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<html> <head> <title>MayaChemTools:Code:Fingerprints::ExtendedConnectivityFingerprints.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::ExtendedConnectivityFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: ExtendedConnectivityFingerprints.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> 5 <span class="c"># $Revision: 1.39 $</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">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> 38 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span> 39 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span> 40 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span> 41 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span> 42 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span> 43 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span> 44 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span> 45 46 <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> 47 48 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> 49 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 50 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> 51 52 <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> 53 54 <span class="c"># Setup class variables...</span> 55 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> 56 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 57 58 <span class="c"># Overload Perl functions...</span> 59 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyExtendedConnectivityFingerprints'</span><span class="sc">;</span> 60 61 <span class="c"># Class constructor...</span> <a name="new-"></a> 62 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 63 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 64 65 <span class="c"># Initialize object...</span> 66 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 67 <span class="k">bless</span> <span class="i">$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> 68 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 69 70 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 71 72 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 73 <span class="s">}</span> 74 75 <span class="c"># Initialize object data...</span> 76 <span class="c">#</span> <a name="_InitializeExtendedConnectivityFingerprints-"></a> 77 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprints</span> <span class="s">{</span> 78 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 79 80 <span class="c"># Type of fingerprint to generate:</span> 81 <span class="c">#</span> 82 <span class="c"># ExtendedConnectivity - Set of integer identifiers corresponding to structurally unique features</span> 83 <span class="c"># ExtendedConnectivityCount - Set of integer identifiers corresponding to structurally unique features and their count</span> 84 <span class="c"># ExtendedConnectivityBits - A bit vector indicating presence/absence of structurally unique features</span> 85 <span class="c">#</span> 86 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivity'</span><span class="sc">;</span> 87 88 <span class="c"># Atomic neighborhoods radius for extended connectivity...</span> 89 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span> 90 91 <span class="c"># Size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...</span> 92 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="n">1024</span><span class="sc">;</span> 93 94 <span class="c"># Min and max size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...</span> 95 <span class="i">$This</span>->{<span class="w">MinSize</span>} = <span class="n">32</span><span class="sc">;</span> 96 <span class="i">$This</span>->{<span class="w">MaxSize</span>} = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span> 97 98 <span class="c"># Type of atom attributes to use for initial identifier assignment to non-hydrogen atoms</span> 99 <span class="c"># during the calculation of extended connectivity fingerprints [ Ref 48, Ref 52 ]...</span> 100 <span class="c">#</span> 101 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes,</span> 102 <span class="c"># DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,</span> 103 <span class="c"># TPSAAtomTypes, UFFAtomTypes</span> 104 <span class="c">#</span> 105 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> 106 107 <span class="c"># Random number generator to use during generation of fingerprints bit-vector</span> 108 <span class="c"># string: Perl CORE::rand or MayaChemTools MathUtil::random function.</span> 109 <span class="c">#</span> 110 <span class="c"># The random number generator implemented in MayaChemTools is a variant of</span> 111 <span class="c"># linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].</span> 112 <span class="c"># It is also referred to as Lehmer random number generator or Park-Miller</span> 113 <span class="c"># random number generator.</span> 114 <span class="c">#</span> 115 <span class="c"># Unlike Perl's core random number generator function rand, the random number</span> 116 <span class="c"># generator implemented in MayaChemTools, MathUtil::random, generates consistent</span> 117 <span class="c"># random values across different platformsfor a specific random seed and leads</span> 118 <span class="c"># to generation of portable fingerprints bit-vector strings.</span> 119 <span class="c">#</span> 120 <span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>} = <span class="n">1</span><span class="sc">;</span> 121 122 <span class="c"># Atom neighorhoods up to specified neighborhood radius...</span> 123 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 124 125 <span class="c"># Atom identifiers at different neighborhoods up to specified neighborhood radius...</span> 126 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 127 128 <span class="c"># Structurally unique atom identifiers at different neighborhoods up to specified neighborhood radius...</span> 129 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 130 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 131 132 <span class="c"># Unique atom identifiers at different neighborhoods up to specified neighborhood radius...</span> 133 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 134 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 135 136 <span class="c"># Structure feature information at different neighborhoods up to specified neighborhood</span> 137 <span class="c"># radius used during removal of atom indentifiers which are structually equivalent...</span> 138 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 139 <span class="s">}</span> 140 141 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 142 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 143 <span class="c">#Class name...</span> 144 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 145 <span class="s">}</span> 146 147 <span class="c"># Initialize object properties....</span> <a name="_InitializeExtendedConnectivityFingerprintsProperties-"></a> 148 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprintsProperties</span> <span class="s">{</span> 149 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 150 151 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> 152 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> 153 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 154 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 155 <span class="s">}</span> 156 157 <span class="c"># Make sure molecule object was specified...</span> 158 <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> 159 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> 160 <span class="s">}</span> 161 162 <span class="c"># Make sure AtomIdentifierType was specified...</span> 163 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> 164 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."</span><span class="sc">;</span> 165 <span class="s">}</span> 166 167 <span class="c"># Make sure it's power of 2...</span> 168 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span> 169 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 170 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Specified size value, $NamesAndValues{Size}, must be power of 2..."</span><span class="sc">;</span> 171 <span class="s">}</span> 172 <span class="s">}</span> 173 174 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span> 175 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 176 <span class="s">}</span> 177 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span> 178 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityCountFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 179 <span class="s">}</span> 180 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> 181 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityBitsFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 182 <span class="s">}</span> 183 <span class="k">else</span> <span class="s">{</span> 184 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeExtendedConnectivityFingerprintsProperties: Unknown ExtendedConnectivity fingerprints type: $This->{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits..."