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<html> <head> <title>MayaChemTools:Code:Molecule.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-Molecule-"></a> 1 <span class="k">package </span><span class="i">Molecule</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: Molecule.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span> 5 <span class="c"># $Revision: 1.59 $</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">Storable</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">MathUtil</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">PeriodicTable</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> 38 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> 39 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> 40 <span class="k">use</span> <span class="w">Graph</span><span class="sc">;</span> 41 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> 42 <span class="k">use</span> <span class="w">Bond</span><span class="sc">;</span> 43 <span class="k">use</span> <span class="w">MolecularFormula</span><span class="sc">;</span> 44 45 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> 46 47 <span class="i">@ISA</span> = <span class="q">qw(Graph ObjectProperty Exporter)</span><span class="sc">;</span> 48 <span class="i">@EXPORT</span> = <span class="q">qw(IsMolecule)</span><span class="sc">;</span> 49 <span class="i">@EXPORT_OK</span> = <span class="q">qw(FormatElementalCompositionInformation GetSupportedAromaticityModels IsSupportedAromaticityModel)</span><span class="sc">;</span> 50 51 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> 52 53 <span class="c"># Setup class variables...</span> 54 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">$ObjectID</span><span class="cm">,</span> <span class="i">%AromaticityModelsDataMap</span><span class="cm">,</span> <span class="i">%CanonicalAromaticityModelNamesMap</span><span class="s">)</span><span class="sc">;</span> 55 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 56 57 <span class="c"># Overload Perl functions...</span> 58 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyMolecule'</span><span class="sc">;</span> 59 60 <span class="c"># Class constructor...</span> <a name="new-"></a> 61 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 62 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 63 64 <span class="c"># Initialize object...</span> 65 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 66 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> 67 <span class="i">$This</span><span class="i">->_InitializeMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 68 69 <span class="k">if</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> <span class="i">$This</span><span class="i">->_InitializeMoleculeProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> <span class="s">}</span> 70 71 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 72 <span class="s">}</span> 73 74 <span class="c"># Initialize object data...</span> <a name="_InitializeMolecule-"></a> 75 <span class="k">sub </span><span class="m">_InitializeMolecule</span> <span class="s">{</span> 76 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 77 <span class="k">my</span><span class="s">(</span><span class="i">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 78 79 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> 80 <span class="c"># are implemented on-demand using ObjectProperty class.</span> 81 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span> 82 <span class="i">$This</span>->{<span class="w">Name</span>} = <span class="q">"Molecule ${ObjectID}"</span><span class="sc">;</span> 83 <span class="s">}</span> 84 85 <span class="c"># Initialize molecule properties...</span> <a name="_InitializeMoleculeProperties-"></a> 86 <span class="k">sub </span><span class="m">_InitializeMoleculeProperties</span> <span class="s">{</span> 87 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 88 89 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> 90 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> 91 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 92 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 93 <span class="s">}</span> 94 <span class="s">}</span> 95 96 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 97 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 98 <span class="c">#Class name...</span> 99 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 100 101 <span class="c"># ID to keep track of objects...</span> 102 <span class="i">$ObjectID</span> = <span class="n">0</span><span class="sc">;</span> 103 104 <span class="c"># Load molecule class data...</span> 105 <span class="i">_LoadMoleculeClassData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 106 <span class="s">}</span> 107 108 <span class="c"># Setup an explicit SetID method to block setting of ID by AUTOLOAD function...</span> <a name="SetID-"></a> 109 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span> 110 <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> 111 112 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> 113 114 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 115 <span class="s">}</span> 116 117 <span class="c"># Add an atom...</span> <a name="AddAtom-"></a> 118 <span class="k">sub </span><span class="m">AddAtom</span> <span class="s">{</span> 119 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 120 121 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Atom</span><span class="s">)</span> <span class="s">{</span> 122 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddAtom: No atom added: Atom must be specified..."</span><span class="sc">;</span> 123 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 124 <span class="s">}</span> 125 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 126 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddAtom: No atom added: Atom already exists..."</span><span class="sc">;</span> 127 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 128 <span class="s">}</span> 129 <span class="k">return</span> <span class="i">$This</span><span class="i">->_AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 130 <span class="s">}</span> 131 132 <span class="c"># Add an atom...</span> <a name="_AddAtom-"></a> 133 <span class="k">sub </span><span class="m">_AddAtom</span> <span class="s">{</span> 134 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 135 136 <span class="c"># Assign atom to this molecule...</span> 137 <span class="i">$Atom</span><span class="i">->_SetMolecule</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 138 139 <span class="c"># Add it to the graph as a vertex...</span> 140 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 141 <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> 142 <span class="i">$This</span><span class="i">->AddVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 143 <span class="i">$This</span><span class="i">->SetVertexProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 144 145 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 146 <span class="s">}</span> 147 148 <span class="c"># Add atoms...</span> <a name="AddAtoms-"></a> 149 <span class="k">sub </span><span class="m">AddAtoms</span> <span class="s">{</span> 150 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 151 152 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 153 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddAtoms: No atoms added: Atoms list must be specified..."</span><span class="sc">;</span> 154 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 155 <span class="s">}</span> 156 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 157 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 158 <span class="i">$This</span><span class="i">->AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 159 <span class="s">}</span> 160 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 161 <span class="s">}</span> 162 163 <span class="c"># Create an atom and add it to molecule...</span> <a name="NewAtom-"></a> 164 <span class="k">sub </span><span class="m">NewAtom</span> <span class="s">{</span> 165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 166 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 167 168 <span class="i">$Atom</span> = <span class="i">new</span> <span class="i">Atom</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 169 <span class="i">$This</span><span class="i">->AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 170 171 <span class="k">return</span> <span class="i">$Atom</span><span class="sc">;</span> 172 <span class="s">}</span> 173 174 <span class="c"># Delete an atom...</span> <a name="DeleteAtom-"></a> 175 <span class="k">sub </span><span class="m">DeleteAtom</span> <span class="s">{</span> 176 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 177 178 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Atom</span><span class="s">)</span> <span class="s">{</span> 179 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteAtom: No atom deleted: Atom must be specified..."</span><span class="sc">;</span> 180 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 181 <span class="s">}</span> 182 <span class="c"># Does the atom exist in molecule?</span> 183 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 184 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteAtom: No atom deleted: Atom doesn't exist..."</span><span class="sc">;</span> 185 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 186 <span class="s">}</span> 187 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 188 <span class="s">}</span> 189 190 <span class="c"># Delete atom...</span> <a name="_DeleteAtom-"></a> 191 <span class="k">sub </span><span class="m">_DeleteAtom</span> <span class="s">{</span> 192 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 193 194 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 195 <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> 196 <span class="i">$This</span><span class="i">->DeleteVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 197 198 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 199 <span class="s">}</span> 200 201 <span class="c"># Delete atoms...</span> <a name="DeleteAtoms-"></a> 202 <span class="k">sub </span><span class="m">DeleteAtoms</span> <span class="s">{</span> 203 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 204 205 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 206 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteAtoms: No atoms added: Atoms list must be specified..."</span><span class="sc">;</span> 207 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 208 <span class="s">}</span> 209 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 210 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 211 <span class="i">$This</span><span class="i">->DeleteAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 212 <span class="s">}</span> 213 214 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 215 <span class="s">}</span> 216 217 <span class="c"># Is this atom present?</span> <a name="HasAtom-"></a> 218 <span class="k">sub </span><span class="m">HasAtom</span> <span class="s">{</span> 219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 220 221 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Atom</span><span class="s">)</span> <span class="s">{</span> 222 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 223 <span class="s">}</span> 224 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 225 <span class="c"># It's not in molecule...</span> 226 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 227 <span class="s">}</span> 228 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 229 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 230 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 231 <span class="c"># It's not in molecule...</span> 232 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 233 <span class="s">}</span> 234 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 235 <span class="i">$Molecule</span> = <span class="i">$Atom</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> 236 237 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Molecule</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 238 <span class="s">}</span> 239 240 <span class="c"># Return an array of atoms. In scalar context, it returns number of atoms. Additionally,</span> 241 <span class="c"># atoms array can be filtered by any user specifiable Atom class method...</span> 242 <span class="c">#</span> <a name="GetAtoms-"></a> 243 <span class="k">sub </span><span class="m">GetAtoms</span> <span class="s">{</span> 244 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomCheckMethodName</span><span class="cm">,</span> <span class="i">$NegateMethodResult</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 245 <span class="k">my</span><span class="s">(</span><span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 246 247 <span class="i">@Atoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 248 249 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 250 <span class="k">if</span> <span class="s">(</span>!<span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span> 251 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@Atoms</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@Atoms</span><span class="sc">;</span> 252 <span class="s">}</span> 253 254 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetVerticesProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 255 256 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$AtomCheckMethodName</span><span class="s">)</span> <span class="s">{</span> 257 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@Atoms</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@Atoms</span><span class="sc">;</span> 258 <span class="s">}</span> 259 <span class="i">$NegateMethodResult</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$NegateMethodResult</span><span class="s">)</span> && <span class="i">$NegateMethodResult</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 260 261 <span class="c"># Filter out atoms...</span> 262 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$KeepAtom</span><span class="cm">,</span> <span class="i">@FilteredAtoms</span><span class="s">)</span><span class="sc">;</span> 263 <span class="i">@FilteredAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 264 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 265 <span class="i">$KeepAtom</span> = <span class="i">$NegateMethodResult</span> ? <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->$AtomCheckMethodName</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="i">$Atom</span><span class="i">->$AtomCheckMethodName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 266 <span class="k">if</span> <span class="s">(</span><span class="i">$KeepAtom</span><span class="s">)</span> <span class="s">{</span> 267 <span class="k">push</span> <span class="i">@FilteredAtoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="sc">;</span> 268 <span class="s">}</span> 269 <span class="s">}</span> 270 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtoms</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtoms</span><span class="sc">;</span> 271 <span class="s">}</span> 272 273 <span class="c"># Return an array of bonds. In scalar context, it returns number of bonds...</span> <a name="GetBonds-"></a> 274 <span class="k">sub </span><span class="m">GetBonds</span> <span class="s">{</span> 275 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 276 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="cm">,</span> <span class="i">@EdgesAtomsIDs</span><span class="s">)</span><span class="sc">;</span> 277 278 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@EdgesAtomsIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 279 280 <span class="i">@EdgesAtomsIDs</span> = <span class="i">$This</span><span class="i">->GetEdges</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 281 <span class="k">if</span> <span class="s">(</span><span class="i">@EdgesAtomsIDs</span><span class="s">)</span> <span class="s">{</span> 282 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetEdgesProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">@EdgesAtomsIDs</span><span class="s">)</span><span class="sc">;</span> 283 <span class="s">}</span> 284 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@Bonds</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@Bonds</span><span class="sc">;</span> 285 <span class="s">}</span> 286 287 <span class="c"># Get number of atoms in molecule...