># PositivelyIonizable: +, NH2</span> + 732 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> + 733 <span class="c">#</span> +<a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 734 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> + 735 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 736 + 737 <span class="c"># Default functional class atom typess to use for generating atom identifiers</span> + 738 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span> + 739 <span class="c">#</span> + 740 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 741 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> + 742 + 743 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 744 <span class="s">}</span> + 745 + 746 <span class="c"># Clear cached molecule data...</span> + 747 <span class="c">#</span> +<a name="_ClearMoleculeDataCache-"></a> 748 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> + 749 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 750 + 751 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 752 + 753 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 754 <span class="s">}</span> + 755 + 756 <span class="c"># Return a string containg data for TopologicalAtomTripletsFingerprints object...</span> + 757 <span class="c">#</span> +<a name="StringifyTopologicalAtomTripletsFingerprints-"></a> 758 <span class="k">sub </span><span class="m">StringifyTopologicalAtomTripletsFingerprints</span> <span class="s">{</span> + 759 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 760 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span> + 761 + 762 <span class="c"># Type of fingerprint...</span> + 763 <span class="i">$FingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomIdentifierType: $This->{AtomIdentifierType}"</span><span class="sc">;</span> + 764 + 765 <span class="c"># Min and max distance...</span> + 766 <span class="i">$FingerprintsString</span> .= <span class="q">"; MinDistance: $This->{MinDistance}; MaxDistance: $This->{MaxDistance}; UseTriangleInequality: "</span> . <span class="s">(</span><span class="i">$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> + 767 + 768 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 769 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomicInvariants</span><span class="s">)</span><span class="sc">;</span> + 770 + 771 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 772 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 773 + 774 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> + 775 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> + 776 <span class="s">}</span> + 777 + 778 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</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> + 779 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> + 780 <span class="i">$FingerprintsString</span> .= <span class="q">"; AvailableAtomicInvariants: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariants</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> + 781 <span class="s">}</span> + 782 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 783 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> + 784 + 785 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 786 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 787 + 788 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> + 789 <span class="k">push</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">"$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}"</span><span class="sc">;</span> + 790 <span class="s">}</span> + 791 + 792 <span class="i">$FingerprintsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</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> + 793 <span class="i">$FingerprintsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> + 794 <span class="i">$FingerprintsString</span> .= <span class="q">"; AvailableFunctionalClasses: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClasses</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> + 795 <span class="s">}</span> + 796 + 797 <span class="c"># Total number of atom triplets...</span> + 798 <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> + 799 + 800 <span class="c"># FingerprintsVector...</span> + 801 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> + 802 + 803 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span> + 804 <span class="s">}</span> + 805 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>