</span><span class="sc">;</span> 185 <span class="s">}</span> 186 187 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 188 <span class="s">}</span> 189 190 <span class="c"># Initialize extended connectivity fingerprints vector...</span> 191 <span class="c">#</span> <a name="_InitializeExtendedConnectivityFingerprintsVector-"></a> 192 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprintsVector</span> <span class="s">{</span> 193 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 194 195 <span class="c"># Type of vector...</span> 196 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> 197 198 <span class="c"># Type of FingerprintsVector...</span> 199 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'AlphaNumericalValues'</span><span class="sc">;</span> 200 201 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 202 203 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 204 <span class="s">}</span> 205 206 <span class="c"># Initialize extended connectivity count fingerprints vector...</span> 207 <span class="c">#</span> <a name="_InitializeExtendedConnectivityCountFingerprintsVector-"></a> 208 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityCountFingerprintsVector</span> <span class="s">{</span> 209 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 210 211 <span class="c"># Type of vector...</span> 212 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> 213 214 <span class="c"># Type of FingerprintsVector...</span> 215 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> 216 217 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 218 219 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 220 <span class="s">}</span> 221 222 <span class="c"># Initialize extended connectivity bit fingerprints vector...</span> 223 <span class="c">#</span> <a name="_InitializeExtendedConnectivityBitsFingerprintsBitVector-"></a> 224 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityBitsFingerprintsBitVector</span> <span class="s">{</span> 225 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 226 227 <span class="c"># Type of vector...</span> 228 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsBitVector'</span><span class="sc">;</span> 229 230 <span class="i">$This</span><span class="i">->_InitializeFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 231 232 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 233 <span class="s">}</span> 234 235 <span class="c"># Set type...</span> 236 <span class="c">#</span> <a name="SetType-"></a> 237 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span> 238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 239 240 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span> 241 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivity'</span><span class="sc">;</span><span class="sc">;</span> 242 <span class="s">}</span> 243 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span> 244 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivityCount'</span><span class="sc">;</span><span class="sc">;</span> 245 <span class="s">}</span> 246 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> 247 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivityBits'</span><span class="sc">;</span><span class="sc">;</span> 248 <span class="s">}</span> 249 <span class="k">else</span> <span class="s">{</span> 250 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Unknown ExtendedConnectivity fingerprints type: $This->{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits..."</span><span class="sc">;</span> 251 <span class="s">}</span> 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 253 <span class="s">}</span> 254 255 <span class="c"># Disable vector type change...</span> 256 <span class="c">#</span> <a name="SetVectorType-"></a> 257 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span> 258 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 259 260 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Can't change vector type..."</span><span class="sc">;</span> 261 262 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 263 <span class="s">}</span> 264 265 <span class="c"># Disable vector type change...</span> 266 <span class="c">#</span> <a name="SetFingerprintsVectorType-"></a> 267 <span class="k">sub </span><span class="m">SetFingerprintsVectorType</span> <span class="s">{</span> 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 269 270 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVectorType: Can't change fingerprints vector type..."</span><span class="sc">;</span> 271 272 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 273 <span class="s">}</span> 274 275 <span class="c"># Set intial atom identifier type..</span> 276 <span class="c">#</span> <a name="SetAtomIdentifierType-"></a> 277 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> 278 <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> 279 280 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> 281 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes."</span><span class="sc">;</span> 282 <span class="s">}</span> 283 284 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> 285 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span> 286 <span class="s">}</span> 287 288 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> 289 290 <span class="c"># Initialize identifier type information...</span> 291 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 292 293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 294 <span class="s">}</span> 295 296 <span class="c"># Set atom neighborhood radius...</span> 297 <span class="c">#</span> <a name="SetNeighborhoodRadius-"></a> 298 <span class="k">sub </span><span class="m">SetNeighborhoodRadius</span> <span class="s">{</span> 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 300 301 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 302 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> 303 <span class="s">}</span> 304 305 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span> 306 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span> 307 <span class="s">}</span> 308 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span> 309 310 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 311 <span class="s">}</span> 312 313 <span class="c"># Generate fingerprints description...</span> 314 <span class="c">#</span> <a name="GetDescription-"></a> 315 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> 316 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 317 318 <span class="c"># Is description explicity set?</span> 319 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> 320 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> 321 <span class="s">}</span> 322 323 <span class="c"># Generate fingerprints description...</span> 324 325 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomIdentifierType}:Radius$This->{NeighborhoodRadius}"</span><span class="sc">;</span> 326 <span class="s">}</span> 327 328 <span class="c"># Generate fingerprints...</span> 329 <span class="c">#</span> 330 <span class="c"># Methodology:</span> 331 <span class="c"># . Assign initial atom identfiers to all non-hydrogen atoms in the molecule</span> 332 <span class="c">#</span> 333 <span class="c"># . Remove duplicates from the initial identifiers and add them to list corresponding</span> 334 <span class="c"># to molecule fingerprint</span> 335 <span class="c">#</span> 336 <span class="c"># . For NeighborhoodRadius value of 0, just return the molecule fingerprint list</span> 337 <span class="c">#</span> 338 <span class="c"># . For each NeighborhoodRadius level</span> 339 <span class="c"># . For each non-hydrogen CentralAtom at this NeighborhoodRadius level</span> 340 <span class="c"># . For each non-hydrogen SuccessorNeighborAtom</span> 341 <span class="c"># . Collect (BondOrder AtomIdentifier) pair of values corresponding to</span> 342 <span class="c"># (CentralAtom SuccessorNeighborAtom) and add it to a list</span> 343 <span class="c">#</span> 344 <span class="c"># . Sort list containing (BondOrder AtomIdentifier) pairs first by BondOrder followed</span> 345 <span class="c"># by AtomIdendifiers to make these values graph invariant</span> 346 <span class="c"># . Generate a hash code for the values in the list</span> 347 <span class="c"># . Assign hash code as new atom identifier at the current NeighborhoodRadius level</span> 348 <span class="c"># . Save all atoms and bonds corresponding to the substructure involved in</span> 349 <span class="c"># generating the hash code to be used for identifying structural duplicate hash code</span> 350 <span class="c">#</span> 351 <span class="c"># . Add the new identifier to the molecule fingerprint list making sure it's not a duplicate</span> 352 <span class="c"># identifier</span> 353 <span class="c">#</span> 354 <span class="c"># Hash code atom identifier deduplication:</span> 355 <span class="c"># . Track/remove the identifier generated at higher neighborhood radius level</span> 356 <span class="c">#</span> 357 <span class="c"># Structural atom identifier deduplication:</span> 358 <span class="c"># . For equivalent atoms and bonds corresponding to substructure at a NeighborhoodRadius level,</span> 359 <span class="c"># track/remove the atom identifier with largest value</span> 360 <span class="c">#</span> 361 <span class="c">#</span> <a name="GenerateFingerprints-"></a> 362 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> 363 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 364 365 <span class="c"># Cache appropriate molecule data...