</span> <a name="GetNumOfAtoms-"></a> 288 <span class="k">sub </span><span class="m">GetNumOfAtoms</span> <span class="s">{</span> 289 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 290 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfAtoms</span><span class="s">)</span><span class="sc">;</span> 291 292 <span class="i">$NumOfAtoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 293 294 <span class="k">return</span> <span class="i">$NumOfAtoms</span><span class="sc">;</span> 295 <span class="s">}</span> 296 297 <span class="c"># Get number of bonds in molecule...</span> <a name="GetNumOfBonds-"></a> 298 <span class="k">sub </span><span class="m">GetNumOfBonds</span> <span class="s">{</span> 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 300 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span> 301 302 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 303 304 <span class="k">return</span> <span class="i">$NumOfBonds</span><span class="sc">;</span> 305 <span class="s">}</span> 306 307 <span class="c"># Get number of heavy atoms in molecule...</span> <a name="GetNumOfHeavyAtoms-"></a> 308 <span class="k">sub </span><span class="m">GetNumOfHeavyAtoms</span> <span class="s">{</span> 309 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 310 311 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 312 <span class="s">}</span> 313 314 <span class="c"># Get number of non-hydrogen atoms in molecule...</span> <a name="GetNumOfNonHydrogenAtoms-"></a> 315 <span class="k">sub </span><span class="m">GetNumOfNonHydrogenAtoms</span> <span class="s">{</span> 316 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 317 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNonHydrogenAtoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> 318 319 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 320 <span class="i">$NumOfNonHydrogenAtoms</span> = <span class="n">0</span><span class="sc">;</span> 321 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 322 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 323 <span class="i">$NumOfNonHydrogenAtoms</span>++<span class="sc">;</span> 324 <span class="s">}</span> 325 <span class="s">}</span> 326 <span class="k">return</span> <span class="i">$NumOfNonHydrogenAtoms</span><span class="sc">;</span> 327 <span class="s">}</span> 328 329 <span class="c"># Get number of hydrogen atoms in molecule...</span> <a name="GetNumOfHydrogenAtoms-"></a> 330 <span class="k">sub </span><span class="m">GetNumOfHydrogenAtoms</span> <span class="s">{</span> 331 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 332 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfHydrogenAtoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> 333 334 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 335 <span class="i">$NumOfHydrogenAtoms</span> = <span class="n">0</span><span class="sc">;</span> 336 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 337 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 338 <span class="i">$NumOfHydrogenAtoms</span>++<span class="sc">;</span> 339 <span class="s">}</span> 340 <span class="s">}</span> 341 <span class="k">return</span> <span class="i">$NumOfHydrogenAtoms</span><span class="sc">;</span> 342 <span class="s">}</span> 343 344 <span class="c"># Get number of missing hydrogen atoms in molecule...</span> <a name="GetNumOfMissingHydrogenAtoms-"></a> 345 <span class="k">sub </span><span class="m">GetNumOfMissingHydrogenAtoms</span> <span class="s">{</span> 346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 347 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> 348 349 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 350 <span class="i">$NumOfMissingHydrogenAtoms</span> = <span class="n">0</span><span class="sc">;</span> 351 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 352 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 353 <span class="i">$NumOfMissingHydrogenAtoms</span> += <span class="i">$Atom</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 354 <span class="s">}</span> 355 <span class="s">}</span> 356 <span class="k">return</span> <span class="i">$NumOfMissingHydrogenAtoms</span><span class="sc">;</span> 357 <span class="s">}</span> 358 359 <span class="c"># Add bond...</span> <a name="AddBond-"></a> 360 <span class="k">sub </span><span class="m">AddBond</span> <span class="s">{</span> 361 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 362 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 363 364 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 365 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 366 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddBond: No bond added: Both atoms must be specified..."</span><span class="sc">;</span> 367 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 368 <span class="s">}</span> 369 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom2</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: ${ClassName}->AddBond: No bond added: Both atoms must be present..."</span><span class="sc">;</span> 371 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 372 <span class="s">}</span> 373 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 374 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddBond: No bond added: Bond already exists..."</span><span class="sc">;</span> 375 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 376 <span class="s">}</span> 377 <span class="k">return</span> <span class="i">$This</span><span class="i">->_AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> 378 <span class="s">}</span> 379 380 <span class="c"># Add bond...</span> <a name="_AddBond-"></a> 381 <span class="k">sub </span><span class="m">_AddBond</span> <span class="s">{</span> 382 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 383 384 <span class="c"># Assign bond to this molecule...</span> 385 <span class="i">$Bond</span><span class="i">->_SetMolecule</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 386 387 <span class="c"># Add it to the graph as an edge...</span> 388 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 389 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 390 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 391 <span class="i">$This</span><span class="i">->AddEdge</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 392 <span class="i">$This</span><span class="i">->SetEdgeProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 393 394 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 395 <span class="s">}</span> 396 397 <span class="c"># Add Bonds...</span> <a name="AddBonds-"></a> 398 <span class="k">sub </span><span class="m">AddBonds</span> <span class="s">{</span> 399 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 400 401 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> 402 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddBonds: No bonds added: Bonds list must be specified..."</span><span class="sc">;</span> 403 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 404 <span class="s">}</span> 405 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> 406 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> 407 <span class="i">$This</span><span class="i">->AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> 408 <span class="s">}</span> 409 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 410 <span class="s">}</span> 411 412 <span class="c"># Create a bond and add it to molecule...</span> <a name="NewBond-"></a> 413 <span class="k">sub </span><span class="m">NewBond</span> <span class="s">{</span> 414 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 415 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> 416 417 <span class="i">$Bond</span> = <span class="i">new</span> <span class="i">Bond</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 418 <span class="i">$This</span><span class="i">->AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> 419 420 <span class="k">return</span> <span class="i">$Bond</span><span class="sc">;</span> 421 <span class="s">}</span> 422 423 <span class="c"># Delete a bond...</span> <a name="DeleteBond-"></a> 424 <span class="k">sub </span><span class="m">DeleteBond</span> <span class="s">{</span> 425 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 426 427 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Bond</span><span class="s">)</span> <span class="s">{</span> 428 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteBond: No bond deleted: Bond must be specified..."</span><span class="sc">;</span> 429 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 430 <span class="s">}</span> 431 <span class="c"># Does the bond exist in molecule?</span> 432 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 433 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteBond: No bond deleted: Bond doesn't exist..."</span><span class="sc">;</span> 434 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 435 <span class="s">}</span> 436 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> 437 <span class="s">}</span> 438 439 <span class="c"># Delete bond...</span> <a name="_DeleteBond-"></a> 440 <span class="k">sub </span><span class="m">_DeleteBond</span> <span class="s">{</span> 441 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 442 443 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 444 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 445 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 446 <span class="i">$This</span><span class="i">->DeleteEdge</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 447 448 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 449 <span class="s">}</span> 450 451 <span class="c"># Delete bonds...</span> <a name="DeleteBonds-"></a> 452 <span class="k">sub </span><span class="m">DeleteBonds</span> <span class="s">{</span> 453 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 454 455 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> 456 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteBonds: No bonds added: Bonds list must be specified..."</span><span class="sc">;</span> 457 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 458 <span class="s">}</span> 459 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> 460 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> 461 <span class="i">$This</span><span class="i">->DeleteBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> 462 <span class="s">}</span> 463 464 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 465 <span class="s">}</span> 466 467 <span class="c"># Has bond...</span> <a name="HasBond-"></a> 468 <span class="k">sub </span><span class="m">HasBond</span> <span class="s">{</span> 469 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 470 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 471 472 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 473 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 474 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 475 <span class="s">}</span> 476 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Bond</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 477 <span class="c"># It's not in molecule...</span> 478 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 479 <span class="s">}</span> 480 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> 481 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 482 <span class="i">$Molecule</span> = <span class="i">$Bond</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 483 484 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasEdge</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Molecule</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 485 <span class="s">}</span> 486 487 <span class="c"># Get atom neighbors...</span> <a name="_GetAtomNeighbors-"></a> 488 <span class="k">sub </span><span class="m">_GetAtomNeighbors</span> <span class="s">{</span> 489 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 490 491 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 492 493 <span class="i">@Atoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 494 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 495 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 496 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span> 497 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetVerticesProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 498 <span class="s">}</span> 499 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@Atoms</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@Atoms</span><span class="sc">;</span> 500 <span class="s">}</span> 501 502 <span class="c"># Get atom bonds...</span> <a name="_GetAtomBonds-"></a> 503 <span class="k">sub </span><span class="m">_GetAtomBonds</span> <span class="s">{</span> 504 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 505 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> 506 507 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 508 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 509 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetEdges</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 510 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span> 511 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetEdgesProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 512 <span class="s">}</span> 513 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@Bonds</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@Bonds</span><span class="sc">;</span> 514 <span class="s">}</span> 515 516 <span class="c"># Get bond to specified atom...</span> <a name="_GetBondToAtom-"></a> 517 <span class="k">sub </span><span class="m">_GetBondToAtom</span> <span class="s">{</span> 518 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 519 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 520 521 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 522 <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 523 524 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetEdgeProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 525 <span class="s">}</span> 526 527 <span class="c"># Are two specified atoms bonded?</span> <a name="_IsBondedToAtom-"></a> 528 <span class="k">sub </span><span class="m">_IsBondedToAtom</span> <span class="s">{</span> 529 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 530 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 531 532 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 533 <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 534 535 <span class="k">return</span> <span class="i">$This</span><span class="i">->HasEdgeProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 536 <span class="s">}</span> 537 538 <span class="c"># Add hydrogens to each atoms in molecule and return total number of hydrogens added...</span> <a name="AddHydrogens-"></a> 539 <span class="k">sub </span><span class="m">AddHydrogens</span> <span class="s">{</span> 540 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 541 542 <span class="k">return</span> <span class="i">$This</span><span class="i">->_AddHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 543 <span class="s">}</span> 544 545 <span class="c"># Add hydrogens to polar atoms (N, O, P, S) in molecule and return total number of hydrogens added...</span> <a name="AddPolarHydrogens-"></a> 546 <span class="k">sub </span><span class="m">AddPolarHydrogens</span> <span class="s">{</span> 547 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 548 <span class="k">my</span><span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> = <span class="n">1</span><span class="sc">;</span> 549 550 <span class="k">return</span> <span class="i">$This</span><span class="i">->_AddHydrogens</span><span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span><span class="sc">;</span> 551 <span class="s">}</span> 552 553 <span class="c"># Add all the hydrogens or hydrogens for polar atoms only...