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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/ExtendedConnectivityFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,1250 @@ +<html> +<head> +<title>MayaChemTools:Code:Fingerprints::ExtendedConnectivityFingerprints.pm</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<pre> +<a name="package-Fingerprints::ExtendedConnectivityFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span> + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: ExtendedConnectivityFingerprints.pm,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> + 5 <span class="c"># $Revision: 1.39 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> + 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> + 32 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span> + 38 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span> + 39 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span> + 40 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span> + 41 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span> + 42 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span> + 43 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span> + 44 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span> + 45 + 46 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> + 47 + 48 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span> + 49 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> + 50 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> + 51 + 52 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> + 53 + 54 <span class="c"># Setup class variables...</span> + 55 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> + 56 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 57 + 58 <span class="c"># Overload Perl functions...</span> + 59 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyExtendedConnectivityFingerprints'</span><span class="sc">;</span> + 60 + 61 <span class="c"># Class constructor...</span> +<a name="new-"></a> 62 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> + 63 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 64 + 65 <span class="c"># Initialize object...</span> + 66 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 67 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> + 68 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 69 + 70 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> + 71 + 72 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 73 <span class="s">}</span> + 74 + 75 <span class="c"># Initialize object data...</span> + 76 <span class="c">#</span> +<a name="_InitializeExtendedConnectivityFingerprints-"></a> 77 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprints</span> <span class="s">{</span> + 78 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 79 + 80 <span class="c"># Type of fingerprint to generate:</span> + 81 <span class="c">#</span> + 82 <span class="c"># ExtendedConnectivity - Set of integer identifiers corresponding to structurally unique features</span> + 83 <span class="c"># ExtendedConnectivityCount - Set of integer identifiers corresponding to structurally unique features and their count</span> + 84 <span class="c"># ExtendedConnectivityBits - A bit vector indicating presence/absence of structurally unique features</span> + 85 <span class="c">#</span> + 86 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivity'</span><span class="sc">;</span> + 87 + 88 <span class="c"># Atomic neighborhoods radius for extended connectivity...</span> + 89 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span> + 90 + 91 <span class="c"># Size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...</span> + 92 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="n">1024</span><span class="sc">;</span> + 93 + 94 <span class="c"># Min and max size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...</span> + 95 <span class="i">$This</span>->{<span class="w">MinSize</span>} = <span class="n">32</span><span class="sc">;</span> + 96 <span class="i">$This</span>->{<span class="w">MaxSize</span>} = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span> + 97 + 98 <span class="c"># Type of atom attributes to use for initial identifier assignment to non-hydrogen atoms</span> + 99 <span class="c"># during the calculation of extended connectivity fingerprints [ Ref 48, Ref 52 ]...</span> + 100 <span class="c">#</span> + 101 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes,</span> + 102 <span class="c"># DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,</span> + 103 <span class="c"># TPSAAtomTypes, UFFAtomTypes</span> + 104 <span class="c">#</span> + 105 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span> + 106 + 107 <span class="c"># Random number generator to use during generation of fingerprints bit-vector</span> + 108 <span class="c"># string: Perl CORE::rand or MayaChemTools MathUtil::random function.</span> + 109 <span class="c">#</span> + 110 <span class="c"># The random number generator implemented in MayaChemTools is a variant of</span> + 111 <span class="c"># linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].</span> + 112 <span class="c"># It is also referred to as Lehmer random number generator or Park-Miller</span> + 113 <span class="c"># random number generator.</span> + 114 <span class="c">#</span> + 115 <span class="c"># Unlike Perl's core random number generator function rand, the random number</span> + 116 <span class="c"># generator implemented in MayaChemTools, MathUtil::random, generates consistent</span> + 117 <span class="c"># random values across different platformsfor a specific random seed and leads</span> + 118 <span class="c"># to generation of portable fingerprints bit-vector strings.</span> + 119 <span class="c">#</span> + 120 <span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>} = <span class="n">1</span><span class="sc">;</span> + 121 + 122 <span class="c"># Atom neighorhoods up to specified neighborhood radius...</span> + 123 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 124 + 125 <span class="c"># Atom identifiers at different neighborhoods up to specified neighborhood radius...</span> + 126 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 127 + 128 <span class="c"># Structurally unique atom identifiers at different neighborhoods up to specified neighborhood radius...</span> + 129 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 130 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 131 + 132 <span class="c"># Unique atom identifiers at different neighborhoods up to specified neighborhood radius...</span> + 133 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 134 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 135 + 136 <span class="c"># Structure feature information at different neighborhoods up to specified neighborhood</span> + 137 <span class="c"># radius used during removal of atom indentifiers which are structually equivalent...</span> + 138 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 139 <span class="s">}</span> + 140 + 141 <span class="c"># Initialize class ...</span> +<a name="_InitializeClass-"></a> 142 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> + 143 <span class="c">#Class name...</span> + 144 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> + 145 <span class="s">}</span> + 146 + 147 <span class="c"># Initialize object properties....</span> +<a name="_InitializeExtendedConnectivityFingerprintsProperties-"></a> 148 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprintsProperties</span> <span class="s">{</span> + 149 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 150 + 151 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span> + 152 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> + 153 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> + 154 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 155 <span class="s">}</span> + 156 + 157 <span class="c"># Make sure molecule object was specified...</span> + 158 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> + 159 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> + 160 <span class="s">}</span> + 161 + 162 <span class="c"># Make sure AtomIdentifierType was specified...</span> + 163 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> + 164 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."</span><span class="sc">;</span> + 165 <span class="s">}</span> + 166 + 167 <span class="c"># Make sure it's power of 2...</span> + 168 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span> + 169 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 170 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Specified size value, $NamesAndValues{Size}, must be power of 2..."</span><span class="sc">;</span> + 171 <span class="s">}</span> + 172 <span class="s">}</span> + 173 + 174 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span> + 175 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 176 <span class="s">}</span> + 177 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span> + 178 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityCountFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 179 <span class="s">}</span> + 180 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> + 181 <span class="i">$This</span><span class="i">->_InitializeExtendedConnectivityBitsFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 182 <span class="s">}</span> + 183 <span class="k">else</span> <span class="s">{</span> + 184 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeExtendedConnectivityFingerprintsProperties: Unknown ExtendedConnectivity fingerprints type: $This->{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits..."