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comparison mayachemtools/docs/modules/html/code/ExtendedConnectivityFingerprints.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:Fingerprints::ExtendedConnectivityFingerprints.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-Fingerprints::ExtendedConnectivityFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: ExtendedConnectivityFingerprints.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> | |
| 18 5 <span class="c"># $Revision: 1.39 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> | |
| 51 38 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span> | |
| 52 39 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span> | |
| 53 40 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span> | |
| 54 41 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span> | |
| 55 42 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span> | |
| 56 43 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span> | |
| 57 44 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span> | |
| 58 45 | |
| 59 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> | |
| 60 47 | |
| 61 48 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> | |
| 62 49 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 63 50 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 64 51 | |
| 65 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> | |
| 66 53 | |
| 67 54 <span class="c"># Setup class variables...</span> | |
| 68 55 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 69 56 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 70 57 | |
| 71 58 <span class="c"># Overload Perl functions...</span> | |
| 72 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> | |
| 73 60 | |
| 74 61 <span class="c"># Class constructor...</span> | |
| 75 <a name="new-"></a> 62 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 76 63 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 77 64 | |
| 78 65 <span class="c"># Initialize object...</span> | |
| 79 66 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 80 67 <span class="k">bless</span> <span class="i">$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> | |
| 81 68 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 82 69 | |
| 83 70 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 84 71 | |
| 85 72 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 86 73 <span class="s">}</span> | |
| 87 74 | |
| 88 75 <span class="c"># Initialize object data...</span> | |
| 89 76 <span class="c">#</span> | |
| 90 <a name="_InitializeExtendedConnectivityFingerprints-"></a> 77 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprints</span> <span class="s">{</span> | |
| 91 78 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 92 79 | |
| 93 80 <span class="c"># Type of fingerprint to generate:</span> | |
| 94 81 <span class="c">#</span> | |
| 95 82 <span class="c"># ExtendedConnectivity - Set of integer identifiers corresponding to structurally unique features</span> | |
| 96 83 <span class="c"># ExtendedConnectivityCount - Set of integer identifiers corresponding to structurally unique features and their count</span> | |
| 97 84 <span class="c"># ExtendedConnectivityBits - A bit vector indicating presence/absence of structurally unique features</span> | |
| 98 85 <span class="c">#</span> | |
| 99 86 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivity'</span><span class="sc">;</span> | |
| 100 87 | |
| 101 88 <span class="c"># Atomic neighborhoods radius for extended connectivity...</span> | |
| 102 89 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span> | |
| 103 90 | |
| 104 91 <span class="c"># Size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...</span> | |
| 105 92 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="n">1024</span><span class="sc">;</span> | |
| 106 93 | |
| 107 94 <span class="c"># Min and max size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...</span> | |
| 108 95 <span class="i">$This</span>->{<span class="w">MinSize</span>} = <span class="n">32</span><span class="sc">;</span> | |
| 109 96 <span class="i">$This</span>->{<span class="w">MaxSize</span>} = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span> | |
| 110 97 | |
| 111 98 <span class="c"># Type of atom attributes to use for initial identifier assignment to non-hydrogen atoms</span> | |
| 112 99 <span class="c"># during the calculation of extended connectivity fingerprints [ Ref 48, Ref 52 ]...</span> | |
| 113 100 <span class="c">#</span> | |
| 114 101 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes,</span> | |
| 115 102 <span class="c"># DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,</span> | |
| 116 103 <span class="c"># TPSAAtomTypes, UFFAtomTypes</span> | |
| 117 104 <span class="c">#</span> | |
| 118 105 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 119 106 | |
| 120 107 <span class="c"># Random number generator to use during generation of fingerprints bit-vector</span> | |
| 121 108 <span class="c"># string: Perl CORE::rand or MayaChemTools MathUtil::random function.</span> | |
| 122 109 <span class="c">#</span> | |
| 123 110 <span class="c"># The random number generator implemented in MayaChemTools is a variant of</span> | |
| 124 111 <span class="c"># linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].</span> | |
| 125 112 <span class="c"># It is also referred to as Lehmer random number generator or Park-Miller</span> | |
| 126 113 <span class="c"># random number generator.</span> | |
| 127 114 <span class="c">#</span> | |
| 128 115 <span class="c"># Unlike Perl's core random number generator function rand, the random number</span> | |
| 129 116 <span class="c"># generator implemented in MayaChemTools, MathUtil::random, generates consistent</span> | |
| 130 117 <span class="c"># random values across different platformsfor a specific random seed and leads</span> | |
| 131 118 <span class="c"># to generation of portable fingerprints bit-vector strings.</span> | |
| 132 119 <span class="c">#</span> | |
| 133 120 <span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 134 121 | |
| 135 122 <span class="c"># Atom neighorhoods up to specified neighborhood radius...</span> | |
| 136 123 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 137 124 | |
| 138 125 <span class="c"># Atom identifiers at different neighborhoods up to specified neighborhood radius...</span> | |
| 139 126 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 140 127 | |
| 141 128 <span class="c"># Structurally unique atom identifiers at different neighborhoods up to specified neighborhood radius...</span> | |
| 142 129 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 143 130 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 144 131 | |
| 145 132 <span class="c"># Unique atom identifiers at different neighborhoods up to specified neighborhood radius...</span> | |
| 146 133 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 147 134 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 148 135 | |
| 149 136 <span class="c"># Structure feature information at different neighborhoods up to specified neighborhood</span> | |
| 150 137 <span class="c"># radius used during removal of atom indentifiers which are structually equivalent...</span> | |
| 151 138 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 152 139 <span class="s">}</span> | |
| 153 140 | |
| 154 141 <span class="c"># Initialize class ...</span> | |
| 155 <a name="_InitializeClass-"></a> 142 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 156 143 <span class="c">#Class name...</span> | |
| 157 144 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 158 145 <span class="s">}</span> | |
| 159 146 | |
| 160 147 <span class="c"># Initialize object properties....</span> | |
| 161 <a name="_InitializeExtendedConnectivityFingerprintsProperties-"></a> 148 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprintsProperties</span> <span class="s">{</span> | |
| 162 149 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 163 150 | |
| 164 151 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
| 165 152 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
| 166 153 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 167 154 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 168 155 <span class="s">}</span> | |
| 169 156 | |
| 170 157 <span class="c"># Make sure molecule object was specified...</span> | |
| 171 158 <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> | |
| 172 159 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> | |
| 173 160 <span class="s">}</span> | |
| 174 161 | |
| 175 162 <span class="c"># Make sure AtomIdentifierType was specified...</span> | |
| 176 163 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 177 164 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."</span><span class="sc">;</span> | |
| 178 165 <span class="s">}</span> | |
| 179 166 | |
| 180 167 <span class="c"># Make sure it's power of 2...</span> | |
| 181 168 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span> | |
| 182 169 <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> | |
| 183 170 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Specified size value, $NamesAndValues{Size}, must be power of 2..."</span><span class="sc">;</span> | |
| 184 171 <span class="s">}</span> | |
| 185 172 <span class="s">}</span> | |
| 186 173 | |
| 187 174 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 188 175 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 189 176 <span class="s">}</span> | |
| 190 177 <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> | |
| 191 178 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityCountFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 192 179 <span class="s">}</span> | |
| 193 180 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 194 181 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityBitsFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 195 182 <span class="s">}</span> | |