</span> 554 <span class="c">#</span> 555 <span class="c"># Note:</span> 556 <span class="c"># . The current release of MayaChemTools doesn't assign any hydrogen positions.</span> 557 <span class="c">#</span> <a name="_AddHydrogens-"></a> 558 <span class="k">sub </span><span class="m">_AddHydrogens</span> <span class="s">{</span> 559 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PolarHydrogensOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 560 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$NumOfHydrogensAdded</span><span class="cm">,</span> <span class="i">$HydrogenPositionsWarning</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> 561 562 <span class="k">if</span> <span class="s">(</span>! <span class="k">defined</span> <span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span> 563 <span class="i">$PolarHydrogensOnly</span> = <span class="n">0</span><span class="sc">;</span> 564 <span class="s">}</span> 565 566 <span class="i">$NumOfHydrogensAdded</span> = <span class="n">0</span><span class="sc">;</span> 567 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 568 <span class="i">$HydrogenPositionsWarning</span> = <span class="n">0</span><span class="sc">;</span> 569 570 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 571 <span class="k">if</span> <span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span> 572 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsPolarAtom</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 573 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 574 <span class="s">}</span> 575 <span class="s">}</span> 576 <span class="i">$NumOfHydrogensAdded</span> += <span class="i">$Atom</span><span class="i">->AddHydrogens</span><span class="s">(</span><span class="i">$HydrogenPositionsWarning</span><span class="s">)</span><span class="sc">;</span> 577 <span class="s">}</span> 578 <span class="k">return</span> <span class="i">$NumOfHydrogensAdded</span><span class="sc">;</span> 579 <span class="s">}</span> 580 581 <span class="c"># Delete all hydrogens atoms in molecule and return total number of hydrogens removed...</span> <a name="DeleteHydrogens-"></a> 582 <span class="k">sub </span><span class="m">DeleteHydrogens</span> <span class="s">{</span> 583 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 584 585 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 586 <span class="s">}</span> 587 588 <span class="c"># Delete hydrogens to polar atoms (N, O, P, S) in molecule and return total number of hydrogens removed...</span> <a name="DeletePolarHydrogens-"></a> 589 <span class="k">sub </span><span class="m">DeletePolarHydrogens</span> <span class="s">{</span> 590 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 591 <span class="k">my</span><span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> = <span class="n">1</span><span class="sc">;</span> 592 593 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteHydrogens</span><span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span><span class="sc">;</span> 594 <span class="s">}</span> 595 596 <span class="c"># Delete all hydrogens atoms in molecule and return total number of hydrogens removed...</span> <a name="_DeleteHydrogens-"></a> 597 <span class="k">sub </span><span class="m">_DeleteHydrogens</span> <span class="s">{</span> 598 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PolarHydrogensOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 599 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$NumOfHydrogensRemoved</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> 600 601 <span class="k">if</span> <span class="s">(</span>! <span class="k">defined</span> <span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span> 602 <span class="i">$PolarHydrogensOnly</span> = <span class="n">0</span><span class="sc">;</span> 603 <span class="s">}</span> 604 605 <span class="i">$NumOfHydrogensRemoved</span> = <span class="n">0</span><span class="sc">;</span> 606 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 607 608 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 609 <span class="k">if</span> <span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span> 610 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsPolarHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 611 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 612 <span class="s">}</span> 613 <span class="s">}</span> 614 <span class="k">elsif</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 615 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 616 <span class="s">}</span> 617 <span class="i">$This</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 618 <span class="i">$NumOfHydrogensRemoved</span>++<span class="sc">;</span> 619 <span class="s">}</span> 620 <span class="k">return</span> <span class="i">$NumOfHydrogensRemoved</span><span class="sc">;</span> 621 <span class="s">}</span> 622 623 <span class="c"># Get molecular weight by summing up atomic weights of all the atoms...</span> <a name="GetMolecularWeight-"></a> 624 <span class="k">sub </span><span class="m">GetMolecularWeight</span> <span class="s">{</span> 625 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 626 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="i">$AtomicWeight</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 627 628 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 629 630 <span class="i">$MolecularWeight</span> = <span class="n">0</span><span class="sc">;</span> 631 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 632 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 633 <span class="i">$AtomicWeight</span> = <span class="i">$Atom</span><span class="i">->GetAtomicWeight</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 634 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicWeight</span><span class="s">)</span> <span class="s">{</span> 635 <span class="i">$MolecularWeight</span> += <span class="i">$AtomicWeight</span><span class="sc">;</span> 636 <span class="s">}</span> 637 <span class="s">}</span> 638 639 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> 640 <span class="k">return</span> <span class="i">$MolecularWeight</span><span class="sc">;</span> 641 <span class="s">}</span> 642 643 <span class="c"># Account for missing hydrogen atoms...</span> 644 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span><span class="sc">;</span> 645 646 <span class="i">$NumOfMissingHydrogenAtoms</span> = <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 647 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span> <span class="s">{</span> 648 <span class="i">$MolecularWeight</span> += <span class="i">$NumOfMissingHydrogenAtoms</span> * <span class="i">PeriodicTable::GetElementAtomicWeight</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span><span class="sc">;</span> 649 <span class="s">}</span> 650 651 <span class="k">return</span> <span class="i">$MolecularWeight</span><span class="sc">;</span> 652 <span class="s">}</span> 653 654 <span class="c"># Get exact mass by summing up exact masses of all the atoms...</span> <a name="GetExactMass-"></a> 655 <span class="k">sub </span><span class="m">GetExactMass</span> <span class="s">{</span> 656 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 657 <span class="k">my</span><span class="s">(</span><span class="i">$ExactMass</span><span class="cm">,</span> <span class="i">$AtomicMass</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 658 659 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 660 661 <span class="i">$ExactMass</span> = <span class="n">0</span><span class="sc">;</span> 662 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 663 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 664 <span class="i">$AtomicMass</span> = <span class="i">$Atom</span><span class="i">->GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 665 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicMass</span><span class="s">)</span> <span class="s">{</span> 666 <span class="i">$ExactMass</span> += <span class="i">$AtomicMass</span><span class="sc">;</span> 667 <span class="s">}</span> 668 <span class="s">}</span> 669 670 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> 671 <span class="k">return</span> <span class="i">$ExactMass</span><span class="sc">;</span> 672 <span class="s">}</span> 673 674 <span class="c"># Account for missing hydrogen atoms...</span> 675 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span><span class="sc">;</span> 676 677 <span class="i">$NumOfMissingHydrogenAtoms</span> = <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 678 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span> <span class="s">{</span> 679 <span class="i">$ExactMass</span> += <span class="i">$NumOfMissingHydrogenAtoms</span> * <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMass</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span><span class="sc">;</span> 680 <span class="s">}</span> 681 682 <span class="k">return</span> <span class="i">$ExactMass</span><span class="sc">;</span> 683 <span class="s">}</span> 684 685 <span class="c"># Get net formal charge on the molecule using one of the following two methods:</span> 686 <span class="c"># . Using explicitly set FormalCharge property</span> 687 <span class="c"># . Adding up formal charge on each atom in the molecule</span> 688 <span class="c">#</span> 689 <span class="c"># Caveats:</span> 690 <span class="c"># . FormalCharge is different from Charge property of the molecule which corresponds to</span> 691 <span class="c"># sum of partial atomic charges explicitly set for each atom using a specific methodology.</span> 692 <span class="c">#</span> <a name="GetFormalCharge-"></a> 693 <span class="k">sub </span><span class="m">GetFormalCharge</span> <span class="s">{</span> 694 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 695 696 <span class="c"># Is FormalCharge property explicitly set?</span> 697 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 698 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="sc">;</span> 699 <span class="s">}</span> 700 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$AtomicFormalCharge</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 701 702 <span class="i">$FormalCharge</span> = <span class="n">0</span><span class="sc">;</span> 703 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 704 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 705 <span class="i">$AtomicFormalCharge</span> = <span class="i">$Atom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 706 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicFormalCharge</span><span class="s">)</span> <span class="s">{</span> 707 <span class="i">$FormalCharge</span> += <span class="i">$AtomicFormalCharge</span><span class="sc">;</span> 708 <span class="s">}</span> 709 <span class="s">}</span> 710 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span> 711 <span class="s">}</span> 712 713 <span class="c"># Get net charge on the molecule using one of the following two methods:</span> 714 <span class="c"># . Using explicitly set Charge property</span> 715 <span class="c"># . Adding up charge on each atom in the molecule</span> 716 <span class="c">#</span> 717 <span class="c"># Caveats:</span> 718 <span class="c"># . FormalCharge is different from Charge property of the molecule which corresponds to</span> 719 <span class="c"># sum of partial atomic charges explicitly set for each atom using a specific methodology.</span> 720 <span class="c">#</span> <a name="GetCharge-"></a> 721 <span class="k">sub </span><span class="m">GetCharge</span> <span class="s">{</span> 722 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 723 724 <span class="c"># Is Charge property explicitly set?</span> 725 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Charge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 726 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Charge'</span><span class="s">)</span><span class="sc">;</span> 727 <span class="s">}</span> 728 <span class="k">my</span><span class="s">(</span><span class="i">$Charge</span><span class="cm">,</span> <span class="i">$AtomicCharge</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 729 730 <span class="i">$Charge</span> = <span class="n">0</span><span class="sc">;</span> 731 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 732 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 733 <span class="i">$AtomicCharge</span> = <span class="i">$Atom</span><span class="i">->GetCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 734 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicCharge</span><span class="s">)</span> <span class="s">{</span> 735 <span class="i">$Charge</span> += <span class="i">$AtomicCharge</span><span class="sc">;</span> 736 <span class="s">}</span> 737 <span class="s">}</span> 738 <span class="k">return</span> <span class="i">$Charge</span><span class="sc">;</span> 739 <span class="s">}</span> 740 741 <span class="c"># Get total SpinMultiplicity for the molecule using one of the following two methods:</span> 742 <span class="c"># . Using explicitly set SpinMultiplicity property</span> 743 <span class="c"># . Adding up SpinMultiplicity on each atom in the molecule</span> 744 <span class="c">#</span> 745 <span class="c">#</span> <a name="GetSpinMultiplicity-"></a> 746 <span class="k">sub </span><span class="m">GetSpinMultiplicity</span> <span class="s">{</span> 747 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 748 749 <span class="c"># Is SpinMultiplicity property explicitly set?</span> 750 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 751 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span> 752 <span class="s">}</span> 753 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicSpinMultiplicity</span><span class="cm">,</span> <span class="i">$SpinMultiplicity</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 754 755 <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span> 756 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 757 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 758 <span class="i">$AtomicSpinMultiplicity</span> = <span class="i">$Atom</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 759 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicSpinMultiplicity</span><span class="s">)</span> <span class="s">{</span> 760 <span class="i">$SpinMultiplicity</span> += <span class="i">$AtomicSpinMultiplicity</span><span class="sc">;</span> 761 <span class="s">}</span> 762 <span class="s">}</span> 763 <span class="k">return</span> <span class="i">$SpinMultiplicity</span><span class="sc">;</span> 764 <span class="s">}</span> 765 766 <span class="c"># Get total FreeRadicalElectrons for the molecule using one of the following two methods:</span> 767 <span class="c"># . Using explicitly set FreeRadicalElectrons property</span> 768 <span class="c"># . Adding up FreeRadicalElectrons on each atom in the molecule</span> 769 <span class="c">#</span> 770 <span class="c">#</span> <a name="GetFreeRadicalElectrons-"></a> 771 <span class="k">sub </span><span class="m">GetFreeRadicalElectrons</span> <span class="s">{</span> 772 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 773 774 <span class="c"># Is FreeRadicalElectrons property explicitly set?</span> 775 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 776 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="sc">;</span> 777 <span class="s">}</span> 778 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicFreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$FreeRadicalElectrons</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 779 780 <span class="i">$FreeRadicalElectrons</span> = <span class="n">0</span><span class="sc">;</span> 781 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 782 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 783 <span class="i">$AtomicFreeRadicalElectrons</span> = <span class="i">$Atom</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 784 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicFreeRadicalElectrons</span><span class="s">)</span> <span class="s">{</span> 785 <span class="i">$FreeRadicalElectrons</span> += <span class="i">$AtomicFreeRadicalElectrons</span><span class="sc">;</span> 786 <span class="s">}</span> 787 <span class="s">}</span> 788 <span class="k">return</span> <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span> 789 <span class="s">}</span> 790 791 <span class="c"># Set valence model...