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<html> <head> <title>MayaChemTools:Code:Fingerprints::TopologicalAtomPairsFingerprints.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::TopologicalAtomPairsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: TopologicalAtomPairsFingerprints.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> 5 <span class="c"># $Revision: 1.30 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">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">'StringifyTopologicalAtomPairsFingerprints'</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">$This</span><span class="i">->_InitializeTopologicalAtomPairsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 68 69 <span class="i">$This</span><span class="i">->_InitializeTopologicalAtomPairsFingerprintsProperties</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">$This</span><span class="sc">;</span> 72 <span class="s">}</span> 73 74 <span class="c"># Initialize object data...</span> 75 <span class="c">#</span> <a name="_InitializeTopologicalAtomPairsFingerprints-"></a> 76 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomPairsFingerprints</span> <span class="s">{</span> 77 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>->{<span class="w">Type</span>} = <span class="q">'TopologicalAtomPairs'</span><span class="sc">;</span> 81 82 <span class="c"># Type of vector...</span> 83 <span class="i">$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">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span> 91 92 <span class="c"># Atom identifier type to use for atom IDs in atom pairs...</span> 93 <span class="c">#</span> 94 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span> 95 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span> 96 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> 97 <span class="c">#</span> 98 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> 99 100 <span class="c"># Atom types assigned to each heavy atom...</span> 101 <span class="c">#</span> 102 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 103 104 <span class="c"># All atom pairs between minimum and maximum distance...</span> 105 <span class="c">#</span> 106 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 107 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 108 <span class="s">}</span> 109 110 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 111 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 112 <span class="c">#Class name...</span> 113 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 114 <span class="s">}</span> 115 116 <span class="c"># Initialize object properties....</span> <a name="_InitializeTopologicalAtomPairsFingerprintsProperties-"></a> 117 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomPairsFingerprintsProperties</span> <span class="s">{</span> 118 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 119 120 <span class="k">my</span><span class="s">(</span><span class="i">$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> 121 <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> 122 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 123 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 124 <span class="s">}</span> 125 126 <span class="c"># Make sure molecule object was specified...</span> 127 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> 128 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> 129 <span class="s">}</span> 130 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> 131 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."</span><span class="sc">;</span> 132 <span class="s">}</span> 133 134 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 135 136 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 137 <span class="s">}</span> 138 139 <span class="c"># Set minimum distance for atom pairs...</span> 140 <span class="c">#</span> <a name="SetMinDistance-"></a> 141 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span> 142 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 143 144 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 145 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> 146 <span class="s">}</span> 147 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> 148 149 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 150 <span class="s">}</span> 151 152 <span class="c"># Set maximum distance for atom pairs...</span> 153 <span class="c">#</span> <a name="SetMaxDistance-"></a> 154 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span> 155 <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> 156 157 <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> 158 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span> 159 <span class="s">}</span> 160 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span> 161 162 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 163 <span class="s">}</span> 164 165 <span class="c"># Set atom identifier type..</span> 166 <span class="c">#</span> <a name="SetAtomIdentifierType-"></a> 167 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> 168 <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> 169 170 <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> 171 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes."</span><span class="sc">;</span> 172 <span class="s">}</span> 173 174 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> 175 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SeAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span> 176 <span class="s">}</span> 177 178 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> 179 180 <span class="c"># Initialize atom identifier type information...</span> 181 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 182 183 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 184 <span class="s">}</span> 185 186 <span class="c"># Generate fingerprints description...</span> 187 <span class="c">#</span> <a name="GetDescription-"></a> 188 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> 189 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 190 191 <span class="c"># Is description explicity set?</span> 192 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> 193 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> 194 <span class="s">}</span> 195 196 <span class="c"># Generate fingerprints description...</span> 197 198 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomIdentifierType}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"</span><span class="sc">;</span> 199 <span class="s">}</span> 200 201 <span class="c"># Generate topological atom pairs [ Ref 57, Ref 59, Ref 72 ] fingerprints...</span> 202 <span class="c">#</span> 203 <span class="c"># Methodology:</span> 204 <span class="c"># . Generate a distance matrix.</span> 205 <span class="c"># . Assign atom types to all the atoms.</span> 206 <span class="c"># . Using distance matrix and atom types, count occurrence of</span> 207 <span class="c"># unique atom pairs within specified distance range - It corresponds to the</span> 208 <span class="c"># correlation-vector for the atom pairs.