</span><span class="sc">;</span> + 185 <span class="s">}</span> + 186 + 187 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 188 <span class="s">}</span> + 189 + 190 <span class="c"># Initialize extended connectivity fingerprints vector...</span> + 191 <span class="c">#</span> +<a name="_InitializeExtendedConnectivityFingerprintsVector-"></a> 192 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprintsVector</span> <span class="s">{</span> + 193 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 194 + 195 <span class="c"># Type of vector...</span> + 196 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> + 197 + 198 <span class="c"># Type of FingerprintsVector...</span> + 199 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'AlphaNumericalValues'</span><span class="sc">;</span> + 200 + 201 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 202 + 203 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 204 <span class="s">}</span> + 205 + 206 <span class="c"># Initialize extended connectivity count fingerprints vector...</span> + 207 <span class="c">#</span> +<a name="_InitializeExtendedConnectivityCountFingerprintsVector-"></a> 208 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityCountFingerprintsVector</span> <span class="s">{</span> + 209 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 210 + 211 <span class="c"># Type of vector...</span> + 212 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> + 213 + 214 <span class="c"># Type of FingerprintsVector...</span> + 215 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span> + 216 + 217 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 218 + 219 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 220 <span class="s">}</span> + 221 + 222 <span class="c"># Initialize extended connectivity bit fingerprints vector...</span> + 223 <span class="c">#</span> +<a name="_InitializeExtendedConnectivityBitsFingerprintsBitVector-"></a> 224 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityBitsFingerprintsBitVector</span> <span class="s">{</span> + 225 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 226 + 227 <span class="c"># Type of vector...</span> + 228 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsBitVector'</span><span class="sc">;</span> + 229 + 230 <span class="i">$This</span><span class="i">->_InitializeFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 231 + 232 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 233 <span class="s">}</span> + 234 + 235 <span class="c"># Set type...</span> + 236 <span class="c">#</span> +<a name="SetType-"></a> 237 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span> + 238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 239 + 240 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span> + 241 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivity'</span><span class="sc">;</span><span class="sc">;</span> + 242 <span class="s">}</span> + 243 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span> + 244 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivityCount'</span><span class="sc">;</span><span class="sc">;</span> + 245 <span class="s">}</span> + 246 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> + 247 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'ExtendedConnectivityBits'</span><span class="sc">;</span><span class="sc">;</span> + 248 <span class="s">}</span> + 249 <span class="k">else</span> <span class="s">{</span> + 250 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Unknown ExtendedConnectivity fingerprints type: $This->{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits..."</span><span class="sc">;</span> + 251 <span class="s">}</span> + 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 253 <span class="s">}</span> + 254 + 255 <span class="c"># Disable vector type change...</span> + 256 <span class="c">#</span> +<a name="SetVectorType-"></a> 257 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span> + 258 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 259 + 260 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Can't change vector type..."</span><span class="sc">;</span> + 261 + 262 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 263 <span class="s">}</span> + 264 + 265 <span class="c"># Disable vector type change...</span> + 266 <span class="c">#</span> +<a name="SetFingerprintsVectorType-"></a> 267 <span class="k">sub </span><span class="m">SetFingerprintsVectorType</span> <span class="s">{</span> + 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 269 + 270 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVectorType: Can't change fingerprints vector type..."</span><span class="sc">;</span> + 271 + 272 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 273 <span class="s">}</span> + 274 + 275 <span class="c"># Set intial atom identifier type..</span> + 276 <span class="c">#</span> +<a name="SetAtomIdentifierType-"></a> 277 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span> + 278 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IdentifierType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 279 + 280 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> + 281 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes."</span><span class="sc">;</span> + 282 <span class="s">}</span> + 283 + 284 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span> + 285 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span> + 286 <span class="s">}</span> + 287 + 288 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span> + 289 + 290 <span class="c"># Initialize identifier type information...</span> + 291 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 292 + 293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 294 <span class="s">}</span> + 295 + 296 <span class="c"># Set atom neighborhood radius...</span> + 297 <span class="c">#</span> +<a name="SetNeighborhoodRadius-"></a> 298 <span class="k">sub </span><span class="m">SetNeighborhoodRadius</span> <span class="s">{</span> + 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 300 + 301 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 302 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer..."</span><span class="sc">;</span> + 303 <span class="s">}</span> + 304 + 305 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> < <span class="n">0</span> <span class="s">)</span> <span class="s">{</span> + 306 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be >= 0..."</span><span class="sc">;</span> + 307 <span class="s">}</span> + 308 <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span> + 309 + 310 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 311 <span class="s">}</span> + 312 + 313 <span class="c"># Generate fingerprints description...</span> + 314 <span class="c">#</span> +<a name="GetDescription-"></a> 315 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> + 316 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 317 + 318 <span class="c"># Is description explicity set?</span> + 319 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span> + 320 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span> + 321 <span class="s">}</span> + 322 + 323 <span class="c"># Generate fingerprints description...</span> + 324 + 325 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomIdentifierType}:Radius$This->{NeighborhoodRadius}"</span><span class="sc">;</span> + 326 <span class="s">}</span> + 327 + 328 <span class="c"># Generate fingerprints...</span> + 329 <span class="c">#</span> + 330 <span class="c"># Methodology:</span> + 331 <span class="c"># . Assign initial atom identfiers to all non-hydrogen atoms in the molecule</span> + 332 <span class="c">#</span> + 333 <span class="c"># . Remove duplicates from the initial identifiers and add them to list corresponding</span> + 334 <span class="c"># to molecule fingerprint</span> + 335 <span class="c">#</span> + 336 <span class="c"># . For NeighborhoodRadius value of 0, just return the molecule fingerprint list</span> + 337 <span class="c">#</span> + 338 <span class="c"># . For each NeighborhoodRadius level</span> + 339 <span class="c"># . For each non-hydrogen CentralAtom at this NeighborhoodRadius level</span> + 340 <span class="c"># . For each non-hydrogen SuccessorNeighborAtom</span> + 341 <span class="c"># . Collect (BondOrder AtomIdentifier) pair of values corresponding to</span> + 342 <span class="c"># (CentralAtom SuccessorNeighborAtom) and add it to a list</span> + 343 <span class="c">#</span> + 344 <span class="c"># . Sort list containing (BondOrder AtomIdentifier) pairs first by BondOrder followed</span> + 345 <span class="c"># by AtomIdendifiers to make these values graph invariant</span> + 346 <span class="c"># . Generate a hash code for the values in the list</span> + 347 <span class="c"># . Assign hash code as new atom identifier at the current NeighborhoodRadius level</span> + 348 <span class="c"># . Save all atoms and bonds corresponding to the substructure involved in</span> + 349 <span class="c"># generating the hash code to be used for identifying structural duplicate hash code</span> + 350 <span class="c">#</span> + 351 <span class="c"># . Add the new identifier to the molecule fingerprint list making sure it's not a duplicate</span> + 352 <span class="c"># identifier</span> + 353 <span class="c">#</span> + 354 <span class="c"># Hash code atom identifier deduplication:</span> + 355 <span class="c"># . Track/remove the identifier generated at higher neighborhood radius level</span> + 356 <span class="c">#</span> + 357 <span class="c"># Structural atom identifier deduplication:</span> + 358 <span class="c"># . For equivalent atoms and bonds corresponding to substructure at a NeighborhoodRadius level,</span> + 359 <span class="c"># track/remove the atom identifier with largest value</span> + 360 <span class="c">#</span> + 361 <span class="c">#</span> +<a name="GenerateFingerprints-"></a> 362 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span> + 363 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 364 + 365 <span class="c"># Cache appropriate molecule data...