</span> 792 <span class="c">#</span> <a name="SetValenceModel-"></a> 793 <span class="k">sub </span><span class="m">SetValenceModel</span> <span class="s">{</span> 794 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ValenceModel</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 795 796 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> !~ <span class="q">/^(MDLValenceModel|DaylightValenceModel|InternalValenceModel|MayaChemToolsValenceModel)$/i</span><span class="s">)</span> <span class="s">{</span> 797 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetValenceModel: The current release of MayaChemTools doesn't support the specified valence model $ValenceModel. Supported valence models: MDLValenceModel, DaylightValenceModel, InternalValenceModel or MayaChemToolsValenceModel. Using internal valence model..."</span><span class="sc">;</span> 798 <span class="i">$ValenceModel</span> = <span class="q">'InternalValenceModel'</span><span class="sc">;</span> 799 <span class="s">}</span> 800 801 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'ValenceModel'</span><span class="cm">,</span> <span class="i">$ValenceModel</span><span class="s">)</span><span class="sc">;</span> 802 803 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 804 <span class="s">}</span> 805 806 <span class="c"># Get valence model...</span> 807 <span class="c">#</span> <a name="GetValenceModel-"></a> 808 <span class="k">sub </span><span class="m">GetValenceModel</span> <span class="s">{</span> 809 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 810 811 <span class="c"># Is ValenceModel property explicitly set?</span> 812 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ValenceModel'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 813 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ValenceModel'</span><span class="s">)</span><span class="sc">;</span> 814 <span class="s">}</span> 815 816 <span class="c"># Used internal valence model as default model...</span> 817 <span class="k">return</span> <span class="q">'InternalValenceModel'</span><span class="sc">;</span> 818 <span class="s">}</span> 819 820 <span class="c"># Get molecular formula by collecting information about all atoms in the molecule and</span> 821 <span class="c"># composing the formula using Hills ordering system:</span> 822 <span class="c"># . C shows up first and H follows assuming C is present</span> 823 <span class="c"># . All other standard elements are sorted alphanumerically</span> 824 <span class="c"># . All other non-stanard atom symbols are also sorted alphanumerically and follow standard elements</span> 825 <span class="c">#</span> 826 <span class="c"># Caveats:</span> 827 <span class="c"># . By default, missing hydrogens and nonelements are also included</span> 828 <span class="c"># . Elements for disconnected fragments are combined into the same formula</span> 829 <span class="c">#</span> 830 <span class="c"># Handle formula generation for disconnected structures. e.g: molecule generated by</span> 831 <span class="c"># [Na+].[O-]c1ccccc1</span> 832 <span class="c">#</span> <a name="GetMolecularFormula-"></a> 833 <span class="k">sub </span><span class="m">GetMolecularFormula</span> <span class="s">{</span> 834 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="cm">,</span> <span class="i">$IncludeNonElements</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 835 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$ElementsCountRef</span><span class="cm">,</span> <span class="i">$NonElementsCountRef</span><span class="s">)</span><span class="sc">;</span> 836 837 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 838 <span class="i">$IncludeNonElements</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeNonElements</span><span class="s">)</span> ? <span class="i">$IncludeNonElements</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 839 840 <span class="c"># Get elements count and setup molecular formula...</span> 841 <span class="s">(</span><span class="i">$ElementsCountRef</span><span class="cm">,</span> <span class="i">$NonElementsCountRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetElementsAndNonElements</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span><span class="sc">;</span> 842 <span class="i">$MolecularFormula</span> = <span class="q">''</span><span class="sc">;</span> 843 844 <span class="c"># Count C and H first...</span> 845 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCountRef</span>->{<span class="w">C</span>} <span class="s">)</span> <span class="s">{</span> 846 <span class="i">$MolecularFormula</span> .= <span class="q">'C'</span> . <span class="s">(</span><span class="i">$ElementsCountRef</span>->{<span class="w">C</span>} > <span class="n">1</span> ? <span class="i">$ElementsCountRef</span>->{<span class="w">C</span>} <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span> 847 <span class="k">delete</span> <span class="i">$ElementsCountRef</span>->{<span class="w">C</span>}<span class="sc">;</span> 848 849 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCountRef</span>->{<span class="w">H</span>} <span class="s">)</span> <span class="s">{</span> 850 <span class="i">$MolecularFormula</span> .= <span class="q">'H'</span> . <span class="s">(</span><span class="i">$ElementsCountRef</span>->{<span class="w">H</span>} > <span class="n">1</span> ? <span class="i">$ElementsCountRef</span>->{<span class="w">H</span>} <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span> 851 <span class="k">delete</span> <span class="i">$ElementsCountRef</span>->{<span class="w">H</span>}<span class="sc">;</span> 852 <span class="s">}</span> 853 <span class="s">}</span> 854 855 <span class="c"># Sort elements...</span> 856 <span class="k">for</span> <span class="i">$AtomSymbol</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span><span class="i">$a</span> <span class="k">cmp</span> <span class="i">$b</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$ElementsCountRef</span>}<span class="s">)</span> <span class="s">{</span> 857 <span class="i">$MolecularFormula</span> .= <span class="i">$AtomSymbol</span> . <span class="s">(</span><span class="i">$ElementsCountRef</span>->{<span class="i">$AtomSymbol</span>} > <span class="n">1</span> ? <span class="i">$ElementsCountRef</span>->{<span class="i">$AtomSymbol</span>} <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span> 858 <span class="s">}</span> 859 860 <span class="c"># Sort non-elements...</span> 861 <span class="k">if</span> <span class="s">(</span><span class="i">$IncludeNonElements</span><span class="s">)</span> <span class="s">{</span> 862 <span class="k">for</span> <span class="i">$AtomSymbol</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span><span class="i">$a</span> <span class="k">cmp</span> <span class="i">$b</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$NonElementsCountRef</span>}<span class="s">)</span> <span class="s">{</span> 863 <span class="i">$MolecularFormula</span> .= <span class="i">$AtomSymbol</span> . <span class="s">(</span><span class="i">$NonElementsCountRef</span>->{<span class="i">$AtomSymbol</span>} > <span class="n">1</span> ? <span class="i">$NonElementsCountRef</span>->{<span class="i">$AtomSymbol</span>} <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span> 864 <span class="s">}</span> 865 <span class="s">}</span> 866 867 <span class="c"># Check formal charge...</span> 868 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span> 869 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 870 <span class="k">if</span> <span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> <span class="s">{</span> 871 <span class="c"># Setup formal charge string...</span> 872 <span class="k">my</span><span class="s">(</span><span class="i">$FormalChargeString</span><span class="s">)</span><span class="sc">;</span> 873 <span class="k">if</span> <span class="s">(</span><span class="i">$FormalCharge</span> == <span class="n">1</span> <span class="s">)</span> <span class="s">{</span> 874 <span class="i">$FormalChargeString</span> = <span class="q">"+"</span><span class="sc">;</span> 875 <span class="s">}</span> 876 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FormalCharge</span> == <span class="n">-1</span> <span class="s">)</span> <span class="s">{</span> 877 <span class="i">$FormalChargeString</span> = <span class="q">"-"</span><span class="sc">;</span> 878 <span class="s">}</span> 879 <span class="k">else</span> <span class="s">{</span> 880 <span class="i">$FormalChargeString</span> = <span class="s">(</span><span class="i">$FormalCharge</span> > <span class="n">0</span><span class="s">)</span> ? <span class="s">(</span><span class="q">"+"</span> . <span class="k">abs</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="q">"-"</span> . <span class="k">abs</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 881 <span class="s">}</span> 882 <span class="i">$MolecularFormula</span> = <span class="q">"${MolecularFormula}${FormalChargeString}"</span><span class="sc">;</span> 883 <span class="s">}</span> 884 885 <span class="k">return</span> <span class="i">$MolecularFormula</span><span class="sc">;</span> 886 <span class="s">}</span> 887 888 <span class="c"># Count elements and non-elements in molecule and return references to hashes</span> 889 <span class="c"># containing count of elements and non-elements respectively. By default, missing</span> 890 <span class="c"># hydrogens are not added to the element hash.</span> 891 <span class="c">#</span> 892 <span class="c">#</span> <a name="GetElementsAndNonElements-"></a> 893 <span class="k">sub </span><span class="m">GetElementsAndNonElements</span> <span class="s">{</span> 894 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 895 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$NumOfMissingHydrogens</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">%ElementsCount</span><span class="cm">,</span> <span class="i">%NonElementsCount</span><span class="s">)</span><span class="sc">;</span> 896 897 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 898 899 <span class="i">%ElementsCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">%NonElementsCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 900 <span class="i">$NumOfMissingHydrogens</span> = <span class="n">0</span><span class="sc">;</span> 901 902 <span class="c"># Count elements and non elements...</span> 903 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 904 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 905 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 906 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 907 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> 908 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> 909 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} += <span class="n">1</span><span class="sc">;</span> 910 <span class="s">}</span> 911 <span class="k">else</span> <span class="s">{</span> 912 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} = <span class="n">1</span><span class="sc">;</span> 913 <span class="s">}</span> 914 <span class="k">if</span> <span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> 915 <span class="i">$NumOfMissingHydrogens</span> += <span class="i">$Atom</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 916 <span class="s">}</span> 917 <span class="s">}</span> 918 <span class="k">else</span> <span class="s">{</span> 919 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NonElementsCount</span>{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> 920 <span class="i">$NonElementsCount</span>{<span class="i">$AtomSymbol</span>} += <span class="n">1</span><span class="sc">;</span> 921 <span class="s">}</span> 922 <span class="k">else</span> <span class="s">{</span> 923 <span class="i">$NonElementsCount</span>{<span class="i">$AtomSymbol</span>} = <span class="n">1</span><span class="sc">;</span> 924 <span class="s">}</span> 925 <span class="s">}</span> 926 <span class="s">}</span> 927 <span class="k">if</span> <span class="s">(</span><span class="i">$IncludeMissingHydrogens</span> && <span class="i">$NumOfMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> 928 <span class="i">$AtomSymbol</span> = <span class="q">'H'</span><span class="sc">;</span> 929 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> 930 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} += <span class="i">$NumOfMissingHydrogens</span><span class="sc">;</span> 931 <span class="s">}</span> 932 <span class="k">else</span> <span class="s">{</span> 933 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} = <span class="i">$NumOfMissingHydrogens</span><span class="sc">;</span> 934 <span class="s">}</span> 935 <span class="s">}</span> 936 937 <span class="k">return</span> <span class="s">(</span>\<span class="i">%ElementsCount</span><span class="cm">,</span> \<span class="i">%NonElementsCount</span><span class="s">)</span><span class="sc">;</span> 938 <span class="s">}</span> 939 940 <span class="c"># Get number of element and non-elements in molecule. By default, missing</span> 941 <span class="c"># hydrogens are not added to element count.</span> 942 <span class="c">#</span> <a name="GetNumOfElementsAndNonElements-"></a> 943 <span class="k">sub </span><span class="m">GetNumOfElementsAndNonElements</span> <span class="s">{</span> 944 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 945 <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 946 947 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 948 949 <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> 950 951 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 952 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 953 <span class="i">$NonElementCount</span>++<span class="sc">;</span> 954 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 955 <span class="s">}</span> 956 <span class="c"># Process element...</span> 957 <span class="i">$ElementCount</span>++<span class="sc">;</span> 958 <span class="k">if</span> <span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> 959 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 960 <span class="i">$ElementCount</span> += <span class="i">$Atom</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 961 <span class="s">}</span> 962 <span class="s">}</span> 963 <span class="s">}</span> 964 965 <span class="k">return</span> <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span> 966 <span class="s">}</span> 967 968 <span class="c"># Calculate elemental composition and return reference to arrays</span> 969 <span class="c"># containing elements and their percent composition.</span> 970 <span class="c">#</span> 971 <span class="c"># Caveats:</span> 972 <span class="c"># . By default, missing hydrogens are included</span> 973 <span class="c"># . Non elemnents are ignored</span> 974 <span class="c"># . Mass number are ignored</span> 975 <span class="c">#</span> <a name="GetElementalComposition-"></a> 976 <span class="k">sub </span><span class="m">GetElementalComposition</span> <span class="s">{</span> 977 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 978 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="cm">,</span> <span class="i">$IncludeNonElements</span><span class="cm">,</span> <span class="i">$ElementsCountRef</span><span class="cm">,</span> <span class="i">$NonElementsCountRef</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="s">)</span><span class="sc">;</span> 979 980 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 981 982 <span class="i">$IncludeNonElements</span> = <span class="n">0</span><span class="sc">;</span> 983 <span class="s">(</span><span class="i">$ElementsCountRef</span><span class="cm">,</span> <span class="i">$NonElementsCountRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetElementsAndNonElements</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span><span class="sc">;</span> 984 985 <span class="i">$MolecularFormula</span> = <span class="i">$This</span><span class="i">->GetMolecularFormula</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="cm">,</span> <span class="i">$IncludeNonElements</span><span class="s">)</span><span class="sc">;</span> 986 987 <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="s">)</span> = <span class="i">MolecularFormula::CalculateElementalComposition</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span> 988 989 <span class="k">return</span> <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="s">)</span><span class="sc">;</span> 990 <span class="s">}</span> 991 992 <span class="c"># Using refernece to element and its composition arrays, format composition information</span> 993 <span class="c"># as: Element: Composition;...