</span> 209 <span class="c">#</span> 210 <span class="c"># Notes:</span> 211 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span> 212 <span class="c">#</span> <a name="GenerateFingerprints-"></a> 213 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> 214 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 215 216 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 217 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateTopologicalAtomPairsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."</span><span class="sc">;</span> 218 <span class="s">}</span> 219 220 <span class="c"># Cache appropriate molecule data...</span> 221 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 222 223 <span class="c"># Generate distance matrix...</span> 224 <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> 225 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't generate distance matrix..."</span><span class="sc">;</span> 226 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 227 <span class="s">}</span> 228 229 <span class="c"># Assign atom types to all heavy atoms...</span> 230 <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> 231 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."</span><span class="sc">;</span> 232 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 233 <span class="s">}</span> 234 235 <span class="c"># Intialize values of toplogical atom pairs...</span> 236 <span class="i">$This</span><span class="i">->_InitializeToplogicalAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 237 238 <span class="c"># Count atom pairs...</span> 239 <span class="i">$This</span><span class="i">->_GenerateAndCountAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 240 241 <span class="c"># Set final fingerprints...</span> 242 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 243 244 <span class="c"># Clear cached molecule data...</span> 245 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 246 247 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 248 <span class="s">}</span> 249 250 <span class="c"># Setup distance matrix...</span> 251 <span class="c">#</span> <a name="_SetupDistanceMatrix-"></a> 252 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span> 253 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 254 255 <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> 256 257 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span> 258 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 259 <span class="s">}</span> 260 261 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 262 <span class="s">}</span> 263 264 <span class="c"># Assign appropriate atom types to all heavy atoms...</span> 265 <span class="c">#</span> <a name="_AssignAtomTypes-"></a> 266 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span> 267 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 268 <span class="k">my</span><span class="s">(</span><span class="i">$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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 269 270 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 271 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span> 272 273 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span> 274 275 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> 276 <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> 277 <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> 278 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 279 <span class="s">}</span> 280 281 <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> 282 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 283 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 284 <span class="s">}</span> 285 286 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 287 <span class="i">$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> 288 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 289 <span class="s">}</span> 290 291 <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> 292 <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> 293 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 294 <span class="s">}</span> 295 296 <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> 297 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 298 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 299 <span class="s">}</span> 300 301 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 302 <span class="i">$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> 303 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 304 <span class="s">}</span> 305 <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> 306 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 307 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 308 <span class="s">}</span> 309 310 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 311 <span class="i">$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">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">0</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> 312 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 313 <span class="s">}</span> 314 315 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 316 <span class="i">$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> 317 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 318 <span class="s">}</span> 319 320 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_AssignAtomTypes: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 321 <span class="s">}</span> 322 323 <span class="c"># Assign atom types...</span> 324 <span class="i">$SpecifiedAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 325 326 <span class="c"># Make sure atom types assignment is successful...</span> 327 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 328 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 329 <span class="s">}</span> 330 331 <span class="c"># Collect assigned atom types...</span> 332 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> 333 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 334 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 335 <span class="s">}</span> 336 <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> 337 <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> 338 <span class="s">}</span> 339 340 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 341 <span class="s">}</span> 342 343 <span class="c"># Initialize topological atom pairs between specified distance range...</span> 344 <span class="c">#</span> <a name="_InitializeToplogicalAtomPairs-"></a> 345 <span class="k">sub </span><span class="m">_InitializeToplogicalAtomPairs</span> <span class="s">{</span> 346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 347 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="s">)</span><span class="sc">;</span> 348 349 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 350 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 351 352 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> 353 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 354 <span class="s">}</span> 355 356 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 357 <span class="s">}</span> 358 359 <span class="c"># Count atom pairs between mininum and maximum distance at each</span> 360 <span class="c"># distance using distance matrix and atom types assiged to each heavy</span> 361 <span class="c"># atom.