</span> + 366 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 367 + 368 <span class="c"># Assign intial atom identifers...</span> + 369 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignInitialAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 370 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."</span><span class="sc">;</span> + 371 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 372 <span class="s">}</span> + 373 + 374 <span class="c"># Identify atom neighborhoods up to specified radius...</span> + 375 <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 376 + 377 <span class="c"># Assign atom identifiers to central atoms considering atom neighborhoods at each</span> + 378 <span class="c"># radius level...</span> + 379 <span class="i">$This</span><span class="i">->_AssignAtomIdentifiersToAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 380 + 381 <span class="c"># Remove duplicates identifiers...</span> + 382 <span class="i">$This</span><span class="i">->_RemoveDuplicateAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 383 + 384 <span class="c"># Set final fingerprints...</span> + 385 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 386 + 387 <span class="c"># Clear cached molecule data...</span> + 388 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 389 + 390 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 391 <span class="s">}</span> + 392 + 393 <span class="c"># Assign appropriate initial atom identifiers...</span> + 394 <span class="c">#</span> + 395 <span class="c"># Generation of initial identifier for a specific atom involves:</span> + 396 <span class="c"># . Values of the specified atom attributes are appended in a specific order to</span> + 397 <span class="c"># generate an initial atom identifier string</span> + 398 <span class="c"># . A 32 bit unsigned integer hash key, using TextUtil::HashCode function, is</span> + 399 <span class="c"># generated for the atom indentifier and assigned to the atom as initial</span> + 400 <span class="c"># atom identifier.</span> + 401 <span class="c">#</span> +<a name="_AssignInitialAtomIdentifiers-"></a> 402 <span class="k">sub </span><span class="m">_AssignInitialAtomIdentifiers</span> <span class="s">{</span> + 403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 404 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$InitialAtomTypeString</span><span class="cm">,</span> <span class="i">$InitialAtomIdentifier</span><span class="s">)</span><span class="sc">;</span> + 405 + 406 <span class="c"># Initialize atom identifiers...</span> + 407 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 408 + 409 <span class="c"># Set up atom types...</span> + 410 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span> + 411 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span> + 412 + 413 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> + 414 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 415 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::AtomicInvariantsAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">'AtomicInvariantsToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}<span class="s">)</span><span class="sc">;</span> + 416 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 417 <span class="s">}</span> + 418 + 419 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 420 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::FunctionalClassAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}<span class="s">)</span><span class="sc">;</span> + 421 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 422 <span class="s">}</span> + 423 + 424 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^DREIDINGAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 425 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::DREIDINGAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 426 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 427 <span class="s">}</span> + 428 + 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 430 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::EStateAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 431 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 432 <span class="s">}</span> + 433 + 434 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^MMFF94AtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 435 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::MMFF94AtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 436 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 437 <span class="s">}</span> + 438 + 439 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 440 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SLogPAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 441 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 442 <span class="s">}</span> + 443 + 444 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SYBYLAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 445 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SYBYLAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 446 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 447 <span class="s">}</span> + 448 + 449 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 450 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">0</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> + 451 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 452 <span class="s">}</span> + 453 + 454 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 455 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::UFFAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span> + 456 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 457 <span class="s">}</span> + 458 + 459 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_AssignInitialAtomIdentifiers: Couldn't assign intial atom identifiers: InitialAtomIdentifierType $This->{AtomIdentifierType} is not supported..."</span><span class="sc">;</span> + 460 <span class="s">}</span> + 461 + 462 <span class="c"># Assign atom types...</span> + 463 <span class="i">$SpecifiedAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 464 + 465 <span class="c"># Make sure atom types assignment is successful...</span> + 466 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 467 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 468 <span class="s">}</span> + 469 + 470 <span class="c"># Assign atom identifiers at radius 0...</span> + 471 <span class="i">$Radius</span> = <span class="n">0</span><span class="sc">;</span> + 472 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> + 473 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 474 + 475 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> + 476 <span class="i">$InitialAtomTypeString</span> = <span class="i">$AtomType</span> ? <span class="i">$AtomType</span> <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span> + 477 + 478 <span class="i">$InitialAtomIdentifier</span> = <span class="i">TextUtil::HashCode</span><span class="s">(</span><span class="i">$InitialAtomTypeString</span><span class="s">)</span><span class="sc">;</span> + 479 <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = <span class="i">$InitialAtomIdentifier</span><span class="sc">;</span> + 480 <span class="s">}</span> + 481 + 482 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 483 <span class="s">}</span> + 484 + 485 <span class="c"># Initialize atom identifiers...</span> + 486 <span class="c">#</span> +<a name="_InitializeAtomIdentifiers-"></a> 487 <span class="k">sub </span><span class="m">_InitializeAtomIdentifiers</span> <span class="s">{</span> + 488 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 489 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="s">)</span><span class="sc">;</span> + 490 + 491 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span> + 492 + 493 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 494 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span> + 495 <span class="c"># Atom idenfiers key and value correspond to AtomID and AtomIdentifier</span> + 496 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 497 + 498 <span class="c"># Unique and strcuturally unique idenfiers key and value correspond to AtomIdentifier and AtomID</span> + 499 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 500 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 501 + 502 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 503 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 504 <span class="s">}</span> + 505 + 506 <span class="s">}</span> + 507 + 508 <span class="c"># Collect atom neighborhoods upto specified neighborhood radius...</span> + 509 <span class="c">#</span> +<a name="_GetAtomNeighborhoods-"></a> 510 <span class="k">sub </span><span class="m">_GetAtomNeighborhoods</span> <span class="s">{</span> + 511 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 512 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> + 513 + 514 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 515 + 516 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span> + 517 <span class="k">if</span> <span class="s">(</span><span class="i">$Radius</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 518 <span class="c"># At radius level 0, it's just the atoms...