</span> 366 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 367 368 <span class="c"># Assign intial atom identifers...</span> 369 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignInitialAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 370 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."</span><span class="sc">;</span> 371 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 372 <span class="s">}</span> 373 374 <span class="c"># Identify atom neighborhoods up to specified radius...</span> 375 <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 376 377 <span class="c"># Assign atom identifiers to central atoms considering atom neighborhoods at each</span> 378 <span class="c"># radius level...</span> 379 <span class="i">$This</span><span class="i">->_AssignAtomIdentifiersToAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 380 381 <span class="c"># Remove duplicates identifiers...</span> 382 <span class="i">$This</span><span class="i">->_RemoveDuplicateAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 383 384 <span class="c"># Set final fingerprints...</span> 385 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 386 387 <span class="c"># Clear cached molecule data...</span> 388 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 389 390 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 391 <span class="s">}</span> 392 393 <span class="c"># Assign appropriate initial atom identifiers...</span> 394 <span class="c">#</span> 395 <span class="c"># Generation of initial identifier for a specific atom involves:</span> 396 <span class="c"># . Values of the specified atom attributes are appended in a specific order to</span> 397 <span class="c"># generate an initial atom identifier string</span> 398 <span class="c"># . A 32 bit unsigned integer hash key, using TextUtil::HashCode function, is</span> 399 <span class="c"># generated for the atom indentifier and assigned to the atom as initial</span> 400 <span class="c"># atom identifier.</span> 401 <span class="c">#</span> <a name="_AssignInitialAtomIdentifiers-"></a> 402 <span class="k">sub </span><span class="m">_AssignInitialAtomIdentifiers</span> <span class="s">{</span> 403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 404 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$InitialAtomTypeString</span><span class="cm">,</span> <span class="i">$InitialAtomIdentifier</span><span class="s">)</span><span class="sc">;</span> 405 406 <span class="c"># Initialize atom identifiers...</span> 407 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 408 409 <span class="c"># Set up atom types...</span> 410 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span> 411 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span> 412 413 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> 414 <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> 415 <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> 416 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 417 <span class="s">}</span> 418 419 <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> 420 <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> 421 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 422 <span class="s">}</span> 423 424 <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> 425 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 426 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 427 <span class="s">}</span> 428 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 430 <span class="i">$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> 431 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 432 <span class="s">}</span> 433 434 <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> 435 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 436 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 437 <span class="s">}</span> 438 439 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 440 <span class="i">$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> 441 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 442 <span class="s">}</span> 443 444 <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> 445 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> 446 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 447 <span class="s">}</span> 448 449 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 450 <span class="i">$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">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">0</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> 451 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 452 <span class="s">}</span> 453 454 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 455 <span class="i">$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> 456 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 457 <span class="s">}</span> 458 459 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_AssignInitialAtomIdentifiers: Couldn't assign intial atom identifiers: InitialAtomIdentifierType $This->{AtomIdentifierType} is not supported..."</span><span class="sc">;</span> 460 <span class="s">}</span> 461 462 <span class="c"># Assign atom types...</span> 463 <span class="i">$SpecifiedAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 464 465 <span class="c"># Make sure atom types assignment is successful...</span> 466 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 467 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 468 <span class="s">}</span> 469 470 <span class="c"># Assign atom identifiers at radius 0...</span> 471 <span class="i">$Radius</span> = <span class="n">0</span><span class="sc">;</span> 472 <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> 473 <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> 474 475 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 476 <span class="i">$InitialAtomTypeString</span> = <span class="i">$AtomType</span> ? <span class="i">$AtomType</span> <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span> 477 478 <span class="i">$InitialAtomIdentifier</span> = <span class="i">TextUtil::HashCode</span><span class="s">(</span><span class="i">$InitialAtomTypeString</span><span class="s">)</span><span class="sc">;</span> 479 <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = <span class="i">$InitialAtomIdentifier</span><span class="sc">;</span> 480 <span class="s">}</span> 481 482 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 483 <span class="s">}</span> 484 485 <span class="c"># Initialize atom identifiers...</span> 486 <span class="c">#</span> <a name="_InitializeAtomIdentifiers-"></a> 487 <span class="k">sub </span><span class="m">_InitializeAtomIdentifiers</span> <span class="s">{</span> 488 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 489 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="s">)</span><span class="sc">;</span> 490 491 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span> 492 493 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 494 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span> 495 <span class="c"># Atom idenfiers key and value correspond to AtomID and AtomIdentifier</span> 496 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 497 498 <span class="c"># Unique and strcuturally unique idenfiers key and value correspond to AtomIdentifier and AtomID</span> 499 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 500 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 501 502 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 503 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 504 <span class="s">}</span> 505 506 <span class="s">}</span> 507 508 <span class="c"># Collect atom neighborhoods upto specified neighborhood radius...</span> 509 <span class="c">#</span> <a name="_GetAtomNeighborhoods-"></a> 510 <span class="k">sub </span><span class="m">_GetAtomNeighborhoods</span> <span class="s">{</span> 511 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 512 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 513 514 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 515 516 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span> 517 <span class="k">if</span> <span class="s">(</span><span class="i">$Radius</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 518 <span class="c"># At radius level 0, it's just the atoms...</span> 519 <span class="k">return</span><span class="sc">;</span> 520 <span class="s">}</span> 521 522 <span class="c"># Initialize neighborhood at different radii...</span> 523 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span> 524 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 525 <span class="s">}</span> 526 527 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 528 529 <span class="c"># Collect available atom neighborhoods at different at different neighborhood level for each atom...