| 196 183 <span class="k">else</span> <span class="s">{</span> | |
| 197 184 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeExtendedConnectivityFingerprintsProperties: Unknown ExtendedConnectivity fingerprints type: $This->{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits..."</span><span class="sc">;</span> | |
| 198 185 <span class="s">}</span> | |
| 199 186 | |
| 200 187 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 201 188 <span class="s">}</span> | |
| 202 189 | |
| 203 190 <span class="c"># Initialize extended connectivity fingerprints vector...</span> | |
| 204 191 <span class="c">#</span> | |
| 205 <a name="_InitializeExtendedConnectivityFingerprintsVector-"></a> 192 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprintsVector</span> <span class="s">{</span> | |
| 206 193 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 207 194 | |
| 208 195 <span class="c"># Type of vector...</span> | |
| 209 196 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> | |
| 210 197 | |
| 211 198 <span class="c"># Type of FingerprintsVector...</span> | |
| 212 199 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'AlphaNumericalValues'</span><span class="sc">;</span> | |
| 213 200 | |
| 214 201 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 215 202 | |
| 216 203 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 217 204 <span class="s">}</span> | |
| 218 205 | |
| 219 206 <span class="c"># Initialize extended connectivity count fingerprints vector...</span> | |
| 220 207 <span class="c">#</span> | |
| 221 <a name="_InitializeExtendedConnectivityCountFingerprintsVector-"></a> 208 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityCountFingerprintsVector</span> <span class="s">{</span> | |
| 222 209 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 223 210 | |
| 224 211 <span class="c"># Type of vector...</span> | |
| 225 212 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> | |
| 226 213 | |
| 227 214 <span class="c"># Type of FingerprintsVector...</span> | |
| 228 215 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> | |
| 229 216 | |
| 230 217 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 231 218 | |
| 232 219 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 233 220 <span class="s">}</span> | |
| 234 221 | |
| 235 222 <span class="c"># Initialize extended connectivity bit fingerprints vector...</span> | |
| 236 223 <span class="c">#</span> | |
| 237 <a name="_InitializeExtendedConnectivityBitsFingerprintsBitVector-"></a> 224 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityBitsFingerprintsBitVector</span> <span class="s">{</span> | |
| 238 225 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 239 226 | |
| 240 227 <span class="c"># Type of vector...</span> | |
| 241 228 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsBitVector'</span><span class="sc">;</span> | |
| 242 229 | |
| 243 230 <span class="i">$This</span><span class="i">->_InitializeFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 244 231 | |
| 245 232 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 246 233 <span class="s">}</span> | |
| 247 234 | |
| 248 235 <span class="c"># Set type...</span> | |
| 249 236 <span class="c">#</span> | |
| 250 <a name="SetType-"></a> 237 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span> | |
| 251 238 <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> | |
| 252 239 | |
| 253 240 <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> | |
| 254 241 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivity'</span><span class="sc">;</span><span class="sc">;</span> | |
| 255 242 <span class="s">}</span> | |
| 256 243 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 257 244 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivityCount'</span><span class="sc">;</span><span class="sc">;</span> | |
| 258 245 <span class="s">}</span> | |
| 259 246 <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> | |
| 260 247 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivityBits'</span><span class="sc">;</span><span class="sc">;</span> | |
| 261 248 <span class="s">}</span> | |
| 262 249 <span class="k">else</span> <span class="s">{</span> | |
| 263 250 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Unknown ExtendedConnectivity fingerprints type: $This->{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits..."</span><span class="sc">;</span> | |
| 264 251 <span class="s">}</span> | |
| 265 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 266 253 <span class="s">}</span> | |
| 267 254 | |
| 268 255 <span class="c"># Disable vector type change...</span> | |
| 269 256 <span class="c">#</span> | |
| 270 <a name="SetVectorType-"></a> 257 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span> | |
| 271 258 <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> | |
| 272 259 | |
| 273 260 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Can't change vector type..."</span><span class="sc">;</span> | |
| 274 261 | |
| 275 262 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 276 263 <span class="s">}</span> | |
| 277 264 | |
| 278 265 <span class="c"># Disable vector type change...</span> | |
| 279 266 <span class="c">#</span> | |
| 280 <a name="SetFingerprintsVectorType-"></a> 267 <span class="k">sub </span><span class="m">SetFingerprintsVectorType</span> <span class="s">{</span> | |
| 281 268 <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> | |
| 282 269 | |
| 283 270 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVectorType: Can't change fingerprints vector type..."</span><span class="sc">;</span> | |
| 284 271 | |
| 285 272 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 286 273 <span class="s">}</span> | |
| 287 274 | |
| 288 275 <span class="c"># Set intial atom identifier type..</span> | |
| 289 276 <span class="c">#</span> | |
| 290 <a name="SetAtomIdentifierType-"></a> 277 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> | |
| 291 278 <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> | |
| 292 279 | |
| 293 280 <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> | |
| 294 281 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes."</span><span class="sc">;</span> | |
| 295 282 <span class="s">}</span> | |
| 296 283 | |
| 297 284 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> | |
| 298 285 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span> | |
| 299 286 <span class="s">}</span> | |
| 300 287 | |
| 301 288 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> | |
| 302 289 | |
| 303 290 <span class="c"># Initialize identifier type information...</span> | |
| 304 291 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 305 292 | |
| 306 293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 307 294 <span class="s">}</span> | |
| 308 295 | |
| 309 296 <span class="c"># Set atom neighborhood radius...</span> | |
| 310 297 <span class="c">#</span> | |
| 311 <a name="SetNeighborhoodRadius-"></a> 298 <span class="k">sub </span><span class="m">SetNeighborhoodRadius</span> <span class="s">{</span> | |
| 312 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 313 300 | |
| 314 301 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 315 302 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> | |
| 316 303 <span class="s">}</span> | |
| 317 304 | |
| 318 305 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span> | |
| 319 306 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span> | |
| 320 307 <span class="s">}</span> | |
| 321 308 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 322 309 | |
| 323 310 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 324 311 <span class="s">}</span> | |
| 325 312 | |
| 326 313 <span class="c"># Generate fingerprints description...</span> | |
| 327 314 <span class="c">#</span> | |
| 328 <a name="GetDescription-"></a> 315 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> | |
| 329 316 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 330 317 | |
| 331 318 <span class="c"># Is description explicity set?</span> | |
| 332 319 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> | |
| 333 320 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> | |
| 334 321 <span class="s">}</span> | |
| 335 322 | |
| 336 323 <span class="c"># Generate fingerprints description...</span> | |
| 337 324 | |
| 338 325 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomIdentifierType}:Radius$This->{NeighborhoodRadius}"</span><span class="sc">;</span> | |
| 339 326 <span class="s">}</span> | |
| 340 327 | |
| 341 328 <span class="c"># Generate fingerprints...</span> | |
| 342 329 <span class="c">#</span> | |
| 343 330 <span class="c"># Methodology:</span> | |
| 344 331 <span class="c"># . Assign initial atom identfiers to all non-hydrogen atoms in the molecule</span> | |
| 345 332 <span class="c">#</span> | |
| 346 333 <span class="c"># . Remove duplicates from the initial identifiers and add them to list corresponding</span> | |
| 347 334 <span class="c"># to molecule fingerprint</span> | |
| 348 335 <span class="c">#</span> | |
| 349 336 <span class="c"># . For NeighborhoodRadius value of 0, just return the molecule fingerprint list</span> | |
| 350 337 <span class="c">#</span> | |
| 351 338 <span class="c"># . For each NeighborhoodRadius level</span> | |
| 352 339 <span class="c"># . For each non-hydrogen CentralAtom at this NeighborhoodRadius level</span> | |
| 353 340 <span class="c"># . For each non-hydrogen SuccessorNeighborAtom</span> | |
| 354 341 <span class="c"># . Collect (BondOrder AtomIdentifier) pair of values corresponding to</span> | |
| 355 342 <span class="c"># (CentralAtom SuccessorNeighborAtom) and add it to a list</span> | |
| 356 343 <span class="c">#</span> | |
| 357 344 <span class="c"># . Sort list containing (BondOrder AtomIdentifier) pairs first by BondOrder followed</span> | |
| 358 345 <span class="c"># by AtomIdendifiers to make these values graph invariant</span> | |