</span> + 519 <span class="k">return</span><span class="sc">;</span> + 520 <span class="s">}</span> + 521 + 522 <span class="c"># Initialize neighborhood at different radii...</span> + 523 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span> + 524 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 525 <span class="s">}</span> + 526 + 527 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 528 + 529 <span class="c"># Collect available atom neighborhoods at different at different neighborhood level for each atom...</span> + 530 <span class="k">my</span><span class="s">(</span><span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span><span class="s">)</span><span class="sc">;</span> + 531 + 532 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> + 533 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 534 <span class="i">$CurrentRadius</span> = <span class="n">0</span><span class="sc">;</span> + 535 <span class="k">for</span> <span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 536 <span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$CurrentRadius</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span><span class="sc">;</span> + 537 <span class="i">$CurrentRadius</span>++<span class="sc">;</span> + 538 <span class="s">}</span> + 539 <span class="s">}</span> + 540 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 541 <span class="s">}</span> + 542 + 543 <span class="c"># Assign atom identifiers to central atom at each neighborhood radius level...</span> + 544 <span class="c">#</span> +<a name="_AssignAtomIdentifiersToAtomNeighborhoods-"></a> 545 <span class="k">sub </span><span class="m">_AssignAtomIdentifiersToAtomNeighborhoods</span> <span class="s">{</span> + 546 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 547 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$NextRadius</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$SuccessorAtom</span><span class="cm">,</span> <span class="i">$SuccessorAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$SuccessorAtomCount</span><span class="s">)</span><span class="sc">;</span> + 548 + 549 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 550 <span class="k">return</span><span class="sc">;</span> + 551 <span class="s">}</span> + 552 + 553 <span class="c"># Go over the atom neighborhoods at each radius upto specified radius and assign atom</span> + 554 <span class="c"># indentifiers using their connected successor atoms and their identifiers.</span> + 555 <span class="c">#</span> + 556 <span class="c"># For a neighborhood atom at a specified radius, the successor connected atoms correpond</span> + 557 <span class="c"># to next radius level and the last set of neighorhood atoms don't have any successor connected</span> + 558 <span class="c"># atoms. Additionally, radius level 0 just correspond to initial atom identifiers.</span> + 559 <span class="c">#</span> + 560 <span class="c"># So in order to process atom neighborhood upto specified radius level, the last atom neighborhood</span> + 561 <span class="c"># doesn't need to be processed: it gets processed at previous radius level as successor connected</span> + 562 <span class="c"># atoms.</span> + 563 <span class="c">#</span> + 564 <span class="j">RADIUS:</span> <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 565 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> + 566 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 567 + 568 <span class="c"># Are there any available atom neighborhoods at this radius?</span> + 569 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span> + 570 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> + 571 <span class="s">}</span> + 572 <span class="i">$NextRadius</span> = <span class="i">$Radius</span> + <span class="n">1</span><span class="sc">;</span> + 573 + 574 <span class="c"># Go over neighborhood atoms and their successor connected atoms at this radius and collect</span> + 575 <span class="c"># (BondOrder AtomIdentifier) values for bonded atom pairs. Additionally, keep track of atom and bonds</span> + 576 <span class="c"># for the neighorhoods to remove identifieres generated from structurally duplicate features.</span> + 577 <span class="c">#</span> + 578 <span class="k">my</span><span class="s">(</span><span class="i">%BondOrdersAndAtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> + 579 + 580 <span class="i">%BondOrdersAndAtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 581 <span class="i">$SuccessorAtomCount</span> = <span class="n">0</span><span class="sc">;</span> + 582 + 583 <span class="j">NEIGHBORHOODS:</span> <span class="k">for</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}}<span class="s">)</span> <span class="s">{</span> + 584 <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span>}<span class="sc">;</span> + 585 + 586 <span class="c"># Any connected successors for the NeighborhoodAtom?</span> + 587 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> + 588 <span class="k">next</span> <span class="j">NEIGHBORHOODS</span><span class="sc">;</span> + 589 <span class="s">}</span> + 590 <span class="j">SUCCESSORATOM:</span> <span class="k">for</span> <span class="i">$SuccessorAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> + 591 <span class="k">if</span> <span class="s">(</span><span class="i">$SuccessorAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 592 <span class="c"># Skip successor hydrogen atom...</span> + 593 <span class="k">next</span> <span class="j">SUCCESSORATOM</span><span class="sc">;</span> + 594 <span class="s">}</span> + 595 <span class="i">$SuccessorAtomID</span> = <span class="i">$SuccessorAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 596 <span class="i">$SuccessorAtomCount</span>++<span class="sc">;</span> + 597 + 598 <span class="i">$Bond</span> = <span class="i">$NeighborhoodAtom</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="i">$SuccessorAtom</span><span class="s">)</span><span class="sc">;</span> + 599 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"1.5"</span> <span class="co">:</span> <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 600 + 601 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}<span class="s">)</span> <span class="s">{</span> + 602 <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 603 <span class="s">}</span> + 604 <span class="k">push</span> <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$SuccessorAtomID</span>}<span class="sc">;</span> + 605 <span class="s">}</span> + 606 <span class="s">}</span> + 607 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SuccessorAtomCount</span><span class="s">)</span> <span class="s">{</span> + 608 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> + 609 <span class="s">}</span> + 610 <span class="c"># Assign a new atom identifier at the NextRadius level...</span> + 611 <span class="i">$This</span><span class="i">->_AssignAtomIdentifierToAtomNeighborhood</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> \<span class="i">%BondOrdersAndAtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> + 612 <span class="s">}</span> + 613 <span class="s">}</span> + 614 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 615 <span class="s">}</span> + 616 + 617 <span class="c"># Generate and assign atom indentifier for AtomID using atom neighborhood at next radius level...</span> + 618 <span class="c">#</span> +<a name="_AssignAtomIdentifierToAtomNeighborhood-"></a> 619 <span class="k">sub </span><span class="m">_AssignAtomIdentifierToAtomNeighborhood</span> <span class="s">{</span> + 620 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$BondOrdersAndAtomIdentifiersRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 621 <span class="k">my</span><span class="s">(</span><span class="i">$NextRadius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$SuccessorAtomIdentifier</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$AtomIdentifierString</span><span class="cm">,</span> <span class="i">@AtomIndentifiersInfo</span><span class="s">)</span><span class="sc">;</span> + 622 + 623 <span class="i">$NextRadius</span> = <span class="i">$Radius</span> + <span class="n">1</span><span class="sc">;</span> + 624 + 625 <span class="i">@AtomIndentifiersInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 626 + 627 <span class="i">$AtomIdentifier</span> = <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> + 628 <span class="k">push</span> <span class="i">@AtomIndentifiersInfo</span><span class="cm">,</span> <span class="s">(</span><span class="i">$NextRadius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> + 629 + 630 <span class="c"># Sort out successor atom bond order and identifier pairs by bond order followed by atom identifiers</span> + 631 <span class="c"># in order to make the final atom identifier graph invariant...</span> + 632 <span class="c">#</span> + 633 <span class="k">for</span> <span class="i">$BondOrder</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$BondOrdersAndAtomIdentifiersRef</span>}<span class="s">)</span> <span class="s">{</span> + 634 <span class="k">for</span> <span class="i">$SuccessorAtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiersRef</span>->{<span class="i">$BondOrder</span>}}<span class="s">)</span> <span class="s">{</span> + 635 <span class="k">push</span> <span class="i">@AtomIndentifiersInfo</span><span class="cm">,</span> <span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$SuccessorAtomIdentifier</span><span class="s">)</span><span class="sc">;</span> + 636 <span class="s">}</span> + 637 <span class="s">}</span> + 638 <span class="i">$AtomIdentifierString</span> = <span class="k">join</span><span class="s">(</span><span class="q">""</span><span class="cm">,</span> <span class="i">@AtomIndentifiersInfo</span><span class="s">)</span><span class="sc">;</span> + 639 <span class="i">$AtomIdentifier</span> = <span class="i">TextUtil::HashCode</span><span class="s">(</span><span class="i">$AtomIdentifierString</span><span class="s">)</span><span class="sc">;</span> + 640 + 641 <span class="c"># Assign atom identifier to the atom at next radius level...