</span> 362 <span class="c">#</span> 363 <span class="c"># Notes:</span> 364 <span class="c"># . The row and column indices of distance matrix correspond to atom indices.</span> 365 <span class="c"># . Distance value of BigNumber implies the atom is not connected to any other atom.</span> 366 <span class="c"># . Due to symmetric nature of distance matrix, only upper or lower triangular matrix</span> 367 <span class="c"># needs to be processed during identification and count of atom pairs.</span> 368 <span class="c">#</span> <a name="_GenerateAndCountAtomPairs-"></a> 369 <span class="k">sub </span><span class="m">_GenerateAndCountAtomPairs</span> <span class="s">{</span> 370 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 371 372 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="cm">,</span> <span class="i">$CountIncrement</span><span class="s">)</span><span class="sc">;</span> 373 374 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span> 375 <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 376 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span> 377 378 <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> 379 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span> 380 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> 381 <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span> 382 <span class="s">}</span> 383 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="sc">;</span> 384 385 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="s">(</span><span class="i">$RowIndex</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> 386 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$ColIndex</span>}<span class="sc">;</span> 387 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> 388 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> 389 <span class="s">}</span> 390 <span class="i">$Distance</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> 391 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance</span> < <span class="i">$This</span>->{<span class="w">MinDistance</span>} || <span class="i">$Distance</span> > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> 392 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> 393 <span class="s">}</span> 394 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="sc">;</span> 395 396 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType1</span> <span class="k">le</span> <span class="i">$AtomType2</span><span class="s">)</span> <span class="s">{</span> 397 <span class="i">$This</span><span class="i">->_SetAtomPairsCount</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span><span class="sc">;</span> 398 <span class="s">}</span> 399 <span class="k">else</span> <span class="s">{</span> 400 <span class="i">$This</span><span class="i">->_SetAtomPairsCount</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="s">)</span><span class="sc">;</span> 401 <span class="s">}</span> 402 <span class="s">}</span> 403 <span class="s">}</span> 404 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 405 <span class="s">}</span> 406 407 <span class="c"># Set atom paris count for a specific atom ID pair at a specific distance...</span> 408 <span class="c">#</span> <a name="_SetAtomPairsCount-"></a> 409 <span class="k">sub </span><span class="m">_SetAtomPairsCount</span> <span class="s">{</span> 410 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 411 412 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}<span class="s">)</span> <span class="s">{</span> 413 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 414 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} = <span class="n">1</span><span class="sc">;</span> 415 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 416 <span class="s">}</span> 417 418 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="s">)</span> <span class="s">{</span> 419 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="n">1</span><span class="sc">;</span> 420 <span class="s">}</span> 421 <span class="k">else</span> <span class="s">{</span> 422 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} = <span class="n">1</span><span class="sc">;</span> 423 <span class="s">}</span> 424 425 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 426 <span class="s">}</span> 427 428 <span class="c"># Set final fingerpritns vector...</span> 429 <span class="c">#</span> <a name="_SetFinalFingerprints-"></a> 430 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> 431 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 432 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> 433 434 <span class="c"># Mark successful generation of fingerprints...</span> 435 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> 436 437 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 438 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 439 440 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span> 441 <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} <span class="s">)</span> <span class="s">{</span> 442 <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span> 443 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="cm">,</span> <span class="q">"${AtomType1}-D${Distance}-${AtomType2}"</span><span class="sc">;</span> 444 <span class="i">$Value</span> = <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span> 445 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span> 446 <span class="s">}</span> 447 <span class="s">}</span> 448 <span class="s">}</span> 449 450 <span class="c"># Add AtomPairsIDs and values to fingerprint vector...</span> 451 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="s">)</span><span class="sc">;</span> 452 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span> 453 454 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 455 <span class="s">}</span> 456 457 <span class="c"># Get atom pair IDs corresponding to atom pairs count values in fingerprint</span> 458 <span class="c"># vector as an array or reference to an array...</span> 459 <span class="c">#</span> 460 <span class="c"># AtomPairIDs list differes in molecules and is generated during finalization</span> 461 <span class="c"># of fingerprints to make sure the fingerprint vector containing count values</span> 462 <span class="c"># matches the atom pairs array.</span> 463 <span class="c">#</span> <a name="GetAtomPairIDs-"></a> 464 <span class="k">sub </span><span class="m">GetAtomPairIDs</span> <span class="s">{</span> 465 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 466 467 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="sc">;</span> 468 <span class="s">}</span> 469 470 <span class="c"># Cache appropriate molecule data...</span> 471 <span class="c">#</span> <a name="_SetupMoleculeDataCache-"></a> 472 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> 473 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 474 475 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span> 476 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span> 477 <span class="c">#</span> 478 <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> 479 480 <span class="c"># Get all atom IDs...