| 359 346 <span class="c"># . Generate a hash code for the values in the list</span> | |
| 360 347 <span class="c"># . Assign hash code as new atom identifier at the current NeighborhoodRadius level</span> | |
| 361 348 <span class="c"># . Save all atoms and bonds corresponding to the substructure involved in</span> | |
| 362 349 <span class="c"># generating the hash code to be used for identifying structural duplicate hash code</span> | |
| 363 350 <span class="c">#</span> | |
| 364 351 <span class="c"># . Add the new identifier to the molecule fingerprint list making sure it's not a duplicate</span> | |
| 365 352 <span class="c"># identifier</span> | |
| 366 353 <span class="c">#</span> | |
| 367 354 <span class="c"># Hash code atom identifier deduplication:</span> | |
| 368 355 <span class="c"># . Track/remove the identifier generated at higher neighborhood radius level</span> | |
| 369 356 <span class="c">#</span> | |
| 370 357 <span class="c"># Structural atom identifier deduplication:</span> | |
| 371 358 <span class="c"># . For equivalent atoms and bonds corresponding to substructure at a NeighborhoodRadius level,</span> | |
| 372 359 <span class="c"># track/remove the atom identifier with largest value</span> | |
| 373 360 <span class="c">#</span> | |
| 374 361 <span class="c">#</span> | |
| 375 <a name="GenerateFingerprints-"></a> 362 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> | |
| 376 363 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 377 364 | |
| 378 365 <span class="c"># Cache appropriate molecule data...</span> | |
| 379 366 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 380 367 | |
| 381 368 <span class="c"># Assign intial atom identifers...</span> | |
| 382 369 <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> | |
| 383 370 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."</span><span class="sc">;</span> | |
| 384 371 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 385 372 <span class="s">}</span> | |
| 386 373 | |
| 387 374 <span class="c"># Identify atom neighborhoods up to specified radius...</span> | |
| 388 375 <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 389 376 | |
| 390 377 <span class="c"># Assign atom identifiers to central atoms considering atom neighborhoods at each</span> | |
| 391 378 <span class="c"># radius level...</span> | |
| 392 379 <span class="i">$This</span><span class="i">->_AssignAtomIdentifiersToAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 393 380 | |
| 394 381 <span class="c"># Remove duplicates identifiers...</span> | |
| 395 382 <span class="i">$This</span><span class="i">->_RemoveDuplicateAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 396 383 | |
| 397 384 <span class="c"># Set final fingerprints...</span> | |
| 398 385 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 399 386 | |
| 400 387 <span class="c"># Clear cached molecule data...</span> | |
| 401 388 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 402 389 | |
| 403 390 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 404 391 <span class="s">}</span> | |
| 405 392 | |
| 406 393 <span class="c"># Assign appropriate initial atom identifiers...</span> | |
| 407 394 <span class="c">#</span> | |
| 408 395 <span class="c"># Generation of initial identifier for a specific atom involves:</span> | |
| 409 396 <span class="c"># . Values of the specified atom attributes are appended in a specific order to</span> | |
| 410 397 <span class="c"># generate an initial atom identifier string</span> | |
| 411 398 <span class="c"># . A 32 bit unsigned integer hash key, using TextUtil::HashCode function, is</span> | |
| 412 399 <span class="c"># generated for the atom indentifier and assigned to the atom as initial</span> | |
| 413 400 <span class="c"># atom identifier.</span> | |
| 414 401 <span class="c">#</span> | |
| 415 <a name="_AssignInitialAtomIdentifiers-"></a> 402 <span class="k">sub </span><span class="m">_AssignInitialAtomIdentifiers</span> <span class="s">{</span> | |
| 416 403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 417 404 <span class="k">my</span><span class="s">(</span><span class="i">$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">$InitialAtomIdentifier</span><span class="s">)</span><span class="sc">;</span> | |
| 418 405 | |
| 419 406 <span class="c"># Initialize atom identifiers...</span> | |
| 420 407 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 421 408 | |
| 422 409 <span class="c"># Set up atom types...</span> | |
| 423 410 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span> | |
| 424 411 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 425 412 | |
| 426 413 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> | |
| 427 414 <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> | |
| 428 415 <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> | |
| 429 416 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 430 417 <span class="s">}</span> | |
| 431 418 | |
| 432 419 <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> | |
| 433 420 <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> | |
| 434 421 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 435 422 <span class="s">}</span> | |
| 436 423 | |
| 437 424 <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> | |
| 438 425 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
| 439 426 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 440 427 <span class="s">}</span> | |
| 441 428 | |
| 442 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 443 430 <span class="i">$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> | |
| 444 431 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 445 432 <span class="s">}</span> | |
| 446 433 | |
| 447 434 <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> | |
| 448 435 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
| 449 436 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 450 437 <span class="s">}</span> | |
| 451 438 | |
| 452 439 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 453 440 <span class="i">$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> | |
| 454 441 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 455 442 <span class="s">}</span> | |
| 456 443 | |
| 457 444 <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> | |
| 458 445 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
| 459 446 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 460 447 <span class="s">}</span> | |
| 461 448 | |
| 462 449 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 463 450 <span class="i">$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">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">0</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> | |
| 464 451 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 465 452 <span class="s">}</span> | |
| 466 453 | |
| 467 454 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 468 455 <span class="i">$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> | |
| 469 456 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 470 457 <span class="s">}</span> | |
| 471 458 | |
| 472 459 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_AssignInitialAtomIdentifiers: Couldn't assign intial atom identifiers: InitialAtomIdentifierType $This->{AtomIdentifierType} is not supported..."</span><span class="sc">;</span> | |
| 473 460 <span class="s">}</span> | |
| 474 461 | |
| 475 462 <span class="c"># Assign atom types...</span> | |
| 476 463 <span class="i">$SpecifiedAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 477 464 | |
| 478 465 <span class="c"># Make sure atom types assignment is successful...</span> | |
| 479 466 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 480 467 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 481 468 <span class="s">}</span> | |
| 482 469 | |
| 483 470 <span class="c"># Assign atom identifiers at radius 0...</span> | |
| 484 471 <span class="i">$Radius</span> = <span class="n">0</span><span class="sc">;</span> | |
| 485 472 <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> | |
| 486 473 <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> | |
| 487 474 | |
| 488 475 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 489 476 <span class="i">$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> | |
| 490 477 | |
| 491 478 <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> | |
| 492 479 <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> | |
| 493 480 <span class="s">}</span> | |
| 494 481 | |
| 495 482 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 496 483 <span class="s">}</span> | |
| 497 484 | |
| 498 485 <span class="c"># Initialize atom identifiers...</span> | |
| 499 486 <span class="c">#</span> | |
| 500 <a name="_InitializeAtomIdentifiers-"></a> 487 <span class="k">sub </span><span class="m">_InitializeAtomIdentifiers</span> <span class="s">{</span> | |
| 501 488 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 502 489 <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> | |
| 503 490 | |
| 504 491 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span> | |
| 505 492 | |
| 506 493 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 507 494 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span> | |
| 508 495 <span class="c"># Atom idenfiers key and value correspond to AtomID and AtomIdentifier</span> | |
| 509 496 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 510 497 | |
| 511 498 <span class="c"># Unique and strcuturally unique idenfiers key and value correspond to AtomIdentifier and AtomID</span> | |
| 512 499 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 513 500 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 514 501 | |
| 515 502 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 516 503 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 517 504 <span class="s">}</span> | |
| 518 505 | |
| 519 506 <span class="s">}</span> | |
| 520 507 | |