</span> + 642 <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$NextRadius</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomIdentifier</span><span class="sc">;</span> + 643 + 644 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 645 <span class="s">}</span> + 646 + 647 <span class="c"># Remove duplicates atom identifiers...</span> + 648 <span class="c">#</span> +<a name="_RemoveDuplicateAtomIdentifiers-"></a> 649 <span class="k">sub </span><span class="m">_RemoveDuplicateAtomIdentifiers</span> <span class="s">{</span> + 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 651 + 652 <span class="i">$This</span><span class="i">->_RemoveDuplicateIdentifiersByValue</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 653 <span class="i">$This</span><span class="i">->_RemoveStructurallyDuplicateIdenfiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 654 + 655 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 656 <span class="s">}</span> + 657 + 658 <span class="c"># Remove duplicate identifiers at each radius level by just using their value...</span> + 659 <span class="c">#</span> +<a name="_RemoveDuplicateIdentifiersByValue-"></a> 660 <span class="k">sub </span><span class="m">_RemoveDuplicateIdentifiersByValue</span> <span class="s">{</span> + 661 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 662 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> + 663 + 664 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> + 665 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> + 666 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 667 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span> + 668 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> + 669 <span class="s">}</span> + 670 <span class="i">$AtomIdentifier</span> = <span class="i">$This</span>->{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> + 671 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="s">)</span> <span class="s">{</span> + 672 <span class="c"># It's a duplicate atom idenfier at this radius level...</span> + 673 <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} += <span class="n">1</span><span class="sc">;</span> + 674 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> + 675 <span class="s">}</span> + 676 <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$AtomID</span><span class="sc">;</span> + 677 <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="n">1</span><span class="sc">;</span> + 678 <span class="s">}</span> + 679 <span class="s">}</span> + 680 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 681 <span class="s">}</span> + 682 + 683 <span class="c"># Remove structurally duplicate identifiers at each radius level...</span> + 684 <span class="c">#</span> + 685 <span class="c"># Methodology:</span> + 686 <span class="c"># . For unquie atom identifiers at each radius level, assign complete structure features</span> + 687 <span class="c"># in terms all the bonds involved to generate that identifier</span> + 688 <span class="c"># . Use the complete structure features to remover atom identifiers which are</span> + 689 <span class="c"># structurally equivalent which can also be at earlier radii levels</span> + 690 <span class="c">#</span> + 691 <span class="c">#</span> +<a name="_RemoveStructurallyDuplicateIdenfiers-"></a> 692 <span class="k">sub </span><span class="m">_RemoveStructurallyDuplicateIdenfiers</span> <span class="s">{</span> + 693 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 694 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifierRadius</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifier</span><span class="s">)</span><span class="sc">;</span> + 695 + 696 <span class="c"># Setup structure features...</span> + 697 <span class="i">$This</span><span class="i">->_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 698 + 699 <span class="c"># Identify structurally unqiue identifiers...</span> + 700 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> + 701 <span class="j">ATOMIDENTIFIER:</span> <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> + 702 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> + 703 + 704 <span class="s">(</span><span class="i">$SimilarAtomIdentifierRadius</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifier</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_FindStructurallySimilarAtomIdentifier</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> + 705 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilarAtomIdentifier</span><span class="s">)</span> <span class="s">{</span> + 706 <span class="c"># Current atom identifier is similar to an earlier structurally unique atom identifier...</span> + 707 <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$SimilarAtomIdentifierRadius</span>}{<span class="i">$SimilarAtomIdentifier</span>} += <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> + 708 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span> + 709 <span class="s">}</span> + 710 <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$AtomID</span><span class="sc">;</span> + 711 + 712 <span class="c"># Set structurally unique atom identifier count to the unique atom identifiers count...</span> + 713 <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> + 714 <span class="s">}</span> + 715 <span class="s">}</span> + 716 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 717 <span class="s">}</span> + 718 + 719 <span class="c"># Set final fingerpritns vector...</span> + 720 <span class="c">#</span> +<a name="_SetFinalFingerprints-"></a> 721 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span> + 722 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 723 + 724 <span class="c"># Mark successful generation of fingerprints...</span> + 725 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> + 726 + 727 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span> + 728 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 729 <span class="s">}</span> + 730 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span> + 731 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityCountFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 732 <span class="s">}</span> + 733 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> + 734 <span class="i">$This</span><span class="i">->_SetFinalExtendedConnectivityBitsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 735 <span class="s">}</span> + 736 + 737 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 738 <span class="s">}</span> + 739 + 740 <span class="c"># Set final extended connectivity fingerpritns vector...</span> + 741 <span class="c">#</span> +<a name="_SetFinalExtendedConnectivityFingerprints-"></a> 742 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityFingerprints</span> <span class="s">{</span> + 743 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 744 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> + 745 + 746 <span class="i">@AtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 747 + 748 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> + 749 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> + 750 <span class="k">push</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="sc">;</span> + 751 <span class="s">}</span> + 752 <span class="s">}</span> + 753 <span class="c"># Add atom identifiers to fingerprint vector...</span> + 754 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> + 755 + 756 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 757 <span class="s">}</span> + 758 + 759 <span class="c"># Set final extended connectivity count fingerpritns vector...</span> + 760 <span class="c">#</span> +<a name="_SetFinalExtendedConnectivityCountFingerprints-"></a> 761 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityCountFingerprints</span> <span class="s">{</span> + 762 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 763 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$AtomIdentifierCount</span><span class="cm">,</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">@AtomIdentifiersCount</span><span class="s">)</span><span class="sc">;</span> + 764 + 765 <span class="i">@AtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIdentifiersCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 766 + 767 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> + 768 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> + 769 <span class="i">$AtomIdentifierCount</span> = <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> + 770 <span class="k">push</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="sc">;</span> + 771 <span class="k">push</span> <span class="i">@AtomIdentifiersCount</span><span class="cm">,</span> <span class="i">$AtomIdentifierCount</span><span class="sc">;</span> + 772 <span class="s">}</span> + 773 <span class="s">}</span> + 774 <span class="c"># Add atom identifiers to fingerprint vector as value IDs...</span> + 775 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span> + 776 + 777 <span class="c"># Add atom identifiers to count to fingerprint vector as values...