</span> 994 <span class="c">#</span> <a name="FormatElementalCompositionInformation-"></a> 995 <span class="k">sub </span><span class="m">FormatElementalCompositionInformation</span> <span class="s">{</span> 996 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="cm">,</span> <span class="i">$FourthParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 997 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span><span class="sc">;</span> 998 999 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecule</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1000 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="cm">,</span> <span class="i">$FourthParameter</span><span class="s">)</span><span class="sc">;</span> 1001 <span class="s">}</span> 1002 <span class="k">else</span> <span class="s">{</span> 1003 <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span><span class="sc">;</span> 1004 <span class="s">}</span> 1005 <span class="k">my</span><span class="s">(</span><span class="i">$FormattedInfo</span><span class="s">)</span> = <span class="q">''</span><span class="sc">;</span> 1006 1007 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ElementsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1008 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->FormatElementalCompositionInformation: Elements list is not defined or empty..."</span><span class="sc">;</span> 1009 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1010 <span class="s">}</span> 1011 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ElementCompositionRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ElementCompositionRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1012 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->FormatElementalCompositionInformation: Elements composition list is not defined or empty..."</span><span class="sc">;</span> 1013 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1014 <span class="s">}</span> 1015 1016 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Precision</span><span class="s">)</span> <span class="s">{</span> 1017 <span class="i">$Precision</span> = <span class="n">2</span><span class="sc">;</span> 1018 <span class="s">}</span> 1019 1020 <span class="i">$FormattedInfo</span> = <span class="i">MolecularFormula::FormatCompositionInfomation</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span><span class="sc">;</span> 1021 1022 <span class="k">return</span> <span class="i">$FormattedInfo</span><span class="sc">;</span> 1023 <span class="s">}</span> 1024 1025 <span class="c"># Copy molecule and its associated data using Storable::dclone and update:</span> 1026 <span class="c">#</span> 1027 <span class="c"># o Atom references corresponding atoms and bonds objects</span> 1028 <span class="c"># o Bond object references</span> 1029 <span class="c">#</span> 1030 <span class="c"># Object IDs for Atoms and Bonds don't get changed. So there is no need to clear</span> 1031 <span class="c"># up any exisiting ring data attached to molecule via graph as vertex IDs.</span> 1032 <span class="c">#</span> <a name="Copy-"></a>1033 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span> 1034 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1035 <span class="k">my</span><span class="s">(</span><span class="i">$NewMolecule</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$NewAtom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">%AtomsIDsToNewAtoms</span><span class="s">)</span><span class="sc">;</span> 1036 1037 <span class="i">$NewMolecule</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> 1038 1039 <span class="c"># Update atom references stored as vertex property...</span> 1040 1041 <span class="i">@Atoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1042 <span class="i">%AtomsIDsToNewAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1043 1044 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1045 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span> 1046 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetVerticesProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 1047 <span class="s">}</span> 1048 1049 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 1050 <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> 1051 1052 <span class="c"># Setup a reference to copied atom object...</span> 1053 <span class="i">$NewAtom</span> = <span class="i">$Atom</span><span class="i">->Copy</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1054 <span class="i">$AtomsIDsToNewAtoms</span>{<span class="i">$AtomID</span>} = <span class="i">$NewAtom</span><span class="sc">;</span> 1055 1056 <span class="c"># Update atom reference to new atom object...</span> 1057 <span class="i">$NewMolecule</span><span class="i">->UpdateVertexProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">$NewAtom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 1058 <span class="s">}</span> 1059 1060 <span class="c"># Update bond object and bond atom references stored as edge property...</span> 1061 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$NewBond</span><span class="cm">,</span> <span class="i">$NewAtom1</span><span class="cm">,</span> <span class="i">$NewAtom2</span><span class="cm">,</span> <span class="i">@EdgesAtomsIDs</span><span class="s">)</span><span class="sc">;</span> 1062 <span class="i">@EdgesAtomsIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1063 <span class="i">@EdgesAtomsIDs</span> = <span class="i">$This</span><span class="i">->GetEdges</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1064 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$#EdgesAtomsIDs</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 1065 <span class="i">$AtomID1</span> = <span class="i">$EdgesAtomsIDs</span>[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$EdgesAtomsIDs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> 1066 1067 <span class="c"># Get reference to bond object...</span> 1068 <span class="i">$Bond</span> = <span class="i">$This</span><span class="i">->GetEdgeProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 1069 1070 <span class="c"># Make a new bond object and update its atom references...</span> 1071 <span class="i">$NewBond</span> = <span class="i">$Bond</span><span class="i">->Copy</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1072 <span class="i">$NewAtom1</span> = <span class="i">$AtomsIDsToNewAtoms</span>{<span class="i">$AtomID1</span>}<span class="sc">;</span> 1073 <span class="i">$NewAtom2</span> = <span class="i">$AtomsIDsToNewAtoms</span>{<span class="i">$AtomID2</span>}<span class="sc">;</span> 1074 <span class="i">$NewBond</span><span class="i">->SetAtoms</span><span class="s">(</span><span class="i">$NewAtom1</span><span class="cm">,</span> <span class="i">$NewAtom2</span><span class="s">)</span><span class="sc">;</span> 1075 1076 <span class="c"># Update bond object reference in the new molecule...</span> 1077 <span class="i">$NewMolecule</span><span class="i">->UpdateEdgeProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">$NewBond</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 1078 <span class="s">}</span> 1079 1080 <span class="k">return</span> <span class="i">$NewMolecule</span><span class="sc">;</span> 1081 <span class="s">}</span> 1082 1083 <span class="c"># Get number of connected components...</span> 1084 <span class="c">#</span> <a name="GetNumOfConnectedComponents-"></a>1085 <span class="k">sub </span><span class="m">GetNumOfConnectedComponents</span> <span class="s">{</span> 1086 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1087 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfComponents</span><span class="s">)</span><span class="sc">;</span> 1088 1089 <span class="i">$NumOfComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1090 1091 <span class="k">return</span> <span class="i">$NumOfComponents</span><span class="sc">;</span> 1092 <span class="s">}</span> 1093 1094 <span class="c"># Return a reference to an array containing molecules corresponding</span> 1095 <span class="c"># to connected components sorted in decreasing order of component size...</span> 1096 <span class="c">#</span> <a name="GetConnectedComponents-"></a>1097 <span class="k">sub </span><span class="m">GetConnectedComponents</span> <span class="s">{</span> 1098 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1099 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">@ComponentMolecules</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span> 1100 1101 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1102 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1103 <span class="i">@ComponentMolecules</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1104 1105 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ConnectedComponents</span><span class="s">)</span> <span class="s">{</span> 1106 <span class="k">push</span> <span class="i">@ComponentMolecules</span><span class="cm">,</span> <span class="i">$This</span><span class="i">->_GetConnectedComponent</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span> 1107 <span class="s">}</span> 1108 <span class="k">return</span> <span class="i">@ComponentMolecules</span><span class="sc">;</span> 1109 <span class="s">}</span> 1110 1111 <span class="c"># Return a reference to largest connected component as a molecule object...</span> 1112 <span class="c">#</span> <a name="GetLargestConnectedComponent-"></a>1113 <span class="k">sub </span><span class="m">GetLargestConnectedComponent</span> <span class="s">{</span> 1114 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1115 <span class="k">my</span><span class="s">(</span><span class="i">$LargestComponentIndex</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span> 1116 1117 <span class="i">$LargestComponentIndex</span> = <span class="n">0</span><span class="sc">;</span> 1118 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1119 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1120 1121 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetConnectedComponent</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$LargestComponentIndex</span><span class="s">)</span><span class="sc">;</span> 1122 <span class="s">}</span> 1123 1124 <span class="c"># Return connected component as a molecule...</span> 1125 <span class="c">#</span> <a name="_GetConnectedComponent-"></a>1126 <span class="k">sub </span><span class="m">_GetConnectedComponent</span> <span class="s">{</span> 1127 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ConnectedComponentsRef</span><span class="cm">,</span> <span class="i">$ComponentIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1128 <span class="k">my</span><span class="s">(</span><span class="i">$ComponentMolecule</span><span class="s">)</span><span class="sc">;</span> 1129 1130 <span class="c"># Copy existing molecule...</span> 1131 <span class="i">$ComponentMolecule</span> = <span class="i">$This</span><span class="i">->Copy</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1132 1133 <span class="c"># Delete all atoms besides the ones in specified component...</span> 1134 <span class="i">$ComponentMolecule</span><span class="i">->_DeleteConnectedComponents</span><span class="s">(</span><span class="i">$ConnectedComponentsRef</span><span class="cm">,</span> <span class="i">$ComponentIndex</span><span class="s">)</span><span class="sc">;</span> 1135 1136 <span class="c"># Clear any deteced rings...</span> 1137 <span class="k">if</span> <span class="s">(</span><span class="i">$ComponentMolecule</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1138 <span class="i">$ComponentMolecule</span><span class="i">->ClearRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1139 <span class="s">}</span> 1140 <span class="k">return</span> <span class="i">$ComponentMolecule</span><span class="sc">;</span> 1141 <span class="s">}</span> 1142 1143 <span class="c"># Delete atoms corresponding to all connected components except the one specified...</span> 1144 <span class="c">#</span> <a name="_DeleteConnectedComponents-"></a>1145 <span class="k">sub </span><span class="m">_DeleteConnectedComponents</span> <span class="s">{</span> 1146 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ConnectedComponentsRef</span><span class="cm">,</span> <span class="i">$KeepComponentIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1147 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 1148 1149 <span class="j">INDEX:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ConnectedComponentsRef</span>}<span class="s">)</span> <span class="s">{</span> 1150 <span class="k">if</span> <span class="s">(</span><span class="i">$Index</span> == <span class="i">$KeepComponentIndex</span><span class="s">)</span> <span class="s">{</span> 1151 <span class="k">next</span> <span class="j">INDEX</span><span class="sc">;</span> 1152 <span class="s">}</span> 1153 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConnectedComponentsRef</span>->[<span class="i">$Index</span>]}<span class="s">)</span> <span class="s">{</span> 1154 <span class="i">$This</span><span class="i">->DeleteVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 1155 <span class="s">}</span> 1156 <span class="s">}</span> 1157 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1158 <span class="s">}</span> 1159 1160 <span class="c"># Return an array containing references to atom arrays corresponding to atoms of</span> 1161 <span class="c"># connected components sorted in order of their decreasing size...</span> 1162 <span class="c">#</span> <a name="GetConnectedComponentsAtoms-"></a>1163 <span class="k">sub </span><span class="m">GetConnectedComponentsAtoms</span> <span class="s">{</span> 1164 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1165 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">@ComponentsAtoms</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span> 1166 1167 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1168 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1169 1170 <span class="i">@ComponentsAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1171 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ConnectedComponents</span><span class="s">)</span> <span class="s">{</span> 1172 <span class="k">my</span><span class="s">(</span><span class="i">@ComponentAtoms</span><span class="s">)</span><span class="sc">;</span> 1173 1174 <span class="i">@ComponentAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1175 <span class="i">@ComponentAtoms</span> = <span class="i">$This</span><span class="i">->_GetConnectedComponentAtoms</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span> 1176 <span class="k">push</span> <span class="i">@ComponentsAtoms</span><span class="cm">,</span> \<span class="i">@ComponentAtoms</span><span class="sc">;</span> 1177 <span class="s">}</span> 1178 <span class="k">return</span> <span class="i">@ComponentsAtoms</span><span class="sc">;</span> 1179 <span class="s">}</span> 1180 1181 <span class="c"># Return an array containing atoms correspondig to largest connected component...</span> 1182 <span class="c">#</span> <a name="GetLargestConnectedComponentAtoms-"></a>1183 <span class="k">sub </span><span class="m">GetLargestConnectedComponentAtoms</span> <span class="s">{</span> 1184 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1185 <span class="k">my</span><span class="s">(</span><span class="i">$LargestComponentIndex</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span> 1186 1187 <span class="i">$LargestComponentIndex</span> = <span class="n">0</span><span class="sc">;</span> 1188 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1189 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1190 1191 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetConnectedComponentAtoms</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$LargestComponentIndex</span><span class="s">)</span><span class="sc">;</span> 1192 <span class="s">}</span> 1193 1194 <span class="c"># Return an array containing atoms corresponding to specified connected component...