</span> 481 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 482 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 483 <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> 484 485 <span class="c"># Set AtomIndex to AtomID hash...</span> 486 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 487 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> } = <span class="i">@AtomIDs</span><span class="sc">;</span> 488 489 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 490 <span class="s">}</span> 491 492 <span class="c"># Clear cached molecule data...</span> 493 <span class="c">#</span> <a name="_ClearMoleculeDataCache-"></a> 494 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> 495 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 496 497 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 498 499 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 500 <span class="s">}</span> 501 502 <span class="c"># Set atomic invariants to use for atom identifiers...</span> 503 <span class="c">#</span> <a name="SetAtomicInvariantsToUse-"></a> 504 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> 505 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 506 <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> 507 508 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 509 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> 510 <span class="k">return</span><span class="sc">;</span> 511 <span class="s">}</span> 512 513 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 514 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 515 516 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 517 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 518 519 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 520 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> 521 <span class="s">}</span> 522 <span class="k">else</span> <span class="s">{</span> 523 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 524 <span class="s">}</span> 525 526 <span class="c"># Make sure specified AtomicInvariants are valid...</span> 527 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> 528 <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> 529 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> 530 <span class="s">}</span> 531 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> 532 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> 533 <span class="s">}</span> 534 535 <span class="c"># Set atomic invariants to use...</span> 536 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 537 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> 538 539 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 540 <span class="s">}</span> 541 542 <span class="c"># Set functional classes to use for atom identifiers...</span> 543 <span class="c">#</span> <a name="SetFunctionalClassesToUse-"></a> 544 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 546 <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> 547 548 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 549 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> 550 <span class="k">return</span><span class="sc">;</span> 551 <span class="s">}</span> 552 553 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 554 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 555 <span class="k">return</span><span class="sc">;</span> 556 <span class="s">}</span> 557 558 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 559 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 560 561 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 562 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 563 564 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 565 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> 566 <span class="s">}</span> 567 <span class="k">else</span> <span class="s">{</span> 568 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 569 <span class="s">}</span> 570 571 <span class="c"># Make sure specified FunctionalClasses are valid...</span> 572 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> 573 <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> 574 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> 575 <span class="s">}</span> 576 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> 577 <span class="s">}</span> 578 579 <span class="c"># Set functional classes to use...</span> 580 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 581 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> 582 583 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 584 <span class="s">}</span> 585 586 <span class="c"># Initialize atom indentifier type information...</span> 587 <span class="c">#</span> 588 <span class="c"># Current supported values:</span> 589 <span class="c">#</span> 590 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span> 591 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> 592 <span class="c">#</span> <a name="_InitializeAtomIdentifierTypeInformation-"></a> 593 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> 594 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 595 596 <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> 597 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 598 <span class="s">}</span> 599 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 600 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 601 <span class="s">}</span> 602 <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> 603 <span class="c"># Nothing to do for now...</span> 604 <span class="s">}</span> 605 <span class="k">else</span> <span class="s">{</span> 606 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 607 <span class="s">}</span> 608 609 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 610 <span class="s">}</span> 611 612 <span class="c"># Initialize atomic invariants atom types to use for generating atom identifiers...</span> 613 <span class="c">#</span> 614 <span class="c"># Let:</span> 615 <span class="c"># AS = Atom symbol corresponding to element symbol</span> 616 <span class="c">#</span> 617 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> 618 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 619 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> 620 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 621 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 622 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 623 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> 624 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> 625 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> 626 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> 627 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> 628 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> 629 <span class="c">#</span> 630 <span class="c"># AtomTypeIDx = Atomic invariants atom type for atom x</span> 631 <span class="c"># AtomTypeIDy = Atomic invariants atom type for atom y</span> 632 <span class="c"># Dn = Topological distance between atom x and y</span> 633 <span class="c">#</span> 634 <span class="c"># Then:</span> 635 <span class="c">#</span> 636 <span class="c"># Atom pair AtomID generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> 637 <span class="c">#</span> 638 <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> 639 <span class="c">#</span> 640 <span class="c"># AtomPairID corresponds to:</span> 641 <span class="c">#</span> 642 <span class="c"># AtomTypeIDx-D<n>-AtomTypeIDy</span> 643 <span class="c">#</span> 644 <span class="c"># Except for AS which is a required atomic invariant in atom pair AtomIDs, all other atomic invariants are</span> 645 <span class="c"># optional. Default atomic invariants used for AtomID are: AS, X<n>, BO<n>, H<n>, FC<+n/-n>.