</span> 530 <span class="k">my</span><span class="s">(</span><span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span><span class="s">)</span><span class="sc">;</span> 531 532 <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> 533 <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> 534 <span class="i">$CurrentRadius</span> = <span class="n">0</span><span class="sc">;</span> 535 <span class="k">for</span> <span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 536 <span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$CurrentRadius</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span><span class="sc">;</span> 537 <span class="i">$CurrentRadius</span>++<span class="sc">;</span> 538 <span class="s">}</span> 539 <span class="s">}</span> 540 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 541 <span class="s">}</span> 542 543 <span class="c"># Assign atom identifiers to central atom at each neighborhood radius level...</span> 544 <span class="c">#</span> <a name="_AssignAtomIdentifiersToAtomNeighborhoods-"></a> 545 <span class="k">sub </span><span class="m">_AssignAtomIdentifiersToAtomNeighborhoods</span> <span class="s">{</span> 546 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 547 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$NextRadius</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">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$SuccessorAtom</span><span class="cm">,</span> <span class="i">$SuccessorAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$SuccessorAtomCount</span><span class="s">)</span><span class="sc">;</span> 548 549 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 550 <span class="k">return</span><span class="sc">;</span> 551 <span class="s">}</span> 552 553 <span class="c"># Go over the atom neighborhoods at each radius upto specified radius and assign atom</span> 554 <span class="c"># indentifiers using their connected successor atoms and their identifiers.</span> 555 <span class="c">#</span> 556 <span class="c"># For a neighborhood atom at a specified radius, the successor connected atoms correpond</span> 557 <span class="c"># to next radius level and the last set of neighorhood atoms don't have any successor connected</span> 558 <span class="c"># atoms. Additionally, radius level 0 just correspond to initial atom identifiers.</span> 559 <span class="c">#</span> 560 <span class="c"># So in order to process atom neighborhood upto specified radius level, the last atom neighborhood</span> 561 <span class="c"># doesn't need to be processed: it gets processed at previous radius level as successor connected</span> 562 <span class="c"># atoms.</span> 563 <span class="c">#</span> 564 <span class="j">RADIUS:</span> <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 565 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> 566 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 567 568 <span class="c"># Are there any available atom neighborhoods at this radius?</span> 569 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span> 570 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 571 <span class="s">}</span> 572 <span class="i">$NextRadius</span> = <span class="i">$Radius</span> + <span class="n">1</span><span class="sc">;</span> 573 574 <span class="c"># Go over neighborhood atoms and their successor connected atoms at this radius and collect</span> 575 <span class="c"># (BondOrder AtomIdentifier) values for bonded atom pairs. Additionally, keep track of atom and bonds</span> 576 <span class="c"># for the neighorhoods to remove identifieres generated from structurally duplicate features.</span> 577 <span class="c">#</span> 578 <span class="k">my</span><span class="s">(</span><span class="i">%BondOrdersAndAtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> 579 580 <span class="i">%BondOrdersAndAtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 581 <span class="i">$SuccessorAtomCount</span> = <span class="n">0</span><span class="sc">;</span> 582 583 <span class="j">NEIGHBORHOODS:</span> <span class="k">for</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}}<span class="s">)</span> <span class="s">{</span> 584 <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span>}<span class="sc">;</span> 585 586 <span class="c"># Any connected successors for the NeighborhoodAtom?</span> 587 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 588 <span class="k">next</span> <span class="j">NEIGHBORHOODS</span><span class="sc">;</span> 589 <span class="s">}</span> 590 <span class="j">SUCCESSORATOM:</span> <span class="k">for</span> <span class="i">$SuccessorAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 591 <span class="k">if</span> <span class="s">(</span><span class="i">$SuccessorAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 592 <span class="c"># Skip successor hydrogen atom...</span> 593 <span class="k">next</span> <span class="j">SUCCESSORATOM</span><span class="sc">;</span> 594 <span class="s">}</span> 595 <span class="i">$SuccessorAtomID</span> = <span class="i">$SuccessorAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 596 <span class="i">$SuccessorAtomCount</span>++<span class="sc">;</span> 597 598 <span class="i">$Bond</span> = <span class="i">$NeighborhoodAtom</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="i">$SuccessorAtom</span><span class="s">)</span><span class="sc">;</span> 599 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"1.5"</span> <span class="co">:</span> <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 600 601 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}<span class="s">)</span> <span class="s">{</span> 602 <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 603 <span class="s">}</span> 604 <span class="k">push</span> <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$SuccessorAtomID</span>}<span class="sc">;</span> 605 <span class="s">}</span> 606 <span class="s">}</span> 607 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SuccessorAtomCount</span><span class="s">)</span> <span class="s">{</span> 608 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 609 <span class="s">}</span> 610 <span class="c"># Assign a new atom identifier at the NextRadius level...</span> 611 <span class="i">$This</span><span class="i">->_AssignAtomIdentifierToAtomNeighborhood</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> \<span class="i">%BondOrdersAndAtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> 612 <span class="s">}</span> 613 <span class="s">}</span> 614 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 615 <span class="s">}</span> 616 617 <span class="c"># Generate and assign atom indentifier for AtomID using atom neighborhood at next radius level...</span> 618 <span class="c">#</span> <a name="_AssignAtomIdentifierToAtomNeighborhood-"></a> 619 <span class="k">sub </span><span class="m">_AssignAtomIdentifierToAtomNeighborhood</span> <span class="s">{</span> 620 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$BondOrdersAndAtomIdentifiersRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 621 <span class="k">my</span><span class="s">(</span><span class="i">$NextRadius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$SuccessorAtomIdentifier</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$AtomIdentifierString</span><span class="cm">,</span> <span class="i">@AtomIndentifiersInfo</span><span class="s">)</span><span class="sc">;</span> 622 623 <span class="i">$NextRadius</span> = <span class="i">$Radius</span> + <span class="n">1</span><span class="sc">;</span> 624 625 <span class="i">@AtomIndentifiersInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 626 627 <span class="i">$AtomIdentifier</span> = <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> 628 <span class="k">push</span> <span class="i">@AtomIndentifiersInfo</span><span class="cm">,</span> <span class="s">(</span><span class="i">$NextRadius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> 629 630 <span class="c"># Sort out successor atom bond order and identifier pairs by bond order followed by atom identifiers</span> 631 <span class="c"># in order to make the final atom identifier graph invariant...</span> 632 <span class="c">#</span> 633 <span class="k">for</span> <span class="i">$BondOrder</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$BondOrdersAndAtomIdentifiersRef</span>}<span class="s">)</span> <span class="s">{</span> 634 <span class="k">for</span> <span class="i">$SuccessorAtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiersRef</span>->{<span class="i">$BondOrder</span>}}<span class="s">)</span> <span class="s">{</span> 635 <span class="k">push</span> <span class="i">@AtomIndentifiersInfo</span><span class="cm">,</span> <span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$SuccessorAtomIdentifier</span><span class="s">)</span><span class="sc">;</span> 636 <span class="s">}</span> 637 <span class="s">}</span> 638 <span class="i">$AtomIdentifierString</span> = <span class="k">join</span><span class="s">(</span><span class="q">""</span><span class="cm">,</span> <span class="i">@AtomIndentifiersInfo</span><span class="s">)</span><span class="sc">;</span> 639 <span class="i">$AtomIdentifier</span> = <span class="i">TextUtil::HashCode</span><span class="s">(</span><span class="i">$AtomIdentifierString</span><span class="s">)</span><span class="sc">;</span> 640 641 <span class="c"># Assign atom identifier to the atom at next radius level...