</span> 1195 <span class="c">#</span> <a name="_GetConnectedComponentAtoms-"></a>1196 <span class="k">sub </span><span class="m">_GetConnectedComponentAtoms</span> <span class="s">{</span> 1197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ConnectedComponentsRef</span><span class="cm">,</span> <span class="i">$ComponentIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1198 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">@ComponentAtoms</span><span class="s">)</span><span class="sc">;</span> 1199 1200 <span class="i">@ComponentAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1201 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1202 1203 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConnectedComponentsRef</span>->[<span class="i">$ComponentIndex</span>]}<span class="s">)</span> <span class="s">{</span> 1204 <span class="k">push</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="sc">;</span> 1205 <span class="s">}</span> 1206 <span class="i">@ComponentAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 1207 1208 <span class="k">return</span> <span class="i">@ComponentAtoms</span><span class="sc">;</span> 1209 <span class="s">}</span> 1210 1211 <span class="c"># Except for the largest connected component, delete atoms corresponding to all other</span> 1212 <span class="c"># connected components...</span> 1213 <span class="c">#</span> <a name="KeepLargestComponent-"></a>1214 <span class="k">sub </span><span class="m">KeepLargestComponent</span> <span class="s">{</span> 1215 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1216 <span class="k">my</span><span class="s">(</span><span class="i">$LargestComponentIndex</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span> 1217 1218 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1219 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1220 <span class="k">if</span> <span class="s">(</span><span class="i">@ConnectedComponents</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 1221 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1222 <span class="s">}</span> 1223 <span class="i">$LargestComponentIndex</span> = <span class="n">0</span><span class="sc">;</span> 1224 <span class="i">$This</span><span class="i">->_DeleteConnectedComponents</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$LargestComponentIndex</span><span class="s">)</span><span class="sc">;</span> 1225 1226 <span class="c"># Clear any deteced rings...</span> 1227 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1228 <span class="i">$This</span><span class="i">->ClearRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1229 <span class="s">}</span> 1230 1231 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1232 <span class="s">}</span> 1233 1234 <span class="c"># Get an array of topologically sorted atoms starting from a specified atom or</span> 1235 <span class="c"># an arbitrary atom in the molecule...</span> 1236 <span class="c">#</span> <a name="GetTopologicallySortedAtoms-"></a>1237 <span class="k">sub </span><span class="m">GetTopologicallySortedAtoms</span> <span class="s">{</span> 1238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1239 <span class="k">my</span><span class="s">(</span><span class="i">@SortedAtoms</span><span class="s">)</span><span class="sc">;</span> 1240 1241 <span class="i">@SortedAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1242 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span> && !<span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1243 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetTopologicallySortedAtoms: No atoms retrieved: Start atom doesn't exist..."</span><span class="sc">;</span> 1244 <span class="k">return</span> <span class="i">@SortedAtoms</span><span class="sc">;</span> 1245 <span class="s">}</span> 1246 <span class="k">my</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 1247 1248 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1249 <span class="i">$StartAtomID</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span> ? <span class="i">$StartAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> 1250 1251 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetTopologicallySortedVertices</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="s">)</span><span class="sc">;</span> 1252 <span class="i">@SortedAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 1253 1254 <span class="k">return</span> <span class="i">@SortedAtoms</span><span class="sc">;</span> 1255 <span class="s">}</span> 1256 1257 <span class="c"># Detect rings in molecule...</span> 1258 <span class="c">#</span> <a name="DetectRings-"></a>1259 <span class="k">sub </span><span class="m">DetectRings</span> <span class="s">{</span> 1260 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1261 1262 <span class="c"># Use graph method to detect all cycles and associate 'em to graph as graph</span> 1263 <span class="c"># and vertex properties...</span> 1264 <span class="k">return</span> <span class="i">$This</span><span class="i">->DetectCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1265 <span class="s">}</span> 1266 1267 <span class="c"># Clear rings in molecule...</span> 1268 <span class="c">#</span> <a name="ClearRings-"></a>1269 <span class="k">sub </span><span class="m">ClearRings</span> <span class="s">{</span> 1270 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1271 1272 <span class="c"># Use graph method to clear all cycles...</span> 1273 <span class="i">$This</span><span class="i">->ClearCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1274 1275 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1276 <span class="s">}</span> 1277 1278 <span class="c"># Setup rings type paths to use during all ring related methods. Possible values:</span> 1279 <span class="c"># Independent or All. Default is to use Independent rings.</span> 1280 <span class="c">#</span> <a name="SetActiveRings-"></a>1281 <span class="k">sub </span><span class="m">SetActiveRings</span> <span class="s">{</span> 1282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1283 1284 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$This</span><span class="i">->SetActiveCyclicPaths</span><span class="s">(</span><span class="i">$RingsType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1285 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1286 <span class="s">}</span> 1287 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1288 <span class="s">}</span> 1289 1290 <span class="c"># Is it a supported aromaticity model?</span> 1291 <span class="c">#</span> <a name="IsSupportedAromaticityModel-"></a>1292 <span class="k">sub </span><span class="m">IsSupportedAromaticityModel</span> <span class="s">{</span> 1293 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1294 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticityModel</span><span class="s">)</span><span class="sc">;</span> 1295 1296 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecule</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1297 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticityModel</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> 1298 <span class="s">}</span> 1299 <span class="k">else</span> <span class="s">{</span> 1300 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticityModel</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span> 1301 <span class="s">}</span> 1302 1303 <span class="k">return</span> <span class="k">exists</span> <span class="i">$CanonicalAromaticityModelNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AromaticityModel</span><span class="s">)</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 1304 <span class="s">}</span> 1305 1306 <span class="c"># Get a list of supported aromaticity model names...</span> 1307 <span class="c">#</span> <a name="GetSupportedAromaticityModels-"></a>1308 <span class="k">sub </span><span class="m">GetSupportedAromaticityModels</span> <span class="s">{</span> 1309 <span class="k">return</span> <span class="s">(</span><span class="k">sort</span> <span class="k">values</span> <span class="i">%CanonicalAromaticityModelNamesMap</span><span class="s">)</span><span class="sc">;</span> 1310 <span class="s">}</span> 1311 1312 <span class="c"># Set aromaticity model...</span> 1313 <span class="c">#</span> <a name="SetAromaticityModel-"></a>1314 <span class="k">sub </span><span class="m">SetAromaticityModel</span> <span class="s">{</span> 1315 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticityModel</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1316 1317 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$AromaticityModel</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1318 <span class="k">my</span><span class="s">(</span><span class="i">@SupportedModels</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetSupportedAromaticityModels</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1319 1320 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAromaticityModel: The current release of MayaChemTools doesn't support the specified aromaticity model $AromaticityModel. Supported aromaticity models defined in AromaticityModelsData.csv file are: @SupportedModels . Using MayaChemToolsAromaticityModel..."</span><span class="sc">;</span> 1321 <span class="i">$AromaticityModel</span> = <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span> 1322 <span class="s">}</span> 1323 1324 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'AromaticityModel'</span><span class="cm">,</span> <span class="i">$AromaticityModel</span><span class="s">)</span><span class="sc">;</span> 1325 1326 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1327 <span class="s">}</span> 1328 1329 <span class="c"># Get aromaticity model...</span> 1330 <span class="c">#</span> <a name="GetAromaticityModel-"></a>1331 <span class="k">sub </span><span class="m">GetAromaticityModel</span> <span class="s">{</span> 1332 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1333 1334 <span class="c"># Is ValenceModel property explicitly set?</span> 1335 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'AromaticityModel'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1336 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'AromaticityModel'</span><span class="s">)</span><span class="sc">;</span> 1337 <span class="s">}</span> 1338 1339 <span class="c"># Used internal aromaticity model as default model...</span> 1340 <span class="k">return</span> <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span> 1341 <span class="s">}</span> 1342 1343 <span class="c"># Identify aromatic rings and ring systems in a molecule and set aromaticity for</span> 1344 <span class="c"># corresponding atoms and bonds.</span> 1345 <span class="c">#</span> 1346 <span class="c"># What is aromaticity? [ Ref 124 ] It's in the code of the implementer, did you</span> 1347 <span class="c"># say? Agree. The implementation of aromaticity varies widely across different</span> 1348 <span class="c"># packages [ Ref 125 ]; additionally, the implementation details are not always</span> 1349 <span class="c"># completely available, and it's not possible to figure out the exact implementation</span> 1350 <span class="c"># of aromaticity across various packages. Using the publicly available information,</span> 1351 <span class="c"># however, one can try to reproduce the available results to the extent possible,</span> 1352 <span class="c"># along with parameterizing all the control parameters used to implement different</span> 1353 <span class="c"># aromaticity models, and that's exactly what the current release of MayaChemTools</span> 1354 <span class="c"># does.</span> 1355 <span class="c">#</span> 1356 <span class="c"># The implementation of aromaticity corresponding to various aromaticity models in</span> 1357 <span class="c"># MayaChemTools package is driven by an external CSV file AromaticityModelsData.csv,</span> 1358 <span class="c"># which is distributed with the package and is available in lib/data directory. The CSV</span> 1359 <span class="c"># files contains names of supported aromaticity models, along with various control</span> 1360 <span class="c"># parameters and their values. This file is loaded and processed during instantiation</span> 1361 <span class="c"># of Molecule class and data corresponding to specific aromaticity model are used</span> 1362 <span class="c"># to detect aromaticity for that model. Any new aromaticity model added to the</span> 1363 <span class="c"># aromaticity data file, using different combinations of values for existing control</span> 1364 <span class="c"># parameters would work without any changes to the code; the addition of any new</span> 1365 <span class="c"># control parameters, however, requires its implementation in the code used to</span> 1366 <span class="c"># calculate number of pi electrons available towards delocalization in a ring or ring</span> 1367 <span class="c"># systems.</span> 1368 <span class="c">#</span> 1369 <span class="c"># The current release of MayaChemTools package supports these aromaticity</span> 1370 <span class="c"># models: MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,</span> 1371 <span class="c"># ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,</span> 1372 <span class="c"># DaylightAromaticityModel, MayaChemToolsAromaticityModel.</span> 1373 <span class="c">#</span> 1374 <span class="c"># The current list of control parameters available to detect aromaticity corresponding</span> 1375 <span class="c"># to different aromaticity models are: AllowHeteroRingAtoms, HeteroRingAtomsList,</span> 1376 <span class="c"># AllowExocyclicDoubleBonds, AllowHomoNuclearExocyclicDoubleBonds,</span> 1377 <span class="c"># AllowElectronegativeRingAtomExocyclicDoubleBonds, AllowRingAtomFormalCharge,</span> 1378 <span class="c"># AllowHeteroRingAtomFormalCharge, MinimumRingSize. The values for these control</span> 1379 <span class="c"># parameters are specified in AromaticityModelsData.csv file.</span> 1380 <span class="c">#</span> 1381 <span class="c"># Although definition of aromaticity differs across various aromaticity models, a ring</span> 1382 <span class="c"># or a ring system containing 4n + 2 pi electrons (Huckel's rule) corresponding to</span> 1383 <span class="c"># alternate single and double bonds, in general, is considered aromatic.</span> 1384 <span class="c">#</span> 1385 <span class="c"># The available valence free electrons on heterocyclic ring atoms, involved in two single</span> 1386 <span class="c"># ring bonds, are also allowed to participate in pi electron delocalizaiton for most of</span> 1387 <span class="c"># the supported aromaticity models.</span> 1388 <span class="c">#</span> 1389 <span class="c"># The presence of exocyclic terminal double bond on ring atoms involved in pi electron</span> 1390 <span class="c"># delocalization is only allowed for some of the aromaticity models. Additionally, the type</span> 1391 <span class="c"># atoms involved in exocyclic terminal double bonds may result in making a ring or ring</span> 1392 <span class="c"># system non-aromatic.</span> 1393 <span class="c">#</span> <a name="DetectAromaticity-"></a>1394 <span class="k">sub </span><span class="m">DetectAromaticity</span> <span class="s">{</span> 1395 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1396 1397 <span class="c"># Delete aromaticity property for atoms and bonds...</span> 1398 <span class="i">$This</span><span class="i">->DeleteAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1399 1400 <span class="c"># Any ring out there...