| 521 508 <span class="c"># Collect atom neighborhoods upto specified neighborhood radius...</span> | |
| 522 509 <span class="c">#</span> | |
| 523 <a name="_GetAtomNeighborhoods-"></a> 510 <span class="k">sub </span><span class="m">_GetAtomNeighborhoods</span> <span class="s">{</span> | |
| 524 511 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 525 512 <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">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 526 513 | |
| 527 514 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 528 515 | |
| 529 516 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span> | |
| 530 517 <span class="k">if</span> <span class="s">(</span><span class="i">$Radius</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 531 518 <span class="c"># At radius level 0, it's just the atoms...</span> | |
| 532 519 <span class="k">return</span><span class="sc">;</span> | |
| 533 520 <span class="s">}</span> | |
| 534 521 | |
| 535 522 <span class="c"># Initialize neighborhood at different radii...</span> | |
| 536 523 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span> | |
| 537 524 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 538 525 <span class="s">}</span> | |
| 539 526 | |
| 540 527 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 541 528 | |
| 542 529 <span class="c"># Collect available atom neighborhoods at different at different neighborhood level for each atom...</span> | |
| 543 530 <span class="k">my</span><span class="s">(</span><span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 544 531 | |
| 545 532 <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> | |
| 546 533 <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> | |
| 547 534 <span class="i">$CurrentRadius</span> = <span class="n">0</span><span class="sc">;</span> | |
| 548 535 <span class="k">for</span> <span class="i">$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">$Radius</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 549 536 <span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$CurrentRadius</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span><span class="sc">;</span> | |
| 550 537 <span class="i">$CurrentRadius</span>++<span class="sc">;</span> | |
| 551 538 <span class="s">}</span> | |
| 552 539 <span class="s">}</span> | |
| 553 540 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 554 541 <span class="s">}</span> | |
| 555 542 | |
| 556 543 <span class="c"># Assign atom identifiers to central atom at each neighborhood radius level...</span> | |
| 557 544 <span class="c">#</span> | |
| 558 <a name="_AssignAtomIdentifiersToAtomNeighborhoods-"></a> 545 <span class="k">sub </span><span class="m">_AssignAtomIdentifiersToAtomNeighborhoods</span> <span class="s">{</span> | |
| 559 546 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 560 547 <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> | |
| 561 548 | |
| 562 549 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 563 550 <span class="k">return</span><span class="sc">;</span> | |
| 564 551 <span class="s">}</span> | |
| 565 552 | |
| 566 553 <span class="c"># Go over the atom neighborhoods at each radius upto specified radius and assign atom</span> | |
| 567 554 <span class="c"># indentifiers using their connected successor atoms and their identifiers.</span> | |
| 568 555 <span class="c">#</span> | |
| 569 556 <span class="c"># For a neighborhood atom at a specified radius, the successor connected atoms correpond</span> | |
| 570 557 <span class="c"># to next radius level and the last set of neighorhood atoms don't have any successor connected</span> | |
| 571 558 <span class="c"># atoms. Additionally, radius level 0 just correspond to initial atom identifiers.</span> | |
| 572 559 <span class="c">#</span> | |
| 573 560 <span class="c"># So in order to process atom neighborhood upto specified radius level, the last atom neighborhood</span> | |
| 574 561 <span class="c"># doesn't need to be processed: it gets processed at previous radius level as successor connected</span> | |
| 575 562 <span class="c"># atoms.</span> | |
| 576 563 <span class="c">#</span> | |
| 577 564 <span class="j">RADIUS:</span> <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 578 565 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 579 566 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 580 567 | |
| 581 568 <span class="c"># Are there any available atom neighborhoods at this radius?</span> | |
| 582 569 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$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> | |
| 583 570 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 584 571 <span class="s">}</span> | |
| 585 572 <span class="i">$NextRadius</span> = <span class="i">$Radius</span> + <span class="n">1</span><span class="sc">;</span> | |
| 586 573 | |
| 587 574 <span class="c"># Go over neighborhood atoms and their successor connected atoms at this radius and collect</span> | |
| 588 575 <span class="c"># (BondOrder AtomIdentifier) values for bonded atom pairs. Additionally, keep track of atom and bonds</span> | |
| 589 576 <span class="c"># for the neighorhoods to remove identifieres generated from structurally duplicate features.</span> | |
| 590 577 <span class="c">#</span> | |
| 591 578 <span class="k">my</span><span class="s">(</span><span class="i">%BondOrdersAndAtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> | |
| 592 579 | |
| 593 580 <span class="i">%BondOrdersAndAtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 594 581 <span class="i">$SuccessorAtomCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 595 582 | |
| 596 583 <span class="j">NEIGHBORHOODS:</span> <span class="k">for</span> <span class="i">$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">$AtomID</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 597 584 <span class="s">(</span><span class="i">$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> | |
| 598 585 | |
| 599 586 <span class="c"># Any connected successors for the NeighborhoodAtom?</span> | |
| 600 587 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 601 588 <span class="k">next</span> <span class="j">NEIGHBORHOODS</span><span class="sc">;</span> | |
| 602 589 <span class="s">}</span> | |
| 603 590 <span class="j">SUCCESSORATOM:</span> <span class="k">for</span> <span class="i">$SuccessorAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 604 591 <span class="k">if</span> <span class="s">(</span><span class="i">$SuccessorAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 605 592 <span class="c"># Skip successor hydrogen atom...</span> | |
| 606 593 <span class="k">next</span> <span class="j">SUCCESSORATOM</span><span class="sc">;</span> | |
| 607 594 <span class="s">}</span> | |
| 608 595 <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> | |
| 609 596 <span class="i">$SuccessorAtomCount</span>++<span class="sc">;</span> | |
| 610 597 | |
| 611 598 <span class="i">$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> | |
| 612 599 <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">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 613 600 | |
| 614 601 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}<span class="s">)</span> <span class="s">{</span> | |
| 615 602 <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 616 603 <span class="s">}</span> | |
| 617 604 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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> | |
| 618 605 <span class="s">}</span> | |
| 619 606 <span class="s">}</span> | |
| 620 607 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SuccessorAtomCount</span><span class="s">)</span> <span class="s">{</span> | |
| 621 608 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 622 609 <span class="s">}</span> | |
| 623 610 <span class="c"># Assign a new atom identifier at the NextRadius level...</span> | |
| 624 611 <span class="i">$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> | |
| 625 612 <span class="s">}</span> | |
| 626 613 <span class="s">}</span> | |
| 627 614 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 628 615 <span class="s">}</span> | |
| 629 616 | |
| 630 617 <span class="c"># Generate and assign atom indentifier for AtomID using atom neighborhood at next radius level...</span> | |
| 631 618 <span class="c">#</span> | |
| 632 <a name="_AssignAtomIdentifierToAtomNeighborhood-"></a> 619 <span class="k">sub </span><span class="m">_AssignAtomIdentifierToAtomNeighborhood</span> <span class="s">{</span> | |
| 633 620 <span class="k">my</span><span class="s">(</span><span class="i">$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">$BondOrdersAndAtomIdentifiersRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 634 621 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 635 622 | |
| 636 623 <span class="i">$NextRadius</span> = <span class="i">$Radius</span> + <span class="n">1</span><span class="sc">;</span> | |
| 637 624 | |
| 638 625 <span class="i">@AtomIndentifiersInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 639 626 | |
| 640 627 <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> | |
| 641 628 <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> | |
| 642 629 | |
| 643 630 <span class="c"># Sort out successor atom bond order and identifier pairs by bond order followed by atom identifiers</span> | |
| 644 631 <span class="c"># in order to make the final atom identifier graph invariant...</span> | |
| 645 632 <span class="c">#</span> | |
| 646 633 <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> | |
| 647 634 <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">$BondOrder</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 648 635 <span class="k">push</span> <span class="i">@AtomIndentifiersInfo</span><span class="cm">,</span> <span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$SuccessorAtomIdentifier</span><span class="s">)</span><span class="sc">;</span> | |