</span> 642 <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$NextRadius</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomIdentifier</span><span class="sc">;</span> 643 644 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 645 <span class="s">}</span> 646 647 <span class="c"># Remove duplicates atom identifiers...</span> 648 <span class="c">#</span> <a name="_RemoveDuplicateAtomIdentifiers-"></a> 649 <span class="k">sub </span><span class="m">_RemoveDuplicateAtomIdentifiers</span> <span class="s">{</span> 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 651 652 <span class="i">$This</span><span class="i">->_RemoveDuplicateIdentifiersByValue</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 653 <span class="i">$This</span><span class="i">->_RemoveStructurallyDuplicateIdenfiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 654 655 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 656 <span class="s">}</span> 657 658 <span class="c"># Remove duplicate identifiers at each radius level by just using their value...</span> 659 <span class="c">#</span> <a name="_RemoveDuplicateIdentifiersByValue-"></a> 660 <span class="k">sub </span><span class="m">_RemoveDuplicateIdentifiersByValue</span> <span class="s">{</span> 661 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 662 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> 663 664 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 665 <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> 666 <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> 667 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span> 668 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 669 <span class="s">}</span> 670 <span class="i">$AtomIdentifier</span> = <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> 671 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="s">)</span> <span class="s">{</span> 672 <span class="c"># It's a duplicate atom idenfier at this radius level...</span> 673 <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} += <span class="n">1</span><span class="sc">;</span> 674 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 675 <span class="s">}</span> 676 <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$AtomID</span><span class="sc">;</span> 677 <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="n">1</span><span class="sc">;</span> 678 <span class="s">}</span> 679 <span class="s">}</span> 680 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 681 <span class="s">}</span> 682 683 <span class="c"># Remove structurally duplicate identifiers at each radius level...</span> 684 <span class="c">#</span> 685 <span class="c"># Methodology:</span> 686 <span class="c"># . For unquie atom identifiers at each radius level, assign complete structure features</span> 687 <span class="c"># in terms all the bonds involved to generate that identifier</span> 688 <span class="c"># . Use the complete structure features to remover atom identifiers which are</span> 689 <span class="c"># structurally equivalent which can also be at earlier radii levels</span> 690 <span class="c">#</span> 691 <span class="c">#</span> <a name="_RemoveStructurallyDuplicateIdenfiers-"></a> 692 <span class="k">sub </span><span class="m">_RemoveStructurallyDuplicateIdenfiers</span> <span class="s">{</span> 693 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 694 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifierRadius</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifier</span><span class="s">)</span><span class="sc">;</span> 695 696 <span class="c"># Setup structure features...</span> 697 <span class="i">$This</span><span class="i">->_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 698 699 <span class="c"># Identify structurally unqiue identifiers...</span> 700 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 701 <span class="j">ATOMIDENTIFIER:</span> <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> 702 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> 703 704 <span class="s">(</span><span class="i">$SimilarAtomIdentifierRadius</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifier</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_FindStructurallySimilarAtomIdentifier</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> 705 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilarAtomIdentifier</span><span class="s">)</span> <span class="s">{</span> 706 <span class="c"># Current atom identifier is similar to an earlier structurally unique atom identifier...</span> 707 <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$SimilarAtomIdentifierRadius</span>}{<span class="i">$SimilarAtomIdentifier</span>} += <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> 708 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span> 709 <span class="s">}</span> 710 <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$AtomID</span><span class="sc">;</span> 711 712 <span class="c"># Set structurally unique atom identifier count to the unique atom identifiers count...</span> 713 <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> 714 <span class="s">}</span> 715 <span class="s">}</span> 716 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 717 <span class="s">}</span> 718 719 <span class="c"># Set final fingerpritns vector...</span> 720 <span class="c">#</span> <a name="_SetFinalFingerprints-"></a> 721 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> 722 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 723 724 <span class="c"># Mark successful generation of fingerprints...</span> 725 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> 726 727 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span> 728 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 729 <span class="s">}</span> 730 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span> 731 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityCountFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 732 <span class="s">}</span> 733 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> 734 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityBitsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 735 <span class="s">}</span> 736 737 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 738 <span class="s">}</span> 739 740 <span class="c"># Set final extended connectivity fingerpritns vector...</span> 741 <span class="c">#</span> <a name="_SetFinalExtendedConnectivityFingerprints-"></a> 742 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityFingerprints</span> <span class="s">{</span> 743 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 744 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> 745 746 <span class="i">@AtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 747 748 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 749 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> 750 <span class="k">push</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="sc">;</span> 751 <span class="s">}</span> 752 <span class="s">}</span> 753 <span class="c"># Add atom identifiers to fingerprint vector...</span> 754 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> 755 756 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 757 <span class="s">}</span> 758 759 <span class="c"># Set final extended connectivity count fingerpritns vector...</span> 760 <span class="c">#</span> <a name="_SetFinalExtendedConnectivityCountFingerprints-"></a> 761 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityCountFingerprints</span> <span class="s">{</span> 762 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 763 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$AtomIdentifierCount</span><span class="cm">,</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">@AtomIdentifiersCount</span><span class="s">)</span><span class="sc">;</span> 764 765 <span class="i">@AtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIdentifiersCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 766 767 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 768 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> 769 <span class="i">$AtomIdentifierCount</span> = <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> 770 <span class="k">push</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="sc">;</span> 771 <span class="k">push</span> <span class="i">@AtomIdentifiersCount</span><span class="cm">,</span> <span class="i">$AtomIdentifierCount</span><span class="sc">;</span> 772 <span class="s">}</span> 773 <span class="s">}</span> 774 <span class="c"># Add atom identifiers to fingerprint vector as value IDs...</span> 775 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> 776 777 <span class="c"># Add atom identifiers to count to fingerprint vector as values...</span> 778 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@AtomIdentifiersCount</span><span class="s">)</span><span class="sc">;</span> 779 780 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 781 <span class="s">}</span> 782 783 <span class="c"># Set final extended connectivity bits fingerpritns vector...