</span> + 778 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@AtomIdentifiersCount</span><span class="s">)</span><span class="sc">;</span> + 779 + 780 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 781 <span class="s">}</span> + 782 + 783 <span class="c"># Set final extended connectivity bits fingerpritns vector...</span> + 784 <span class="c">#</span> +<a name="_SetFinalExtendedConnectivityBitsFingerprints-"></a> 785 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityBitsFingerprints</span> <span class="s">{</span> + 786 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 787 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="cm">,</span> <span class="i">$Size</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="cm">,</span> <span class="i">$AtomIdentifierBitPos</span><span class="cm">,</span> <span class="i">$SetBitNum</span><span class="s">)</span><span class="sc">;</span> + 788 + 789 <span class="i">$FingerprintsBitVector</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="sc">;</span> + 790 + 791 <span class="i">$Size</span> = <span class="i">$This</span>->{<span class="w">Size</span>}<span class="sc">;</span> + 792 + 793 <span class="i">$SkipBitPosCheck</span> = <span class="n">1</span><span class="sc">;</span> + 794 + 795 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> + 796 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> + 797 <span class="c"># Set random number seed...</span> + 798 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span> <span class="s">{</span> + 799 <span class="i">CORE::</span><span class="k">srand</span><span class="s">(</span><span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> + 800 <span class="s">}</span> + 801 <span class="k">else</span> <span class="s">{</span> + 802 <span class="i">MathUtil::srandom</span><span class="s">(</span><span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> + 803 <span class="s">}</span> + 804 + 805 <span class="c"># Set bit position...</span> + 806 <span class="i">$AtomIdentifierBitPos</span> = <span class="i">$This</span>->{<span class="w">UsePerlCoreRandom</span>} ? <span class="k">int</span><span class="s">(</span><span class="i">CORE::</span><span class="k">rand</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="k">int</span><span class="s">(</span><span class="i">MathUtil::random</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> + 807 <span class="i">$FingerprintsBitVector</span><span class="i">->SetBit</span><span class="s">(</span><span class="i">$AtomIdentifierBitPos</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="s">)</span><span class="sc">;</span> + 808 <span class="s">}</span> + 809 <span class="s">}</span> + 810 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 811 <span class="s">}</span> + 812 + 813 + 814 <span class="c"># Identify structurally unique identifiers by comparing structure features involved in</span> + 815 <span class="c"># generating identifiear by comparing it agains all the previous structurally unique</span> + 816 <span class="c"># identifiers...</span> + 817 <span class="c">#</span> +<a name="_FindStructurallySimilarAtomIdentifier-"></a> 818 <span class="k">sub </span><span class="m">_FindStructurallySimilarAtomIdentifier</span> <span class="s">{</span> + 819 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$SpecifiedRadius</span><span class="cm">,</span> <span class="i">$SpecifiedAtomID</span><span class="cm">,</span> <span class="i">$SpecifiedAtomIdentifier</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 820 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$FeatureAtomCount</span><span class="cm">,</span> <span class="i">$FeatureAtomIDsRef</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomID</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomCount</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomIDsRef</span><span class="s">)</span><span class="sc">;</span> + 821 + 822 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedRadius</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span> + 823 <span class="c"># After duplicate removal by value, all identifier at radius level 0 would be structurally unique...</span> + 824 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> + 825 <span class="s">}</span> + 826 + 827 <span class="i">$SpecifiedFeatureAtomCount</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$SpecifiedRadius</span>}{<span class="i">$SpecifiedAtomID</span>}<span class="sc">;</span> + 828 <span class="i">$SpecifiedFeatureAtomIDsRef</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$SpecifiedRadius</span>}{<span class="i">$SpecifiedAtomID</span>}<span class="sc">;</span> + 829 + 830 <span class="c"># No need to compare features at radius 0...</span> + 831 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$SpecifiedRadius</span><span class="s">)</span> <span class="s">{</span> + 832 <span class="j">ATOMIDENTIFIER:</span> <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> + 833 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> + 834 + 835 <span class="i">$FeatureAtomCount</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> + 836 <span class="i">$FeatureAtomIDsRef</span> = <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> + 837 + 838 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedFeatureAtomCount</span> != <span class="i">$FeatureAtomCount</span><span class="s">)</span> <span class="s">{</span> + 839 <span class="c"># Couldn't be structurally equivalent...</span> + 840 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span> + 841 <span class="s">}</span> + 842 <span class="k">for</span> <span class="i">$SpecifiedFeatureAtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span> {<span class="i">$SpecifiedFeatureAtomIDsRef</span>}<span class="s">)</span> <span class="s">{</span> + 843 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$FeatureAtomIDsRef</span>->{<span class="i">$SpecifiedFeatureAtomID</span>}<span class="s">)</span> <span class="s">{</span> + 844 <span class="c"># For structural equivalency, all atom in specified feature must also be present in a previously</span> + 845 <span class="c"># identified structurally unique structure feature...</span> + 846 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span> + 847 <span class="s">}</span> + 848 <span class="s">}</span> + 849 <span class="c"># Found structurally equivalent feature...</span> + 850 <span class="k">return</span> <span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span> + 851 <span class="s">}</span> + 852 <span class="s">}</span> + 853 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> + 854 <span class="s">}</span> + 855 + 856 <span class="c"># Setup structure features for atom IDs involved in unique atom identifiers at all</span> + 857 <span class="c"># radii level...</span> + 858 <span class="c">#</span> +<a name="_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers-"></a> 859 <span class="k">sub </span><span class="m">_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers</span> <span class="s">{</span> + 860 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 861 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$PreviousRadius</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">%AtomIDs</span><span class="s">)</span><span class="sc">;</span> + 862 + 863 <span class="i">$This</span><span class="i">->_InitializeStructureFeatures</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 864 + 865 <span class="c"># Collect atom IDs involved in unique atom identifiers...</span> + 866 <span class="i">%AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 867 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> + 868 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span> + 869 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span> + 870 <span class="i">$AtomIDs</span>{<span class="i">$AtomID</span>} = <span class="i">$AtomID</span><span class="sc">;</span> + 871 <span class="s">}</span> + 872 <span class="s">}</span> + 873 + 874 <span class="c"># Setup structure features...</span> + 875 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span> + 876 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AtomIDs</span><span class="s">)</span> <span class="s">{</span> + 877 <span class="k">my</span><span class="s">(</span><span class="i">$StructureFeatureAtomCount</span><span class="cm">,</span> <span class="i">%StructureFeatureAtomIDs</span><span class="s">)</span><span class="sc">;</span> + 878 + 879 <span class="i">$StructureFeatureAtomCount</span> = <span class="n">0</span><span class="sc">;</span> + 880 <span class="i">%StructureFeatureAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 881 + 882 <span class="c"># Get partial structure features for the atom at previous radius level...</span> + 883 <span class="i">$PreviousRadius</span> = <span class="i">$Radius</span> - <span class="n">1</span><span class="sc">;</span> + 884 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRadius</span> >= <span class="n">0</span><span class="s">)</span> <span class="s">{</span> + 885 <span class="i">$StructureFeatureAtomCount</span> += <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$PreviousRadius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> + 886 <span class="i">%StructureFeatureAtomIDs</span> = <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$PreviousRadius</span>}{<span class="i">$AtomID</span>}}<span class="sc">;</span> + 887 <span class="s">}</span> + 888 + 889 <span class="c"># Get all neighborhood atom at this radius level...