</span> 1401 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1402 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1403 <span class="s">}</span> 1404 1405 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasFusedRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1406 <span class="i">$This</span><span class="i">->_DetectAromaticityUsingFusedRingSets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1407 <span class="s">}</span> 1408 <span class="k">else</span> <span class="s">{</span> 1409 <span class="i">$This</span><span class="i">->_DetectAromaticityUsingIndividualRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1410 <span class="s">}</span> 1411 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1412 <span class="s">}</span> 1413 1414 <span class="c"># Go over all rings and set aromaticity property for corresponding ring atoms</span> 1415 <span class="c"># and bonds involved in aromatic rings...</span> 1416 <span class="c">#</span> <a name="_DetectAromaticityUsingIndividualRings-"></a>1417 <span class="k">sub </span><span class="m">_DetectAromaticityUsingIndividualRings</span> <span class="s">{</span> 1418 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1419 1420 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DetectRingsAromaticity</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 1421 <span class="s">}</span> 1422 1423 <span class="c"># For each fused ring set, detect aromaticity by treating all of its ring as one aromatic</span> 1424 <span class="c"># system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in</span> 1425 <span class="c"># fused set are treated individually for aromaticity detection. Additionally, non-fused</span> 1426 <span class="c"># rings are handled on their own during aromaticity detection.</span> 1427 <span class="c">#</span> 1428 <span class="c"># Note:</span> 1429 <span class="c"># . pi electrons in common bonds involved in fused ring sets are only counted once.</span> 1430 <span class="c">#</span> 1431 <span class="c">#</span> <a name="_DetectAromaticityUsingFusedRingSets-"></a>1432 <span class="k">sub </span><span class="m">_DetectAromaticityUsingFusedRingSets</span> <span class="s">{</span> 1433 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1434 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$FusedRingSetRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedRingsRef</span><span class="cm">,</span> <span class="i">@FusedRingSetIsAromatic</span><span class="s">)</span><span class="sc">;</span> 1435 1436 <span class="s">(</span><span class="i">$FusedRingSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedRingsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetFusedAndNonFusedRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1437 1438 <span class="i">@FusedRingSetIsAromatic</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1439 <span class="j">RINGSET:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 1440 <span class="i">$FusedRingSetRef</span> = <span class="i">$FusedRingSetsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 1441 <span class="i">$FusedRingSetIsAromatic</span>[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> 1442 1443 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfPiElectronsInRingSet</span><span class="cm">,</span> <span class="i">$NumOfPiElectronsInRing</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">%FusedRingSetsBondsMap</span><span class="cm">,</span> <span class="i">%FusedRingSetsBondsVisitedMap</span><span class="cm">,</span> <span class="i">%FusedRingBondsMap</span><span class="s">)</span><span class="sc">;</span> 1444 1445 <span class="i">$NumOfPiElectronsInRingSet</span> = <span class="n">0</span><span class="sc">;</span> 1446 1447 <span class="i">%FusedRingSetsBondsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1448 <span class="i">%FusedRingSetsBondsVisitedMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1449 <span class="i">%FusedRingBondsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1450 1451 <span class="c"># Setup a bond ID map for all bonds in fused ring set and another one</span> 1452 <span class="c"># for bonds involved in more than one ring...</span> 1453 <span class="c">#</span> 1454 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span> <span class="s">{</span> 1455 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1456 <span class="i">$BondID</span> = <span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1457 <span class="i">$FusedRingSetsBondsMap</span>{<span class="i">$BondID</span>} = <span class="i">$BondID</span><span class="sc">;</span> 1458 1459 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 1460 <span class="i">$FusedRingBondsMap</span>{<span class="i">$BondID</span>} = <span class="i">$BondID</span><span class="sc">;</span> 1461 <span class="s">}</span> 1462 <span class="s">}</span> 1463 <span class="s">}</span> 1464 1465 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span> <span class="s">{</span> 1466 <span class="k">my</span><span class="s">(</span><span class="i">@RingBonds</span><span class="s">)</span><span class="sc">;</span> 1467 1468 <span class="i">@RingBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1469 <span class="i">@RingBonds</span> = <span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="sc">;</span> 1470 <span class="i">$NumOfPiElectronsInRing</span> = <span class="i">$This</span><span class="i">->_GetNumOfPiElectronsAvailableForDelocalization</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> \<span class="i">@RingBonds</span><span class="cm">,</span> \<span class="i">%FusedRingSetsBondsMap</span><span class="cm">,</span> \<span class="i">%FusedRingSetsBondsVisitedMap</span><span class="cm">,</span> \<span class="i">%FusedRingBondsMap</span><span class="s">)</span><span class="sc">;</span> 1471 1472 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfPiElectronsInRing</span><span class="s">)</span> <span class="s">{</span> 1473 <span class="k">next</span> <span class="j">RINGSET</span><span class="sc">;</span> 1474 <span class="s">}</span> 1475 <span class="i">$NumOfPiElectronsInRingSet</span> += <span class="i">$NumOfPiElectronsInRing</span><span class="sc">;</span> 1476 <span class="s">}</span> 1477 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->_DoPiElectronSatifyHuckelsRule</span><span class="s">(</span><span class="i">$NumOfPiElectronsInRingSet</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1478 <span class="i">$FusedRingSetIsAromatic</span>[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> 1479 <span class="s">}</span> 1480 <span class="s">}</span> 1481 1482 <span class="c"># Set atom and bond aromatic flags for ring sets whose pi electrons satisfy Huckel's rule; otherwise,</span> 1483 <span class="c"># treat rings in a ring set as individual rings for detecting aromaticity...</span> 1484 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 1485 <span class="i">$FusedRingSetRef</span> = <span class="i">$FusedRingSetsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 1486 <span class="k">if</span> <span class="s">(</span><span class="i">$FusedRingSetIsAromatic</span>[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span> 1487 <span class="i">$This</span><span class="i">->_SetRingsAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span><span class="sc">;</span> 1488 <span class="s">}</span> 1489 <span class="k">else</span> <span class="s">{</span> 1490 <span class="i">$This</span><span class="i">->_DetectRingsAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span><span class="sc">;</span> 1491 <span class="s">}</span> 1492 <span class="s">}</span> 1493 1494 <span class="i">$This</span><span class="i">->_DetectRingsAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedRingsRef</span>}<span class="s">)</span><span class="sc">;</span> 1495 1496 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1497 <span class="s">}</span> 1498 1499 <span class="c"># Detect and set aromaticity for rings...</span> 1500 <span class="c">#</span> <a name="_DetectRingsAromaticity-"></a>1501 <span class="k">sub </span><span class="m">_DetectRingsAromaticity</span> <span class="s">{</span> 1502 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1503 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="s">)</span><span class="sc">;</span> 1504 1505 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span> 1506 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckRingAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1507 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span> 1508 <span class="s">}</span> 1509 <span class="i">$This</span><span class="i">->_SetRingAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="sc">;</span> 1510 <span class="s">}</span> 1511 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1512 <span class="s">}</span> 1513 1514 <span class="c"># Set aromatic property for all all atoms and bonds involved in all specified rings..</span> 1515 <span class="c">#</span> <a name="_SetRingsAromaticity-"></a>1516 <span class="k">sub </span><span class="m">_SetRingsAromaticity</span> <span class="s">{</span> 1517 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1518 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomsRef</span> <span class="s">)</span><span class="sc">;</span> 1519 1520 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span> 1521 <span class="i">$This</span><span class="i">->_SetRingAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="sc">;</span> 1522 <span class="s">}</span> 1523 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1524 <span class="s">}</span> 1525 1526 <span class="c"># Set aromatic property for all all atoms and bonds involved in ring..</span> 1527 <span class="c">#</span> <a name="_SetRingAromaticity-"></a>1528 <span class="k">sub </span><span class="m">_SetRingAromaticity</span> <span class="s">{</span> 1529 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1530 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="s">)</span><span class="sc">;</span> 1531 1532 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span> 1533 <span class="i">$RingAtom</span><span class="i">->SetAromatic</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> 1534 <span class="s">}</span> 1535 <span class="k">for</span> <span class="i">$RingBond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1536 <span class="i">$RingBond</span><span class="i">->SetAromatic</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> 1537 <span class="s">}</span> 1538 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1539 <span class="s">}</span> 1540 1541 1542 <span class="c"># For a ring to be an aromatic ring, all of its atoms must have aromatic property</span> 1543 <span class="c"># set.</span> 1544 <span class="c">#</span> <a name="IsRingAromatic-"></a>1545 <span class="k">sub </span><span class="m">IsRingAromatic</span> <span class="s">{</span> 1546 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1547 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtom</span><span class="s">)</span><span class="sc">;</span> 1548 1549 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span> 1550 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1551 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1552 <span class="s">}</span> 1553 <span class="s">}</span> 1554 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 1555 <span class="s">}</span> 1556 1557 <span class="c"># Delete aromatic property for all atoms and bonds...</span> 1558 <span class="c">#</span> <a name="DeleteAromaticity-"></a>1559 <span class="k">sub </span><span class="m">DeleteAromaticity</span> <span class="s">{</span> 1560 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1561 1562 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteAtomsAndBondsAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1563 <span class="s">}</span> 1564 1565 <span class="c"># Check ring aromaticity...</span> 1566 <span class="c">#</span> <a name="_CheckRingAromaticity-"></a>1567 <span class="k">sub </span><span class="m">_CheckRingAromaticity</span> <span class="s">{</span> 1568 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1569 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfPiElectrons</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">@RingBonds</span><span class="s">)</span><span class="sc">;</span> 1570 1571 <span class="i">@RingBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1572 <span class="i">@RingBonds</span> = <span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span> 1573 1574 <span class="i">$NumOfPiElectrons</span> = <span class="i">$This</span><span class="i">->_GetNumOfPiElectronsAvailableForDelocalization</span><span class="s">(</span>\<span class="i">@RingAtoms</span><span class="cm">,</span> \<span class="i">@RingBonds</span><span class="s">)</span><span class="sc">;</span> 1575 1576 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DoPiElectronSatifyHuckelsRule</span><span class="s">(</span><span class="i">$NumOfPiElectrons</span><span class="s">)</span><span class="sc">;</span> 1577 <span class="s">}</span> 1578 1579 <span class="c"># Get number of pi electrons available for delocalizaiton in a ring or ring system...</span> 1580 <span class="c">#</span> <a name="_GetNumOfPiElectronsAvailableForDelocalization-"></a>1581 <span class="k">sub </span><span class="m">_GetNumOfPiElectronsAvailableForDelocalization</span> <span class="s">{</span> 1582 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsBondsMapRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsBondsVisitedMapRef</span><span class="cm">,</span> <span class="i">$FusedRingBondsMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1583 <span class="k">my</span><span class="s">(</span><span class="i">$AromaticityModelName</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="cm">,</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="cm">,</span> <span class="i">$NumOfConjugatedDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfExplicitAromaticBonds</span><span class="cm">,</span> <span class="i">$NumOfRingAtomElectronPairs</span><span class="cm">,</span> <span class="i">$NumOfRingBondsProcessed</span><span class="cm">,</span> <span class="i">$NumOfPiElectrons</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingAtomSymbol</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$RingAtomID</span><span class="cm">,</span> <span class="i">$RingBondID</span><span class="cm">,</span> <span class="i">$PreviousIndex</span><span class="cm">,</span> <span class="i">$PreviousRingBond</span><span class="cm">,</span> <span class="i">$ExcludeFreeRadicalElectrons</span><span class="cm">,</span> <span class="i">%ElectronPairContributionProcessedMap</span><span class="s">)</span><span class="sc">;</span> 1584 1585 <span class="i">$AromaticityModelName</span> = <span class="i">$CanonicalAromaticityModelNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetAromaticityModel</span><span class="s">(</span><span class="s">)</span><span class="s">)</span>}<span class="sc">;</span> 1586 <span class="i">$AromaticityModelDataRef</span> = \<span class="i">%</span>{<span class="i">$AromaticityModelsDataMap</span>{<span class="i">$AromaticityModelName</span>}}<span class="sc">;</span> 1587 1588 <span class="c"># Perform an intial check for potential atomatic ring atoms..</span> 1589 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckRingAtomsForPotentialAromaticity</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1590 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1591 <span class="s">}</span> 1592 1593 <span class="i">$ExocyclicDoubleBondsDataMapRef</span> = <span class="k">undef</span><span class="sc">;</span> 1594 <span class="i">$ExcludeFreeRadicalElectrons</span> = <span class="n">1</span><span class="sc">;</span> 1595 1596 <span class="i">%ElectronPairContributionProcessedMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1597 1598 <span class="s">(</span><span class="i">$NumOfPiElectrons</span><span class="cm">,</span> <span class="i">$NumOfRingBondsProcessed</span><span class="cm">,</span> <span class="i">$NumOfConjugatedDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfExplicitAromaticBonds</span><span class="cm">,</span> <span class="i">$NumOfRingAtomElectronPairs</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">5</span><span class="sc">;</span> 1599 1600 <span class="c"># Go over ring atoms and bonds to check their participation in aromaticity and count</span> 1601 <span class="c"># pi electrons available for delocalization corresponding to various aromaticity models...