</span> 784 <span class="c">#</span> <a name="_SetFinalExtendedConnectivityBitsFingerprints-"></a> 785 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityBitsFingerprints</span> <span class="s">{</span> 786 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 787 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="cm">,</span> <span class="i">$Size</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="cm">,</span> <span class="i">$AtomIdentifierBitPos</span><span class="cm">,</span> <span class="i">$SetBitNum</span><span class="s">)</span><span class="sc">;</span> 788 789 <span class="i">$FingerprintsBitVector</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="sc">;</span> 790 791 <span class="i">$Size</span> = <span class="i">$This</span>->{<span class="w">Size</span>}<span class="sc">;</span> 792 793 <span class="i">$SkipBitPosCheck</span> = <span class="n">1</span><span class="sc">;</span> 794 795 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 796 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> 797 <span class="c"># Set random number seed...</span> 798 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span> <span class="s">{</span> 799 <span class="i">CORE::</span><span class="k">srand</span><span class="s">(</span><span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> 800 <span class="s">}</span> 801 <span class="k">else</span> <span class="s">{</span> 802 <span class="i">MathUtil::srandom</span><span class="s">(</span><span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> 803 <span class="s">}</span> 804 805 <span class="c"># Set bit position...</span> 806 <span class="i">$AtomIdentifierBitPos</span> = <span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>} ? <span class="k">int</span><span class="s">(</span><span class="i">CORE::</span><span class="k">rand</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="k">int</span><span class="s">(</span><span class="i">MathUtil::random</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 807 <span class="i">$FingerprintsBitVector</span><span class="i">->SetBit</span><span class="s">(</span><span class="i">$AtomIdentifierBitPos</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="s">)</span><span class="sc">;</span> 808 <span class="s">}</span> 809 <span class="s">}</span> 810 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 811 <span class="s">}</span> 812 813 814 <span class="c"># Identify structurally unique identifiers by comparing structure features involved in</span> 815 <span class="c"># generating identifiear by comparing it agains all the previous structurally unique</span> 816 <span class="c"># identifiers...</span> 817 <span class="c">#</span> <a name="_FindStructurallySimilarAtomIdentifier-"></a> 818 <span class="k">sub </span><span class="m">_FindStructurallySimilarAtomIdentifier</span> <span class="s">{</span> 819 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$SpecifiedRadius</span><span class="cm">,</span> <span class="i">$SpecifiedAtomID</span><span class="cm">,</span> <span class="i">$SpecifiedAtomIdentifier</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 820 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$FeatureAtomCount</span><span class="cm">,</span> <span class="i">$FeatureAtomIDsRef</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomID</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomCount</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomIDsRef</span><span class="s">)</span><span class="sc">;</span> 821 822 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedRadius</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 823 <span class="c"># After duplicate removal by value, all identifier at radius level 0 would be structurally unique...</span> 824 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> 825 <span class="s">}</span> 826 827 <span class="i">$SpecifiedFeatureAtomCount</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$SpecifiedRadius</span>}{<span class="i">$SpecifiedAtomID</span>}<span class="sc">;</span> 828 <span class="i">$SpecifiedFeatureAtomIDsRef</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$SpecifiedRadius</span>}{<span class="i">$SpecifiedAtomID</span>}<span class="sc">;</span> 829 830 <span class="c"># No need to compare features at radius 0...</span> 831 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$SpecifiedRadius</span><span class="s">)</span> <span class="s">{</span> 832 <span class="j">ATOMIDENTIFIER:</span> <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> 833 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> 834 835 <span class="i">$FeatureAtomCount</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> 836 <span class="i">$FeatureAtomIDsRef</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> 837 838 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedFeatureAtomCount</span> != <span class="i">$FeatureAtomCount</span><span class="s">)</span> <span class="s">{</span> 839 <span class="c"># Couldn't be structurally equivalent...</span> 840 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span> 841 <span class="s">}</span> 842 <span class="k">for</span> <span class="i">$SpecifiedFeatureAtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span> {<span class="i">$SpecifiedFeatureAtomIDsRef</span>}<span class="s">)</span> <span class="s">{</span> 843 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$FeatureAtomIDsRef</span>->{<span class="i">$SpecifiedFeatureAtomID</span>}<span class="s">)</span> <span class="s">{</span> 844 <span class="c"># For structural equivalency, all atom in specified feature must also be present in a previously</span> 845 <span class="c"># identified structurally unique structure feature...</span> 846 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span> 847 <span class="s">}</span> 848 <span class="s">}</span> 849 <span class="c"># Found structurally equivalent feature...</span> 850 <span class="k">return</span> <span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> 851 <span class="s">}</span> 852 <span class="s">}</span> 853 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> 854 <span class="s">}</span> 855 856 <span class="c"># Setup structure features for atom IDs involved in unique atom identifiers at all</span> 857 <span class="c"># radii level...</span> 858 <span class="c">#</span> <a name="_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers-"></a> 859 <span class="k">sub </span><span class="m">_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers</span> <span class="s">{</span> 860 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 861 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$PreviousRadius</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">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">%AtomIDs</span><span class="s">)</span><span class="sc">;</span> 862 863 <span class="i">$This</span><span class="i">->_InitializeStructureFeatures</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 864 865 <span class="c"># Collect atom IDs involved in unique atom identifiers...</span> 866 <span class="i">%AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 867 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 868 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> 869 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> 870 <span class="i">$AtomIDs</span>{<span class="i">$AtomID</span>} = <span class="i">$AtomID</span><span class="sc">;</span> 871 <span class="s">}</span> 872 <span class="s">}</span> 873 874 <span class="c"># Setup structure features...</span> 875 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> 876 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AtomIDs</span><span class="s">)</span> <span class="s">{</span> 877 <span class="k">my</span><span class="s">(</span><span class="i">$StructureFeatureAtomCount</span><span class="cm">,</span> <span class="i">%StructureFeatureAtomIDs</span><span class="s">)</span><span class="sc">;</span> 878 879 <span class="i">$StructureFeatureAtomCount</span> = <span class="n">0</span><span class="sc">;</span> 880 <span class="i">%StructureFeatureAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 881 882 <span class="c"># Get partial structure features for the atom at previous radius level...</span> 883 <span class="i">$PreviousRadius</span> = <span class="i">$Radius</span> - <span class="n">1</span><span class="sc">;</span> 884 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRadius</span> >= <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 885 <span class="i">$StructureFeatureAtomCount</span> += <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$PreviousRadius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> 886 <span class="i">%StructureFeatureAtomIDs</span> = <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$PreviousRadius</span>}{<span class="i">$AtomID</span>}}<span class="sc">;</span> 887 <span class="s">}</span> 888 889 <span class="c"># Get all neighborhood atom at this radius level...