| 649 636 <span class="s">}</span> | |
| 650 637 <span class="s">}</span> | |
| 651 638 <span class="i">$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> | |
| 652 639 <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> | |
| 653 640 | |
| 654 641 <span class="c"># Assign atom identifier to the atom at next radius level...</span> | |
| 655 642 <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> | |
| 656 643 | |
| 657 644 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 658 645 <span class="s">}</span> | |
| 659 646 | |
| 660 647 <span class="c"># Remove duplicates atom identifiers...</span> | |
| 661 648 <span class="c">#</span> | |
| 662 <a name="_RemoveDuplicateAtomIdentifiers-"></a> 649 <span class="k">sub </span><span class="m">_RemoveDuplicateAtomIdentifiers</span> <span class="s">{</span> | |
| 663 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 664 651 | |
| 665 652 <span class="i">$This</span><span class="i">->_RemoveDuplicateIdentifiersByValue</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 666 653 <span class="i">$This</span><span class="i">->_RemoveStructurallyDuplicateIdenfiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 667 654 | |
| 668 655 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 669 656 <span class="s">}</span> | |
| 670 657 | |
| 671 658 <span class="c"># Remove duplicate identifiers at each radius level by just using their value...</span> | |
| 672 659 <span class="c">#</span> | |
| 673 <a name="_RemoveDuplicateIdentifiersByValue-"></a> 660 <span class="k">sub </span><span class="m">_RemoveDuplicateIdentifiersByValue</span> <span class="s">{</span> | |
| 674 661 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 675 662 <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> | |
| 676 663 | |
| 677 664 <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> | |
| 678 665 <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> | |
| 679 666 <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> | |
| 680 667 <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">$AtomID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 681 668 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 682 669 <span class="s">}</span> | |
| 683 670 <span class="i">$AtomIdentifier</span> = <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
| 684 671 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$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> | |
| 685 672 <span class="c"># It's a duplicate atom idenfier at this radius level...</span> | |
| 686 673 <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 687 674 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 688 675 <span class="s">}</span> | |
| 689 676 <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$AtomID</span><span class="sc">;</span> | |
| 690 677 <span class="i">$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> | |
| 691 678 <span class="s">}</span> | |
| 692 679 <span class="s">}</span> | |
| 693 680 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 694 681 <span class="s">}</span> | |
| 695 682 | |
| 696 683 <span class="c"># Remove structurally duplicate identifiers at each radius level...</span> | |
| 697 684 <span class="c">#</span> | |
| 698 685 <span class="c"># Methodology:</span> | |
| 699 686 <span class="c"># . For unquie atom identifiers at each radius level, assign complete structure features</span> | |
| 700 687 <span class="c"># in terms all the bonds involved to generate that identifier</span> | |
| 701 688 <span class="c"># . Use the complete structure features to remover atom identifiers which are</span> | |
| 702 689 <span class="c"># structurally equivalent which can also be at earlier radii levels</span> | |
| 703 690 <span class="c">#</span> | |
| 704 691 <span class="c">#</span> | |
| 705 <a name="_RemoveStructurallyDuplicateIdenfiers-"></a> 692 <span class="k">sub </span><span class="m">_RemoveStructurallyDuplicateIdenfiers</span> <span class="s">{</span> | |
| 706 693 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 707 694 <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">$SimilarAtomIdentifier</span><span class="s">)</span><span class="sc">;</span> | |
| 708 695 | |
| 709 696 <span class="c"># Setup structure features...</span> | |
| 710 697 <span class="i">$This</span><span class="i">->_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 711 698 | |
| 712 699 <span class="c"># Identify structurally unqiue identifiers...</span> | |
| 713 700 <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> | |
| 714 701 <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">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 715 702 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> | |
| 716 703 | |
| 717 704 <span class="s">(</span><span class="i">$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">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> | |
| 718 705 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilarAtomIdentifier</span><span class="s">)</span> <span class="s">{</span> | |
| 719 706 <span class="c"># Current atom identifier is similar to an earlier structurally unique atom identifier...</span> | |
| 720 707 <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> | |
| 721 708 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span> | |
| 722 709 <span class="s">}</span> | |
| 723 710 <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> | |
| 724 711 | |
| 725 712 <span class="c"># Set structurally unique atom identifier count to the unique atom identifiers count...</span> | |
| 726 713 <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> | |
| 727 714 <span class="s">}</span> | |
| 728 715 <span class="s">}</span> | |
| 729 716 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 730 717 <span class="s">}</span> | |
| 731 718 | |
| 732 719 <span class="c"># Set final fingerpritns vector...</span> | |
| 733 720 <span class="c">#</span> | |
| 734 <a name="_SetFinalFingerprints-"></a> 721 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> | |
| 735 722 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 736 723 | |
| 737 724 <span class="c"># Mark successful generation of fingerprints...</span> | |
| 738 725 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 739 726 | |
| 740 727 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 741 728 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 742 729 <span class="s">}</span> | |
| 743 730 <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> | |
| 744 731 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityCountFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 745 732 <span class="s">}</span> | |
| 746 733 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 747 734 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityBitsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 748 735 <span class="s">}</span> | |
| 749 736 | |
| 750 737 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 751 738 <span class="s">}</span> | |
| 752 739 | |
| 753 740 <span class="c"># Set final extended connectivity fingerpritns vector...</span> | |
| 754 741 <span class="c">#</span> | |
| 755 <a name="_SetFinalExtendedConnectivityFingerprints-"></a> 742 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityFingerprints</span> <span class="s">{</span> | |
| 756 743 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 757 744 <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> | |
| 758 745 | |
| 759 746 <span class="i">@AtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 760 747 | |
| 761 748 <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> | |
| 762 749 <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">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 763 750 <span class="k">push</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="sc">;</span> | |
| 764 751 <span class="s">}</span> | |
| 765 752 <span class="s">}</span> | |
| 766 753 <span class="c"># Add atom identifiers to fingerprint vector...</span> | |
| 767 754 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> | |
| 768 755 | |
| 769 756 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 770 757 <span class="s">}</span> | |
| 771 758 | |
| 772 759 <span class="c"># Set final extended connectivity count fingerpritns vector...</span> | |
| 773 760 <span class="c">#</span> | |
| 774 <a name="_SetFinalExtendedConnectivityCountFingerprints-"></a> 761 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityCountFingerprints</span> <span class="s">{</span> | |
| 775 762 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 776 763 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 777 764 | |
| 778 765 <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> | |
| 779 766 | |
| 780 767 <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> | |
| 781 768 <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">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 782 769 <span class="i">$AtomIdentifierCount</span> = <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> | |
| 783 770 <span class="k">push</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="sc">;</span> | |
| 784 771 <span class="k">push</span> <span class="i">@AtomIdentifiersCount</span><span class="cm">,</span> <span class="i">$AtomIdentifierCount</span><span class="sc">;</span> | |
| 785 772 <span class="s">}</span> | |
| 786 773 <span class="s">}</span> | |
| 787 774 <span class="c"># Add atom identifiers to fingerprint vector as value IDs...</span> | |
| 788 775 <span class="i">$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> | |
| 789 776 | |
| 790 777 <span class="c"># Add atom identifiers to count to fingerprint vector as values...</span> | |
| 791 778 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@AtomIdentifiersCount</span><span class="s">)</span><span class="sc">;</span> | |
| 792 779 | |
| 793 780 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 794 781 <span class="s">}</span> | |