</span> + 890 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}<span class="s">)</span> && <span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 891 <span class="j">NEIGHBORHOODS:</span> <span class="k">for</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}}<span class="s">)</span> <span class="s">{</span> + 892 <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span>}<span class="sc">;</span> + 893 <span class="k">if</span> <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 894 <span class="k">next</span> <span class="j">NEIGHBORHOODS</span><span class="sc">;</span> + 895 <span class="s">}</span> + 896 <span class="i">$NeighborhoodAtomID</span> = <span class="i">$NeighborhoodAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 897 <span class="i">$StructureFeatureAtomCount</span>++<span class="sc">;</span> + 898 <span class="i">$StructureFeatureAtomIDs</span>{<span class="i">$NeighborhoodAtomID</span>} = <span class="i">$NeighborhoodAtomID</span><span class="sc">;</span> + 899 <span class="s">}</span> + 900 <span class="s">}</span> + 901 + 902 <span class="c"># Assign structure features to atom at this radius level...</span> + 903 <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = <span class="i">$StructureFeatureAtomCount</span><span class="sc">;</span> + 904 <span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = \<span class="i">%StructureFeatureAtomIDs</span><span class="sc">;</span> + 905 <span class="s">}</span> + 906 <span class="s">}</span> + 907 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 908 <span class="s">}</span> + 909 + 910 <span class="c"># Intialize structure features at each radius level...</span> + 911 <span class="c">#</span> +<a name="_InitializeStructureFeatures-"></a> 912 <span class="k">sub </span><span class="m">_InitializeStructureFeatures</span> <span class="s">{</span> + 913 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 914 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> + 915 + 916 <span class="c"># Initialize all structure features...</span> + 917 + 918 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 919 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 920 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 921 + 922 <span class="i">$Radius</span> = <span class="i">$This</span>->{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span> + 923 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span> + 924 <span class="c"># Structure features for at specific radii accessed using atom IDs...</span> + 925 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 926 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 927 <span class="s">}</span> + 928 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 929 <span class="s">}</span> + 930 + 931 <span class="c"># Cache appropriate molecule data...</span> + 932 <span class="c">#</span> +<a name="_SetupMoleculeDataCache-"></a> 933 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> + 934 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 935 + 936 <span class="c"># Get all non-hydrogen atoms...</span> + 937 <span class="k">my</span><span class="s">(</span><span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> + 938 <span class="i">$NegateAtomCheckMethod</span> = <span class="n">1</span><span class="sc">;</span> + 939 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="q">"IsHydrogen"</span><span class="cm">,</span> <span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span> + 940 + 941 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 942 <span class="s">}</span> + 943 + 944 <span class="c"># Clear cached molecule data...</span> + 945 <span class="c">#</span> +<a name="_ClearMoleculeDataCache-"></a> 946 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> + 947 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 948 + 949 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 950 + 951 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 952 <span class="s">}</span> + 953 + 954 <span class="c"># Initialize atom indentifier type information...</span> + 955 <span class="c">#</span> + 956 <span class="c"># Current supported values:</span> + 957 <span class="c">#</span> + 958 <span class="c"># AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,</span> + 959 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span> + 960 <span class="c">#</span> +<a name="_InitializeAtomIdentifierTypeInformation-"></a> 961 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span> + 962 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 963 + 964 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span> + 965 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 966 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 967 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 968 <span class="s">}</span> + 969 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> + 970 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 971 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 972 <span class="s">}</span> + 973 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span> + 974 <span class="c"># Nothing to do for now...</span> + 975 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span> + 976 <span class="s">}</span> + 977 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span> + 978 <span class="s">}</span> + 979 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 980 <span class="s">}</span> + 981 + 982 <span class="c"># Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes</span> + 983 <span class="c"># class, to use for generating initial atom identifiers...</span> + 984 <span class="c">#</span> + 985 <span class="c"># Let:</span> + 986 <span class="c"># AS = Atom symbol corresponding to element symbol</span> + 987 <span class="c">#</span> + 988 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 989 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 990 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 991 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 992 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 993 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> + 994 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span> + 995 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span> + 996 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span> + 997 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> + 998 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> + 999 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span> +1000 <span class="c">#</span> +1001 <span class="c"># Then:</span> +1002 <span class="c">#</span> +1003 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span> +1004 <span class="c">#</span> +1005 <span class="c"># AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></span> +1006 <span class="c">#</span> +1007 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span> +1008 <span class="c"># optional.</span> +1009 <span class="c">#</span> +1010 <span class="c"># Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:</span> +1011 <span class="c">#</span> +1012 <span class="c"># AS, X<n>, BO<n>, H<n>, FC<+n/-n>, MN<n></span> +1013 <span class="c">#</span> +1014 <span class="c"># In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words</span> +1015 <span class="c"># are also allowed:</span> +1016 <span class="c">#</span> +1017 <span class="c"># X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors</span> +1018 <span class="c"># BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms</span> +1019 <span class="c"># LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms</span> +1020 <span class="c"># SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms</span> +1021 <span class="c"># DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms</span> +1022 <span class="c"># TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms</span> +1023 <span class="c"># H : NumOfImplicitAndExplicitHydrogens</span> +1024 <span class="c"># Ar : Aromatic</span> +1025 <span class="c"># RA : RingAtom</span> +1026 <span class="c"># FC : FormalCharge</span> +1027 <span class="c"># MN : MassNumber</span> +1028 <span class="c"># SM : SpinMultiplicity</span> +1029 <span class="c">#</span> +<a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a>1030 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span> +1031 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1032 +1033 <span class="c"># Default atomic invariants to use for generating initial atom identifiers are: AS, X, BO, LBO, H, FC</span> +1034 <span class="c">#</span> +1035 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1036 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="cm">,</span> <span class="q">'MN'</span><span class="s">)</span><span class="sc">;</span> +1037 +1038 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1039 <span class="s">}</span> +1040 +1041 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span> +1042 <span class="c"># class, to use for generating initial atom identifiers...