</span> 890 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}<span class="s">)</span> && <span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 891 <span class="j">NEIGHBORHOODS:</span> <span class="k">for</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}}<span class="s">)</span> <span class="s">{</span> 892 <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span>}<span class="sc">;</span> 893 <span class="k">if</span> <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 894 <span class="k">next</span> <span class="j">NEIGHBORHOODS</span><span class="sc">;</span> 895 <span class="s">}</span> 896 <span class="i">$NeighborhoodAtomID</span> = <span class="i">$NeighborhoodAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 897 <span class="i">$StructureFeatureAtomCount</span>++<span class="sc">;</span> 898 <span class="i">$StructureFeatureAtomIDs</span>{<span class="i">$NeighborhoodAtomID</span>} = <span class="i">$NeighborhoodAtomID</span><span class="sc">;</span> 899 <span class="s">}</span> 900 <span class="s">}</span> 901 902 <span class="c"># Assign structure features to atom at this radius level...</span> 903 <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = <span class="i">$StructureFeatureAtomCount</span><span class="sc">;</span> 904 <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = \<span class="i">%StructureFeatureAtomIDs</span><span class="sc">;</span> 905 <span class="s">}</span> 906 <span class="s">}</span> 907 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 908 <span class="s">}</span> 909 910 <span class="c"># Intialize structure features at each radius level...</span> 911 <span class="c">#</span> <a name="_InitializeStructureFeatures-"></a> 912 <span class="k">sub </span><span class="m">_InitializeStructureFeatures</span> <span class="s">{</span> 913 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 914 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 915 916 <span class="c"># Initialize all structure features...</span> 917 918 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 919 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 920 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 921 922 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span> 923 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span> 924 <span class="c"># Structure features for at specific radii accessed using atom IDs...</span> 925 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 926 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 927 <span class="s">}</span> 928 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 929 <span class="s">}</span> 930 931 <span class="c"># Cache appropriate molecule data...</span> 932 <span class="c">#</span> <a name="_SetupMoleculeDataCache-"></a> 933 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> 934 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 935 936 <span class="c"># Get all non-hydrogen atoms...</span> 937 <span class="k">my</span><span class="s">(</span><span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> 938 <span class="i">$NegateAtomCheckMethod</span> = <span class="n">1</span><span class="sc">;</span> 939 <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="q">"IsHydrogen"</span><span class="cm">,</span> <span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> 940 941 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 942 <span class="s">}</span> 943 944 <span class="c"># Clear cached molecule data...</span> 945 <span class="c">#</span> <a name="_ClearMoleculeDataCache-"></a> 946 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> 947 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 948 949 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 950 951 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 952 <span class="s">}</span> 953 954 <span class="c"># Initialize atom indentifier type information...</span> 955 <span class="c">#</span> 956 <span class="c"># Current supported values:</span> 957 <span class="c">#</span> 958 <span class="c"># AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,</span> 959 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> 960 <span class="c">#</span> <a name="_InitializeAtomIdentifierTypeInformation-"></a> 961 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> 962 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 963 964 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> 965 <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> 966 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 967 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 968 <span class="s">}</span> 969 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 970 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 971 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 972 <span class="s">}</span> 973 <span class="k">if</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> 974 <span class="c"># Nothing to do for now...</span> 975 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> 976 <span class="s">}</span> 977 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 978 <span class="s">}</span> 979 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 980 <span class="s">}</span> 981 982 <span class="c"># Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes</span> 983 <span class="c"># class, to use for generating initial atom identifiers...</span> 984 <span class="c">#</span> 985 <span class="c"># Let:</span> 986 <span class="c"># AS = Atom symbol corresponding to element symbol</span> 987 <span class="c">#</span> 988 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> 989 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 990 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> 991 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 992 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 993 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> 994 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> 995 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> 996 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> 997 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> 998 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> 999 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> 1000 <span class="c">#</span> 1001 <span class="c"># Then:</span> 1002 <span class="c">#</span> 1003 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> 1004 <span class="c">#</span> 1005 <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> 1006 <span class="c">#</span> 1007 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span> 1008 <span class="c"># optional.</span> 1009 <span class="c">#</span> 1010 <span class="c"># Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:</span> 1011 <span class="c">#</span> 1012 <span class="c"># AS, X<n>, BO<n>, H<n>, FC<+n/-n>, MN<n></span> 1013 <span class="c">#</span> 1014 <span class="c"># In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words</span> 1015 <span class="c"># are also allowed:</span> 1016 <span class="c">#</span> 1017 <span class="c"># X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors</span> 1018 <span class="c"># BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms</span> 1019 <span class="c"># LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms</span> 1020 <span class="c"># SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms</span> 1021 <span class="c"># DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms</span> 1022 <span class="c"># TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms</span> 1023 <span class="c"># H : NumOfImplicitAndExplicitHydrogens</span> 1024 <span class="c"># Ar : Aromatic</span> 1025 <span class="c"># RA : RingAtom</span> 1026 <span class="c"># FC : FormalCharge</span> 1027 <span class="c"># MN : MassNumber</span> 1028 <span class="c"># SM : SpinMultiplicity</span> 1029 <span class="c">#</span> <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a>1030 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> 1031 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1032 1033 <span class="c"># Default atomic invariants to use for generating initial atom identifiers are: AS, X, BO, LBO, H, FC</span> 1034 <span class="c">#</span> 1035 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1036 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="cm">,</span> <span class="q">'MN'</span><span class="s">)</span><span class="sc">;</span> 1037 1038 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1039 <span class="s">}</span> 1040 1041 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> 1042 <span class="c"># class, to use for generating initial atom identifiers...