</span> 646 <span class="c"># AtomID specification doesn't include atomic invariants with zero or undefined values.</span> 647 <span class="c">#</span> 648 <span class="c"># Examples of atom pair AtomIDs:</span> 649 <span class="c">#</span> 650 <span class="c"># O.X1.BO1.H1 - Hydroxyl oxygen in carboxylate with attached hydrogen and no explicit charge</span> 651 <span class="c"># O.X1.BO1.FC-1 - Hydroxyl ozygen in carboxylate with explicit negative charge</span> 652 <span class="c"># O.X1.BO2 - Carbonyl oxygen in carboxylate with double bond to carbon</span> 653 <span class="c"># O.X2.BO2 - Hydroxyl ozygen in carboxylate attached to carbonyl carbon and another heavy atom</span> 654 <span class="c">#</span> 655 <span class="c"># C.X2.BO3.H1.Ar - Aromatic carbon</span> 656 <span class="c">#</span> 657 <span class="c"># Examples of AtomPairIDs:</span> 658 <span class="c">#</span> 659 <span class="c"># C.X2.BO2.H3-D1-O.X1.BO1 - Carbon with two heavy atom neighbors attached to oxygen at bond distance 1(methanol)</span> 660 <span class="c">#</span> 661 <span class="c"># C.X2.BO3.H1.Ar-D3-C.X2.BO3.H1.Ar - Two aromatic carbons at bond distance 3 where each carbon has</span> 662 <span class="c"># two heavy atom neighbors and bond order of 3 (benzene)</span> 663 <span class="c">#</span> <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 664 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> 665 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 666 667 <span class="c"># Default atomic invariants to use for generating atom neighborhood atom IDs: AS, X, BO, H, FC</span> 668 <span class="c">#</span> 669 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 670 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span> 671 672 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 673 <span class="s">}</span> 674 675 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> 676 <span class="c"># class, to use for generating atom identifiers...</span> 677 <span class="c">#</span> 678 <span class="c"># Let:</span> 679 <span class="c"># HBD: HydrogenBondDonor</span> 680 <span class="c"># HBA: HydrogenBondAcceptor</span> 681 <span class="c"># PI : PositivelyIonizable</span> 682 <span class="c"># NI : NegativelyIonizable</span> 683 <span class="c"># Ar : Aromatic</span> 684 <span class="c"># Hal : Halogen</span> 685 <span class="c"># H : Hydrophobic</span> 686 <span class="c"># RA : RingAtom</span> 687 <span class="c"># CA : ChainAtom</span> 688 <span class="c">#</span> 689 <span class="c"># Then:</span> 690 <span class="c">#</span> 691 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> 692 <span class="c">#</span> 693 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> 694 <span class="c">#</span> 695 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> 696 <span class="c">#</span> 697 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> 698 <span class="c">#</span> 699 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> 700 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> 701 <span class="c"># PositivelyIonizable: +, NH2</span> 702 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> 703 <span class="c">#</span> <a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 704 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> 705 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 706 707 <span class="c"># Default functional class atom typess to use for generating atom identifiers</span> 708 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span> 709 <span class="c">#</span> 710 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 711 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> 712 713 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 714 <span class="s">}</span> 715 716 <span class="c"># Return a string containg data for TopologicalAtomPairsFingerprints object...</span> 717 <span class="c">#</span> <a name="StringifyTopologicalAtomPairsFingerprints-"></a> 718 <span class="k">sub </span><span class="m">StringifyTopologicalAtomPairsFingerprints</span> <span class="s">{</span> 719 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 720 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span> 721 722 <span class="c"># Type of fingerprint...</span> 723 <span class="i">$FingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomIdentifierType: $This->{AtomIdentifierType}"</span><span class="sc">;</span> 724 725 <span class="c"># Min and max distance...</span> 726 <span class="i">$FingerprintsString</span> .= <span class="q">"; MinDistance: $This->{MinDistance}; MaxDistance: $This->{MaxDistance}"</span><span class="sc">;</span> 727 728 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 729 <span class="k">my</span><span class="s">(</span><span class="i">$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> 730 731 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 732 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 733 734 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> 735 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> 736 <span class="s">}</span> 737 738 <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> 739 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 740 <span class="i">$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> 741 <span class="s">}</span> 742 <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> 743 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> 744 745 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 746 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 747 748 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> 749 <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> 750 <span class="s">}</span> 751 752 <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> 753 <span class="i">$FingerprintsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 754 <span class="i">$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> 755 <span class="s">}</span> 756 757 <span class="c"># Total number of atom pairs...</span> 758 <span class="i">$FingerprintsString</span> .= <span class="q">"; NumOfAtomPairs: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 759 760 <span class="c"># FingerprintsVector...</span> 761 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> 762 763 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span> 764 <span class="s">}</span> 765 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>