| 795 782 | |
| 796 783 <span class="c"># Set final extended connectivity bits fingerpritns vector...</span> | |
| 797 784 <span class="c">#</span> | |
| 798 <a name="_SetFinalExtendedConnectivityBitsFingerprints-"></a> 785 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityBitsFingerprints</span> <span class="s">{</span> | |
| 799 786 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 800 787 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 801 788 | |
| 802 789 <span class="i">$FingerprintsBitVector</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="sc">;</span> | |
| 803 790 | |
| 804 791 <span class="i">$Size</span> = <span class="i">$This</span>->{<span class="w">Size</span>}<span class="sc">;</span> | |
| 805 792 | |
| 806 793 <span class="i">$SkipBitPosCheck</span> = <span class="n">1</span><span class="sc">;</span> | |
| 807 794 | |
| 808 795 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> | |
| 809 796 <span class="k">for</span> <span class="i">$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> | |
| 810 797 <span class="c"># Set random number seed...</span> | |
| 811 798 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span> <span class="s">{</span> | |
| 812 799 <span class="i">CORE::</span><span class="k">srand</span><span class="s">(</span><span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> | |
| 813 800 <span class="s">}</span> | |
| 814 801 <span class="k">else</span> <span class="s">{</span> | |
| 815 802 <span class="i">MathUtil::srandom</span><span class="s">(</span><span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> | |
| 816 803 <span class="s">}</span> | |
| 817 804 | |
| 818 805 <span class="c"># Set bit position...</span> | |
| 819 806 <span class="i">$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">$Size</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 820 807 <span class="i">$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> | |
| 821 808 <span class="s">}</span> | |
| 822 809 <span class="s">}</span> | |
| 823 810 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 824 811 <span class="s">}</span> | |
| 825 812 | |
| 826 813 | |
| 827 814 <span class="c"># Identify structurally unique identifiers by comparing structure features involved in</span> | |
| 828 815 <span class="c"># generating identifiear by comparing it agains all the previous structurally unique</span> | |
| 829 816 <span class="c"># identifiers...</span> | |
| 830 817 <span class="c">#</span> | |
| 831 <a name="_FindStructurallySimilarAtomIdentifier-"></a> 818 <span class="k">sub </span><span class="m">_FindStructurallySimilarAtomIdentifier</span> <span class="s">{</span> | |
| 832 819 <span class="k">my</span><span class="s">(</span><span class="i">$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">$SpecifiedAtomIdentifier</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 833 820 <span class="k">my</span><span class="s">(</span><span class="i">$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">$SpecifiedFeatureAtomIDsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 834 821 | |
| 835 822 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedRadius</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 836 823 <span class="c"># After duplicate removal by value, all identifier at radius level 0 would be structurally unique...</span> | |
| 837 824 <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> | |
| 838 825 <span class="s">}</span> | |
| 839 826 | |
| 840 827 <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> | |
| 841 828 <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> | |
| 842 829 | |
| 843 830 <span class="c"># No need to compare features at radius 0...</span> | |
| 844 831 <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> | |
| 845 832 <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">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 846 833 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> | |
| 847 834 | |
| 848 835 <span class="i">$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">$AtomID</span>}<span class="sc">;</span> | |
| 849 836 <span class="i">$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">$AtomID</span>}<span class="sc">;</span> | |
| 850 837 | |
| 851 838 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedFeatureAtomCount</span> != <span class="i">$FeatureAtomCount</span><span class="s">)</span> <span class="s">{</span> | |
| 852 839 <span class="c"># Couldn't be structurally equivalent...</span> | |
| 853 840 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span> | |
| 854 841 <span class="s">}</span> | |
| 855 842 <span class="k">for</span> <span class="i">$SpecifiedFeatureAtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span> {<span class="i">$SpecifiedFeatureAtomIDsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 856 843 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$FeatureAtomIDsRef</span>->{<span class="i">$SpecifiedFeatureAtomID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 857 844 <span class="c"># For structural equivalency, all atom in specified feature must also be present in a previously</span> | |
| 858 845 <span class="c"># identified structurally unique structure feature...</span> | |
| 859 846 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span> | |
| 860 847 <span class="s">}</span> | |
| 861 848 <span class="s">}</span> | |
| 862 849 <span class="c"># Found structurally equivalent feature...</span> | |
| 863 850 <span class="k">return</span> <span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> | |
| 864 851 <span class="s">}</span> | |
| 865 852 <span class="s">}</span> | |
| 866 853 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 867 854 <span class="s">}</span> | |
| 868 855 | |
| 869 856 <span class="c"># Setup structure features for atom IDs involved in unique atom identifiers at all</span> | |
| 870 857 <span class="c"># radii level...</span> | |
| 871 858 <span class="c">#</span> | |
| 872 <a name="_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers-"></a> 859 <span class="k">sub </span><span class="m">_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers</span> <span class="s">{</span> | |
| 873 860 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 874 861 <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">$NeighborhoodAtomSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">%AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 875 862 | |
| 876 863 <span class="i">$This</span><span class="i">->_InitializeStructureFeatures</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 877 864 | |
| 878 865 <span class="c"># Collect atom IDs involved in unique atom identifiers...</span> | |
| 879 866 <span class="i">%AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 880 867 <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> | |
| 881 868 <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">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 882 869 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> | |
| 883 870 <span class="i">$AtomIDs</span>{<span class="i">$AtomID</span>} = <span class="i">$AtomID</span><span class="sc">;</span> | |
| 884 871 <span class="s">}</span> | |
| 885 872 <span class="s">}</span> | |
| 886 873 | |
| 887 874 <span class="c"># Setup structure features...</span> | |
| 888 875 <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> | |
| 889 876 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AtomIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 890 877 <span class="k">my</span><span class="s">(</span><span class="i">$StructureFeatureAtomCount</span><span class="cm">,</span> <span class="i">%StructureFeatureAtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 891 878 | |
| 892 879 <span class="i">$StructureFeatureAtomCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 893 880 <span class="i">%StructureFeatureAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 894 881 | |
| 895 882 <span class="c"># Get partial structure features for the atom at previous radius level...</span> | |
| 896 883 <span class="i">$PreviousRadius</span> = <span class="i">$Radius</span> - <span class="n">1</span><span class="sc">;</span> | |
| 897 884 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRadius</span> >= <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 898 885 <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> | |
| 899 886 <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">$AtomID</span>}}<span class="sc">;</span> | |
| 900 887 <span class="s">}</span> | |
| 901 888 | |
| 902 889 <span class="c"># Get all neighborhood atom at this radius level...</span> | |
| 903 890 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$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> | |
| 904 891 <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> | |
| 905 892 <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">$NeighborhoodAtomsWithSuccessorAtomsRef</span>}<span class="sc">;</span> | |
| 906 893 <span class="k">if</span> <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 907 894 <span class="k">next</span> <span class="j">NEIGHBORHOODS</span><span class="sc">;</span> | |
| 908 895 <span class="s">}</span> | |
| 909 896 <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> | |
| 910 897 <span class="i">$StructureFeatureAtomCount</span>++<span class="sc">;</span> | |
| 911 898 <span class="i">$StructureFeatureAtomIDs</span>{<span class="i">$NeighborhoodAtomID</span>} = <span class="i">$NeighborhoodAtomID</span><span class="sc">;</span> | |
| 912 899 <span class="s">}</span> | |
| 913 900 <span class="s">}</span> | |
| 914 901 | |
| 915 902 <span class="c"># Assign structure features to atom at this radius level...</span> | |
| 916 903 <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> | |
| 917 904 <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = \<span class="i">%StructureFeatureAtomIDs</span><span class="sc">;</span> | |
