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| author | deepakjadmin |
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| date | Thu, 15 Dec 2016 14:18:03 -0500 |
| parents | 73ae111cf86f |
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<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>