</span> +1043 <span class="c">#</span> +1044 <span class="c"># Let:</span> +1045 <span class="c"># HBD: HydrogenBondDonor</span> +1046 <span class="c"># HBA: HydrogenBondAcceptor</span> +1047 <span class="c"># PI : PositivelyIonizable</span> +1048 <span class="c"># NI : NegativelyIonizable</span> +1049 <span class="c"># Ar : Aromatic</span> +1050 <span class="c"># Hal : Halogen</span> +1051 <span class="c"># H : Hydrophobic</span> +1052 <span class="c"># RA : RingAtom</span> +1053 <span class="c"># CA : ChainAtom</span> +1054 <span class="c">#</span> +1055 <span class="c"># Then:</span> +1056 <span class="c">#</span> +1057 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span> +1058 <span class="c">#</span> +1059 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span> +1060 <span class="c">#</span> +1061 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span> +1062 <span class="c">#</span> +1063 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span> +1064 <span class="c">#</span> +1065 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span> +1066 <span class="c"># HydrogenBondAcceptor: N[!H], O</span> +1067 <span class="c"># PositivelyIonizable: +, NH2</span> +1068 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span> +1069 <span class="c">#</span> +<a name="_InitializeFunctionalClassAtomTypesInformation-"></a>1070 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span> +1071 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1072 +1073 <span class="c"># Default functional class atom typess to use for generating initial atom identifiers</span> +1074 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span> +1075 <span class="c">#</span> +1076 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1077 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span> +1078 +1079 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1080 <span class="s">}</span> +1081 +1082 <span class="c"># Set atomic invariants to use for generation of intial atom indentifiers...</span> +1083 <span class="c">#</span> +<a name="SetAtomicInvariantsToUse-"></a>1084 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span> +1085 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1086 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$SpecifiedAtomicInvariant</span><span class="cm">,</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span> +1087 +1088 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> +1089 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span> +1090 <span class="k">return</span><span class="sc">;</span> +1091 <span class="s">}</span> +1092 +1093 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> +1094 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalAtomTypesToUse: AtomicInvariantsToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> +1095 <span class="k">return</span><span class="sc">;</span> +1096 <span class="s">}</span> +1097 +1098 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> +1099 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> +1100 +1101 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1102 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1103 +1104 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> +1105 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> +1106 <span class="s">}</span> +1107 <span class="k">else</span> <span class="s">{</span> +1108 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> +1109 <span class="s">}</span> +1110 +1111 <span class="c"># Make sure specified AtomicInvariants are valid...</span> +1112 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span> +1113 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1114 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span> +1115 <span class="s">}</span> +1116 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span> +1117 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span> +1118 <span class="s">}</span> +1119 +1120 <span class="c"># Set atomic invariants to use...</span> +1121 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1122 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span> +1123 +1124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1125 <span class="s">}</span> +1126 +1127 <span class="c"># Set functional classes to use for generation of intial atom indentifiers...</span> +1128 <span class="c">#</span> +<a name="SetFunctionalClassesToUse-"></a>1129 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span> +1130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1131 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="cm">,</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span> +1132 +1133 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> +1134 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span> +1135 <span class="k">return</span><span class="sc">;</span> +1136 <span class="s">}</span> +1137 +1138 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> +1139 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span> +1140 <span class="k">return</span><span class="sc">;</span> +1141 <span class="s">}</span> +1142 +1143 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> +1144 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> +1145 +1146 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1147 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1148 +1149 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> +1150 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> +1151 <span class="s">}</span> +1152 <span class="k">else</span> <span class="s">{</span> +1153 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> +1154 <span class="s">}</span> +1155 +1156 <span class="c"># Make sure specified FunctionalClasses are valid...</span> +1157 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span> +1158 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedFunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1159 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span> +1160 <span class="s">}</span> +1161 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span> +1162 <span class="s">}</span> +1163 +1164 <span class="c"># Set functional classes to use...</span> +1165 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1166 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span> +1167 +1168 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> +1169 <span class="s">}</span> +1170 +1171 <span class="c"># Return a string containg data for ExtendedConnectivityFingerprints object...</span> +<a name="StringifyExtendedConnectivityFingerprints-"></a>1172 <span class="k">sub </span><span class="m">StringifyExtendedConnectivityFingerprints</span> <span class="s">{</span> +1173 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1174 <span class="k">my</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprintsString</span><span class="s">)</span><span class="sc">;</span> +1175 +1176 <span class="i">$ExtendedConnectivityFingerprintsString</span> = <span class="q">"InitialAtomIdentifierType: $This->{AtomIdentifierType}; NeighborhoodRadius: $This->{NeighborhoodRadius}"</span><span class="sc">;</span> +1177 +1178 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> +1179 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomicInvariants</span><span class="s">)</span><span class="sc">;</span> +1180 +1181 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1182 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1183 +1184 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span> +1185 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span> +1186 <span class="s">}</span> +1187 +1188 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1189 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1190 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; AvailableAtomicInvariants: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1191 <span class="s">}</span> +1192 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span> +1193 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span> +1194 +1195 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1196 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1197 +1198 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span> +1199 <span class="k">push</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">"$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}"</span><span class="sc">;</span> +1200 <span class="s">}</span> +1201 +1202 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1203 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1204 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; AvailableFunctionalClasses: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> +1205 <span class="s">}</span> +1206 +1207 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span> +1208 <span class="c"># Size...</span> +1209 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; Size: $This->{Size}; MinSize: $This->{MinSize}; MaxSize: $This->{MaxSize}"</span><span class="sc">;</span> +1210 +1211 <span class="c"># Fingerprint bit density and num of bits set...</span> +1212 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSetBits</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span> +1213 <span class="i">$NumOfSetBits</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1214 <span class="i">$BitDensity</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetFingerprintsBitDensity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1215 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity"</span><span class="sc">;</span> +1216 +1217 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FingerprintsBitVector: < $This->{FingerprintsBitVector} >"</span><span class="sc">;</span> +1218 <span class="s">}</span> +1219 <span class="k">else</span> <span class="s">{</span> +1220 <span class="c"># Number of identifiers...</span> +1221 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; NumOfIdentifiers: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1222 +1223 <span class="c"># FingerprintsVector...</span> +1224 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span> +1225 <span class="s">}</span> +1226 +1227 <span class="k">return</span> <span class="i">$ExtendedConnectivityFingerprintsString</span><span class="sc">;</span> +1228 <span class="s">}</span> +1229 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>