| 918 905 <span class="s">}</span> | |
| 919 906 <span class="s">}</span> | |
| 920 907 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 921 908 <span class="s">}</span> | |
| 922 909 | |
| 923 910 <span class="c"># Intialize structure features at each radius level...</span> | |
| 924 911 <span class="c">#</span> | |
| 925 <a name="_InitializeStructureFeatures-"></a> 912 <span class="k">sub </span><span class="m">_InitializeStructureFeatures</span> <span class="s">{</span> | |
| 926 913 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 927 914 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 928 915 | |
| 929 916 <span class="c"># Initialize all structure features...</span> | |
| 930 917 | |
| 931 918 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 932 919 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 933 920 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 934 921 | |
| 935 922 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span> | |
| 936 923 <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> | |
| 937 924 <span class="c"># Structure features for at specific radii accessed using atom IDs...</span> | |
| 938 925 <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> | |
| 939 926 <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> | |
| 940 927 <span class="s">}</span> | |
| 941 928 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 942 929 <span class="s">}</span> | |
| 943 930 | |
| 944 931 <span class="c"># Cache appropriate molecule data...</span> | |
| 945 932 <span class="c">#</span> | |
| 946 <a name="_SetupMoleculeDataCache-"></a> 933 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> | |
| 947 934 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 948 935 | |
| 949 936 <span class="c"># Get all non-hydrogen atoms...</span> | |
| 950 937 <span class="k">my</span><span class="s">(</span><span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> | |
| 951 938 <span class="i">$NegateAtomCheckMethod</span> = <span class="n">1</span><span class="sc">;</span> | |
| 952 939 <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">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> | |
| 953 940 | |
| 954 941 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 955 942 <span class="s">}</span> | |
| 956 943 | |
| 957 944 <span class="c"># Clear cached molecule data...</span> | |
| 958 945 <span class="c">#</span> | |
| 959 <a name="_ClearMoleculeDataCache-"></a> 946 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> | |
| 960 947 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 961 948 | |
| 962 949 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 963 950 | |
| 964 951 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 965 952 <span class="s">}</span> | |
| 966 953 | |
| 967 954 <span class="c"># Initialize atom indentifier type information...</span> | |
| 968 955 <span class="c">#</span> | |
| 969 956 <span class="c"># Current supported values:</span> | |
| 970 957 <span class="c">#</span> | |
| 971 958 <span class="c"># AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,</span> | |
| 972 959 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> | |
| 973 960 <span class="c">#</span> | |
| 974 <a name="_InitializeAtomIdentifierTypeInformation-"></a> 961 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> | |
| 975 962 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 976 963 | |
| 977 964 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> | |
| 978 965 <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> | |
| 979 966 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 980 967 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 981 968 <span class="s">}</span> | |
| 982 969 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 983 970 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 984 971 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 985 972 <span class="s">}</span> | |
| 986 973 <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> | |
| 987 974 <span class="c"># Nothing to do for now...</span> | |
| 988 975 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> | |
| 989 976 <span class="s">}</span> | |
| 990 977 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
| 991 978 <span class="s">}</span> | |
| 992 979 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 993 980 <span class="s">}</span> | |
| 994 981 | |
| 995 982 <span class="c"># Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes</span> | |
| 996 983 <span class="c"># class, to use for generating initial atom identifiers...</span> | |
| 997 984 <span class="c">#</span> | |
| 998 985 <span class="c"># Let:</span> | |
| 999 986 <span class="c"># AS = Atom symbol corresponding to element symbol</span> | |
| 1000 987 <span class="c">#</span> | |
| 1001 988 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1002 989 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1003 990 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1004 991 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1005 992 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1006 993 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 1007 994 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> | |
| 1008 995 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> | |
| 1009 996 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> | |
| 1010 997 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> | |
| 1011 998 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> | |
| 1012 999 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> | |
| 1013 1000 <span class="c">#</span> | |
| 1014 1001 <span class="c"># Then:</span> | |
| 1015 1002 <span class="c">#</span> | |
| 1016 1003 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> | |
| 1017 1004 <span class="c">#</span> | |
| 1018 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> | |
| 1019 1006 <span class="c">#</span> | |
| 1020 1007 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span> | |
| 1021 1008 <span class="c"># optional.</span> | |
| 1022 1009 <span class="c">#</span> | |
| 1023 1010 <span class="c"># Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:</span> | |
| 1024 1011 <span class="c">#</span> | |
| 1025 1012 <span class="c"># AS, X<n>, BO<n>, H<n>, FC<+n/-n>, MN<n></span> | |
| 1026 1013 <span class="c">#</span> | |
| 1027 1014 <span class="c"># In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words</span> | |
| 1028 1015 <span class="c"># are also allowed:</span> | |
| 1029 1016 <span class="c">#</span> | |
| 1030 1017 <span class="c"># X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors</span> | |
| 1031 1018 <span class="c"># BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms</span> | |
| 1032 1019 <span class="c"># LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms</span> | |
| 1033 1020 <span class="c"># SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms</span> | |
| 1034 1021 <span class="c"># DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms</span> | |
| 1035 1022 <span class="c"># TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms</span> | |
| 1036 1023 <span class="c"># H : NumOfImplicitAndExplicitHydrogens</span> | |
| 1037 1024 <span class="c"># Ar : Aromatic</span> | |
| 1038 1025 <span class="c"># RA : RingAtom</span> | |
| 1039 1026 <span class="c"># FC : FormalCharge</span> | |
| 1040 1027 <span class="c"># MN : MassNumber</span> | |
| 1041 1028 <span class="c"># SM : SpinMultiplicity</span> | |
| 1042 1029 <span class="c">#</span> | |
| 1043 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a>1030 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> | |
| 1044 1031 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1045 1032 | |
| 1046 1033 <span class="c"># Default atomic invariants to use for generating initial atom identifiers are: AS, X, BO, LBO, H, FC</span> | |
| 1047 1034 <span class="c">#</span> | |
| 1048 1035 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1049 1036 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="cm">,</span> <span class="q">'MN'</span><span class="s">)</span><span class="sc">;</span> | |
| 1050 1037 | |
| 1051 1038 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1052 1039 <span class="s">}</span> | |
| 1053 1040 | |
| 1054 1041 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> | |
| 1055 1042 <span class="c"># class, to use for generating initial atom identifiers...</span> | |
| 1056 1043 <span class="c">#</span> | |
| 1057 1044 <span class="c"># Let:</span> | |
| 1058 1045 <span class="c"># HBD: HydrogenBondDonor</span> | |
| 1059 1046 <span class="c"># HBA: HydrogenBondAcceptor</span> | |
| 1060 1047 <span class="c"># PI : PositivelyIonizable</span> | |
| 1061 1048 <span class="c"># NI : NegativelyIonizable</span> | |
| 1062 1049 <span class="c"># Ar : Aromatic</span> | |
| 1063 1050 <span class="c"># Hal : Halogen</span> | |
| 1064 1051 <span class="c"># H : Hydrophobic</span> | |
| 1065 1052 <span class="c"># RA : RingAtom</span> | |
| 1066 1053 <span class="c"># CA : ChainAtom</span> | |
| 1067 1054 <span class="c">#</span> | |
| 1068 1055 <span class="c"># Then:</span> | |
| 1069 1056 <span class="c">#</span> | |
| 1070 1057 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> | |
| 1071 1058 <span class="c">#</span> | |
| 1072 1059 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> | |
| 1073 1060 <span class="c">#</span> | |
| 1074 1061 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> | |
| 1075 1062 <span class="c">#</span> | |
| 1076 1063 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> | |
| 1077 1064 <span class="c">#</span> | |
| 1078 1065 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> | |
| 1079 1066 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> | |
| 1080 1067 <span class="c"># PositivelyIonizable: +, NH2</span> | |
| 1081 1068 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> | |