</span> 1043 <span class="c">#</span> 1044 <span class="c"># Let:</span> 1045 <span class="c"># HBD: HydrogenBondDonor</span> 1046 <span class="c"># HBA: HydrogenBondAcceptor</span> 1047 <span class="c"># PI : PositivelyIonizable</span> 1048 <span class="c"># NI : NegativelyIonizable</span> 1049 <span class="c"># Ar : Aromatic</span> 1050 <span class="c"># Hal : Halogen</span> 1051 <span class="c"># H : Hydrophobic</span> 1052 <span class="c"># RA : RingAtom</span> 1053 <span class="c"># CA : ChainAtom</span> 1054 <span class="c">#</span> 1055 <span class="c"># Then:</span> 1056 <span class="c">#</span> 1057 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> 1058 <span class="c">#</span> 1059 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> 1060 <span class="c">#</span> 1061 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> 1062 <span class="c">#</span> 1063 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> 1064 <span class="c">#</span> 1065 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> 1066 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> 1067 <span class="c"># PositivelyIonizable: +, NH2</span> 1068 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> 1069 <span class="c">#</span> <a name="_InitializeFunctionalClassAtomTypesInformation-"></a>1070 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> 1071 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1072 1073 <span class="c"># Default functional class atom typess to use for generating initial atom identifiers</span> 1074 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span> 1075 <span class="c">#</span> 1076 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1077 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> 1078 1079 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1080 <span class="s">}</span> 1081 1082 <span class="c"># Set atomic invariants to use for generation of intial atom indentifiers...</span> 1083 <span class="c">#</span> <a name="SetAtomicInvariantsToUse-"></a>1084 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> 1085 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1086 <span class="k">my</span><span class="s">(</span><span class="i">$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">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span> 1087 1088 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 1089 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> 1090 <span class="k">return</span><span class="sc">;</span> 1091 <span class="s">}</span> 1092 1093 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 1094 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalAtomTypesToUse: AtomicInvariantsToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 1095 <span class="k">return</span><span class="sc">;</span> 1096 <span class="s">}</span> 1097 1098 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 1099 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 1100 1101 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1102 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1103 1104 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 1105 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> 1106 <span class="s">}</span> 1107 <span class="k">else</span> <span class="s">{</span> 1108 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 1109 <span class="s">}</span> 1110 1111 <span class="c"># Make sure specified AtomicInvariants are valid...</span> 1112 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> 1113 <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> 1114 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> 1115 <span class="s">}</span> 1116 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> 1117 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> 1118 <span class="s">}</span> 1119 1120 <span class="c"># Set atomic invariants to use...</span> 1121 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1122 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> 1123 1124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1125 <span class="s">}</span> 1126 1127 <span class="c"># Set functional classes to use for generation of intial atom indentifiers...</span> 1128 <span class="c">#</span> <a name="SetFunctionalClassesToUse-"></a>1129 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> 1130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1131 <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> 1132 1133 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 1134 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> 1135 <span class="k">return</span><span class="sc">;</span> 1136 <span class="s">}</span> 1137 1138 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 1139 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> 1140 <span class="k">return</span><span class="sc">;</span> 1141 <span class="s">}</span> 1142 1143 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 1144 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 1145 1146 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1147 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1148 1149 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 1150 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> 1151 <span class="s">}</span> 1152 <span class="k">else</span> <span class="s">{</span> 1153 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 1154 <span class="s">}</span> 1155 1156 <span class="c"># Make sure specified FunctionalClasses are valid...</span> 1157 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> 1158 <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> 1159 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> 1160 <span class="s">}</span> 1161 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> 1162 <span class="s">}</span> 1163 1164 <span class="c"># Set functional classes to use...</span> 1165 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1166 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> 1167 1168 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1169 <span class="s">}</span> 1170 1171 <span class="c"># Return a string containg data for ExtendedConnectivityFingerprints object...</span> <a name="StringifyExtendedConnectivityFingerprints-"></a>1172 <span class="k">sub </span><span class="m">StringifyExtendedConnectivityFingerprints</span> <span class="s">{</span> 1173 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1174 <span class="k">my</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprintsString</span><span class="s">)</span><span class="sc">;</span> 1175 1176 <span class="i">$ExtendedConnectivityFingerprintsString</span> = <span class="q">"InitialAtomIdentifierType: $This->{AtomIdentifierType}; NeighborhoodRadius: $This->{NeighborhoodRadius}"</span><span class="sc">;</span> 1177 1178 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> 1179 <span class="k">my</span><span class="s">(</span><span class="i">$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> 1180 1181 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1182 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1183 1184 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> 1185 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> 1186 <span class="s">}</span> 1187 1188 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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> 1189 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 1190 <span class="i">$ExtendedConnectivityFingerprintsString</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> 1191 <span class="s">}</span> 1192 <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> 1193 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> 1194 1195 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1196 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1197 1198 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> 1199 <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> 1200 <span class="s">}</span> 1201 1202 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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> 1203 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 1204 <span class="i">$ExtendedConnectivityFingerprintsString</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> 1205 <span class="s">}</span> 1206 1207 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> 1208 <span class="c"># Size...</span> 1209 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; Size: $This->{Size}; MinSize: $This->{MinSize}; MaxSize: $This->{MaxSize}"</span><span class="sc">;</span> 1210 1211 <span class="c"># Fingerprint bit density and num of bits set...</span> 1212 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSetBits</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span> 1213 <span class="i">$NumOfSetBits</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1214 <span class="i">$BitDensity</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetFingerprintsBitDensity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1215 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity"</span><span class="sc">;</span> 1216 1217 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FingerprintsBitVector: < $This->{FingerprintsBitVector} >"</span><span class="sc">;</span> 1218 <span class="s">}</span> 1219 <span class="k">else</span> <span class="s">{</span> 1220 <span class="c"># Number of identifiers...</span> 1221 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; NumOfIdentifiers: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1222 1223 <span class="c"># FingerprintsVector...</span> 1224 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> 1225 <span class="s">}</span> 1226 1227 <span class="k">return</span> <span class="i">$ExtendedConnectivityFingerprintsString</span><span class="sc">;</span> 1228 <span class="s">}</span> 1229 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>