| 1082 1069 <span class="c">#</span> | |
| 1083 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a>1070 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> | |
| 1084 1071 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1085 1072 | |
| 1086 1073 <span class="c"># Default functional class atom typess to use for generating initial atom identifiers</span> | |
| 1087 1074 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span> | |
| 1088 1075 <span class="c">#</span> | |
| 1089 1076 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1090 1077 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> | |
| 1091 1078 | |
| 1092 1079 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1093 1080 <span class="s">}</span> | |
| 1094 1081 | |
| 1095 1082 <span class="c"># Set atomic invariants to use for generation of intial atom indentifiers...</span> | |
| 1096 1083 <span class="c">#</span> | |
| 1097 <a name="SetAtomicInvariantsToUse-"></a>1084 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> | |
| 1098 1085 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1099 1086 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1100 1087 | |
| 1101 1088 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
| 1102 1089 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> | |
| 1103 1090 <span class="k">return</span><span class="sc">;</span> | |
| 1104 1091 <span class="s">}</span> | |
| 1105 1092 | |
| 1106 1093 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1107 1094 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalAtomTypesToUse: AtomicInvariantsToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
| 1108 1095 <span class="k">return</span><span class="sc">;</span> | |
| 1109 1096 <span class="s">}</span> | |
| 1110 1097 | |
| 1111 1098 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 1112 1099 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
| 1113 1100 | |
| 1114 1101 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1115 1102 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1116 1103 | |
| 1117 1104 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
| 1118 1105 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
| 1119 1106 <span class="s">}</span> | |
| 1120 1107 <span class="k">else</span> <span class="s">{</span> | |
| 1121 1108 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
| 1122 1109 <span class="s">}</span> | |
| 1123 1110 | |
| 1124 1111 <span class="c"># Make sure specified AtomicInvariants are valid...</span> | |
| 1125 1112 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> | |
| 1126 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> | |
| 1127 1114 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> | |
| 1128 1115 <span class="s">}</span> | |
| 1129 1116 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> | |
| 1130 1117 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> | |
| 1131 1118 <span class="s">}</span> | |
| 1132 1119 | |
| 1133 1120 <span class="c"># Set atomic invariants to use...</span> | |
| 1134 1121 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1135 1122 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> | |
| 1136 1123 | |
| 1137 1124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1138 1125 <span class="s">}</span> | |
| 1139 1126 | |
| 1140 1127 <span class="c"># Set functional classes to use for generation of intial atom indentifiers...</span> | |
| 1141 1128 <span class="c">#</span> | |
| 1142 <a name="SetFunctionalClassesToUse-"></a>1129 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> | |
| 1143 1130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1144 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> | |
| 1145 1132 | |
| 1146 1133 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
| 1147 1134 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> | |
| 1148 1135 <span class="k">return</span><span class="sc">;</span> | |
| 1149 1136 <span class="s">}</span> | |
| 1150 1137 | |
| 1151 1138 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1152 1139 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> | |
| 1153 1140 <span class="k">return</span><span class="sc">;</span> | |
| 1154 1141 <span class="s">}</span> | |
| 1155 1142 | |
| 1156 1143 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 1157 1144 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
| 1158 1145 | |
| 1159 1146 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1160 1147 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1161 1148 | |
| 1162 1149 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
| 1163 1150 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
| 1164 1151 <span class="s">}</span> | |
| 1165 1152 <span class="k">else</span> <span class="s">{</span> | |
| 1166 1153 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> | |
| 1167 1154 <span class="s">}</span> | |
| 1168 1155 | |
| 1169 1156 <span class="c"># Make sure specified FunctionalClasses are valid...</span> | |
| 1170 1157 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> | |
| 1171 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> | |
| 1172 1159 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> | |
| 1173 1160 <span class="s">}</span> | |
| 1174 1161 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> | |
| 1175 1162 <span class="s">}</span> | |
| 1176 1163 | |
| 1177 1164 <span class="c"># Set functional classes to use...</span> | |
| 1178 1165 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1179 1166 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> | |
| 1180 1167 | |
| 1181 1168 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1182 1169 <span class="s">}</span> | |
| 1183 1170 | |
| 1184 1171 <span class="c"># Return a string containg data for ExtendedConnectivityFingerprints object...</span> | |
| 1185 <a name="StringifyExtendedConnectivityFingerprints-"></a>1172 <span class="k">sub </span><span class="m">StringifyExtendedConnectivityFingerprints</span> <span class="s">{</span> | |
| 1186 1173 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1187 1174 <span class="k">my</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprintsString</span><span class="s">)</span><span class="sc">;</span> | |
| 1188 1175 | |
| 1189 1176 <span class="i">$ExtendedConnectivityFingerprintsString</span> = <span class="q">"InitialAtomIdentifierType: $This->{AtomIdentifierType}; NeighborhoodRadius: $This->{NeighborhoodRadius}"</span><span class="sc">;</span> | |
| 1190 1177 | |
| 1191 1178 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 1192 1179 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1193 1180 | |
| 1194 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> | |
| 1195 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> | |
| 1196 1183 | |
| 1197 1184 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 1198 1185 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> | |
| 1199 1186 <span class="s">}</span> | |
| 1200 1187 | |
| 1201 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> | |
| 1202 1189 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
| 1203 1190 <span class="i">$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> | |
| 1204 1191 <span class="s">}</span> | |
| 1205 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> | |
| 1206 1193 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> | |
| 1207 1194 | |
| 1208 1195 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1209 1196 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1210 1197 | |
| 1211 1198 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> | |
| 1212 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> | |
| 1213 1200 <span class="s">}</span> | |
| 1214 1201 | |
| 1215 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> | |
| 1216 1203 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
| 1217 1204 <span class="i">$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> | |
| 1218 1205 <span class="s">}</span> | |
| 1219 1206 | |
| 1220 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> | |
| 1221 1208 <span class="c"># Size...</span> | |
| 1222 1209 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; Size: $This->{Size}; MinSize: $This->{MinSize}; MaxSize: $This->{MaxSize}"</span><span class="sc">;</span> | |
| 1223 1210 | |
| 1224 1211 <span class="c"># Fingerprint bit density and num of bits set...</span> | |
| 1225 1212 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSetBits</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span> | |
| 1226 1213 <span class="i">$NumOfSetBits</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1227 1214 <span class="i">$BitDensity</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetFingerprintsBitDensity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1228 1215 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity"</span><span class="sc">;</span> | |
| 1229 1216 | |
| 1230 1217 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FingerprintsBitVector: < $This->{FingerprintsBitVector} >"</span><span class="sc">;</span> | |
| 1231 1218 <span class="s">}</span> | |
| 1232 1219 <span class="k">else</span> <span class="s">{</span> | |
| 1233 1220 <span class="c"># Number of identifiers...</span> | |
| 1234 1221 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; NumOfIdentifiers: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1235 1222 | |
| 1236 1223 <span class="c"># FingerprintsVector...</span> | |
| 1237 1224 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> | |
| 1238 1225 <span class="s">}</span> | |
| 1239 1226 | |
| 1240 1227 <span class="k">return</span> <span class="i">$ExtendedConnectivityFingerprintsString</span><span class="sc">;</span> | |
| 1241 1228 <span class="s">}</span> | |
| 1242 1229 | |
| 1243 <a name="EOF-"></a></pre> | |
| 1244 <p> </p> | |
| 1245 <br /> | |
| 1246 <center> | |
| 1247 <img src="../../../images/h2o2.png"> | |
| 1248 </center> | |
| 1249 </body> | |
| 1250 </html> |