</span> 1602 <span class="c">#</span> 1603 <span class="j">RINGBOND:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span> 1604 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 1605 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 1606 <span class="i">$BondOrder</span> = <span class="i">$RingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1607 1608 <span class="c"># Is this ring bond part of a fused ring system which has been already processed?</span> 1609 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FusedRingSetsBondsVisitedMapRef</span><span class="s">)</span> && <span class="i">$RingBond</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 1610 <span class="i">$RingBondID</span> = <span class="i">$RingBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1611 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$FusedRingSetsBondsVisitedMapRef</span>->{<span class="i">$RingBondID</span>}<span class="s">)</span> <span class="s">{</span> 1612 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> 1613 <span class="s">}</span> 1614 <span class="i">$FusedRingSetsBondsVisitedMapRef</span>->{<span class="i">$RingBondID</span>} = <span class="i">$RingBondID</span><span class="sc">;</span> 1615 <span class="s">}</span> 1616 <span class="i">$NumOfRingBondsProcessed</span>++<span class="sc">;</span> 1617 1618 <span class="c"># For first ring, previous ring bond corrresponds to last ring bond...</span> 1619 <span class="i">$PreviousIndex</span> = <span class="i">$Index</span> ? <span class="s">(</span><span class="i">$Index</span> -<span class="n">1</span><span class="s">)</span> <span class="co">:</span> <span class="i">$#</span>{<span class="i">$RingBondsRef</span>}<span class="sc">;</span> 1620 <span class="i">$PreviousRingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$PreviousIndex</span>]<span class="sc">;</span> 1621 1622 <span class="c"># Check for presence of alternate single/double bond configuration, and pesence of</span> 1623 <span class="c"># hetero atoms with two single ring bonds along with any exocyclic double bonds...</span> 1624 <span class="c">#</span> 1625 <span class="j">BONDORDER:</span> <span class="s">{</span> 1626 <span class="c"># Is current ring double bond in an alternate single/double bond configuration?</span> 1627 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 1628 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 1629 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1630 <span class="s">}</span> 1631 <span class="i">$NumOfConjugatedDoubleBonds</span> += <span class="n">1</span><span class="sc">;</span> 1632 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> 1633 <span class="s">}</span> 1634 1635 <span class="c"># Is current ring bond order correspond to an explicit aromatic bond?</span> 1636 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1.5</span><span class="s">)</span> <span class="s">{</span> 1637 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span> != <span class="n">1.5</span><span class="s">)</span> <span class="s">{</span> 1638 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1639 <span class="s">}</span> 1640 <span class="i">$NumOfExplicitAromaticBonds</span> += <span class="n">1</span><span class="sc">;</span> 1641 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> 1642 <span class="s">}</span> 1643 1644 <span class="c"># Check for potential hetero atoms involved in two single ring bonds along</span> 1645 <span class="c"># with any terminal exocyclic bonds...</span> 1646 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 1647 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 1648 <span class="c"># Part of a conjugated system...</span> 1649 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> 1650 <span class="s">}</span> 1651 1652 <span class="c"># Identify any exocylic bonds on rings atoms...</span> 1653 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="s">)</span> <span class="s">{</span> 1654 <span class="i">$ExocyclicDoubleBondsDataMapRef</span> = <span class="i">$This</span><span class="i">->_IdentifyRingAtomsInvolvedInExocyclicDoubleBonds</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsBondsMapRef</span><span class="s">)</span><span class="sc">;</span> 1655 <span class="s">}</span> 1656 1657 <span class="c"># Is current ring atom part of an allowed exocyclic terminal bond?</span> 1658 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckPotentialAromaticRingAtomForExocylicDoubleBonds</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="cm">,</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1659 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1660 <span class="s">}</span> 1661 1662 <span class="c"># Is it allowed to have any formal charge?</span> 1663 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckPotentialAromaticRingAtomForFormalCharge</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1664 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1665 <span class="s">}</span> 1666 1667 <span class="c"># It it an allowed hetero ring atom or a carbon atom?</span> 1668 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1669 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1670 <span class="s">}</span> 1671 1672 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1673 <span class="i">$ElectronPairContributionProcessedMap</span>{<span class="i">$RingAtomID</span>} = <span class="i">$RingAtomID</span><span class="sc">;</span> 1674 1675 <span class="c"># Is it able to donate a pair for electrons towards pi electron delocalization?</span> 1676 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetValenceFreeElectrons</span><span class="s">(</span><span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 1677 <span class="c"># Possibilites:</span> 1678 <span class="c"># . Hetero atom with or without formal charge and an available electron pair</span> 1679 <span class="c"># . Carbon atom with -ve formal charge and with an available electron pair</span> 1680 <span class="c">#</span> 1681 <span class="i">$NumOfRingAtomElectronPairs</span> += <span class="n">1</span><span class="sc">;</span> 1682 <span class="s">}</span> 1683 <span class="k">else</span> <span class="s">{</span> 1684 <span class="c"># Is ring atom involved in two single bonds without any electron pair allowed?</span> 1685 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AllowRingAtomInTwoSingleBondsWithoutElectronPair</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$PreviousRingBond</span><span class="cm">,</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="cm">,</span> <span class="i">$FusedRingBondsMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1686 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1687 <span class="s">}</span> 1688 <span class="s">}</span> 1689 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> 1690 <span class="s">}</span> 1691 1692 <span class="c"># Any other type of ring atom/bond is not allowed to contribute towards pi electron count</span> 1693 <span class="c"># and caused loss of aromaticity...</span> 1694 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1695 <span class="s">}</span> 1696 <span class="s">}</span> 1697 1698 <span class="c"># Check for any electron pair contributions towards pi electron delocalization due to</span> 1699 <span class="c"># -ve formal charge on ring atoms which haven't been already processed and part of</span> 1700 <span class="c"># conjugated single/double bond system...</span> 1701 <span class="c">#</span> 1702 <span class="i">$NumOfRingAtomElectronPairs</span> += <span class="i">$This</span><span class="i">->_GetElectronPairsContributionFromConjugatedRingAtoms</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$ExcludeFreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="cm">,</span> \<span class="i">%ElectronPairContributionProcessedMap</span><span class="s">)</span><span class="sc">;</span> 1703 1704 <span class="c"># Setup pi electron count available for delocalization...</span> 1705 <span class="j">COUNT:</span> <span class="s">{</span> 1706 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfExplicitAromaticBonds</span> == <span class="i">$NumOfRingBondsProcessed</span><span class="s">)</span> <span class="s">{</span> 1707 <span class="c"># Each aromatic bond contribute one electron towards pi electron delocalization...</span> 1708 <span class="i">$NumOfPiElectrons</span> = <span class="i">$NumOfExplicitAromaticBonds</span><span class="sc">;</span> 1709 <span class="k">last</span> <span class="j">COUNT</span><span class="sc">;</span> 1710 <span class="s">}</span> 1711 1712 <span class="c"># Each conjugated double bond contribute two electrons towards pi electron delocalization...</span> 1713 <span class="i">$NumOfPiElectrons</span> = <span class="n">2</span>*<span class="i">$NumOfConjugatedDoubleBonds</span> + <span class="n">2</span>*<span class="i">$NumOfRingAtomElectronPairs</span><span class="sc">;</span> 1714 <span class="s">}</span> 1715 1716 <span class="k">return</span> <span class="i">$NumOfPiElectrons</span><span class="sc">;</span> 1717 <span class="s">}</span> 1718 1719 <span class="c"># Check ring atoms for their potential participation in aromatic systems..</span> 1720 <span class="c">#</span> <a name="_CheckRingAtomsForPotentialAromaticity-"></a>1721 <span class="k">sub </span><span class="m">_CheckRingAtomsForPotentialAromaticity</span> <span class="s">{</span> 1722 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1723 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="s">)</span><span class="sc">;</span> 1724 1725 <span class="c"># Check availability of ring atoms and bonds...</span> 1726 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1727 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1728 <span class="s">}</span> 1729 1730 <span class="c"># Is there any minimum ring size limit?</span> 1731 <span class="k">if</span> <span class="s">(</span><span class="i">$AromaticityModelDataRef</span>->{<span class="w">MinimumRingSize</span>}<span class="s">)</span> <span class="s">{</span> 1732 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>} < <span class="i">$AromaticityModelDataRef</span>->{<span class="w">MinimumRingSize</span>}<span class="s">)</span> <span class="s">{</span> 1733 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1734 <span class="s">}</span> 1735 <span class="s">}</span> 1736 1737 <span class="c"># Make sure ring bond order is not greater than 2 and ring atom is not connected to more</span> 1738 <span class="c"># than 3 other atoms to eliminate any non sp2 carbon atoms and still allow for hetero atoms</span> 1739 <span class="c"># to contrbute towards electron delocalization...</span> 1740 <span class="c">#</span> 1741 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span> 1742 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 1743 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 1744 1745 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$RingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span> > <span class="n">2</span><span class="s">)</span> || <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetNumOfBonds</span><span class="s">(</span><span class="s">)</span> + <span class="i">$RingAtom</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> > <span class="n">3</span><span class="s">)</span> <span class="s">{</span> 1746 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1747 <span class="s">}</span> 1748 <span class="s">}</span> 1749 1750 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 1751 <span class="s">}</span> 1752 1753 <span class="c"># Identify any exocylic double bonds on ring atoms...</span> 1754 <span class="c">#</span> <a name="_IdentifyRingAtomsInvolvedInExocyclicDoubleBonds-"></a>1755 <span class="k">sub </span><span class="m">_IdentifyRingAtomsInvolvedInExocyclicDoubleBonds</span> <span class="s">{</span> 1756 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsBondsMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1757 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$RingAtomID</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$RingBondsMapRef</span><span class="cm">,</span> <span class="i">%RingBondsMap</span><span class="cm">,</span> <span class="i">%ExocyclicDoubleBondsDataMap</span><span class="s">)</span><span class="sc">;</span> 1758 1759 <span class="c"># Setup a ring bond map to process exocyclic bonds...</span> 1760 <span class="i">$RingBondsMapRef</span> = <span class="k">undef</span><span class="sc">;</span> 1761 <span class="i">%RingBondsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1762 1763 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$FusedRingSetsBondsMapRef</span><span class="s">)</span> <span class="s">{</span> 1764 <span class="i">$RingBondsMapRef</span> = <span class="i">$FusedRingSetsBondsMapRef</span><span class="sc">;</span> 1765 <span class="s">}</span> 1766 <span class="k">else</span> <span class="s">{</span> 1767 <span class="k">for</span> <span class="i">$BondID</span> <span class="s">(</span><span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span> 1768 <span class="i">$RingBondsMap</span>{<span class="i">$BondID</span>} = <span class="i">$BondID</span><span class="sc">;</span> 1769 <span class="s">}</span> 1770 <span class="i">$RingBondsMapRef</span> = \<span class="i">%RingBondsMap</span><span class="sc">;</span> 1771 <span class="s">}</span> 1772 1773 <span class="c"># Intialize exocyclic terminal double bond data...</span> 1774 <span class="i">%ExocyclicDoubleBondsDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1775 <span class="i">%</span>{<span class="i">$ExocyclicDoubleBondsDataMap</span>{<span class="w">RingAtomID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1776 1777 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span> 1778 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 1779 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 1780 1781 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1782 1783 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1784 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->GetBondOrder</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 1785 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 1786 <span class="s">}</span> 1787 1788 <span class="c"># Is it part of ring or ring system under consideration?</span> 1789 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$RingBondsMapRef</span>->{<span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 1790 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 1791 <span class="s">}</span> 1792 1793 <span class="c"># Is bonded atom in a ring or a non-terminal atom?</span> 1794 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$RingAtom</span><span class="s">)</span><span class="sc">;</span> 1795 <span class="k">if</span> <span class="s">(</span><span class="i">$BondedAtom</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span> || !<span class="i">$BondedAtom</span><span class="i">->IsTerminal</span><span class="s">(</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> 1796 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 1797 <span class="s">}</span> 1798 1799 <span class="c"># Track exocyclic terminal double bond information...</span> 1800 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ExocyclicDoubleBondsDataMap</span>{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span> 1801 <span class="i">@</span>{<span class="i">$ExocyclicDoubleBondsDataMap</span>{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1802 <span class="s">}</span> 1803 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ExocyclicDoubleBondsDataMap</span>{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}}<span class="cm">,</span> <span class="i">$BondedAtom</span><span class="sc">;</span> 1804 <span class="s">}</span> 1805 <span class="s">}</span> 1806 1807 <span class="k">return</span> \<span class="i">%ExocyclicDoubleBondsDataMap</span><span class="sc">;</span> 1808 <span class="s">}</span> 1809 1810 <span class="c"># Check to see whether ring atoms are allowed to participate in exocyclic terminal double</span> 1811 <span class="c"># bonds...</span> 1812 <span class="c">#</span> <a name="_CheckPotentialAromaticRingAtomForExocylicDoubleBonds-"></a>1813 <span class="k">sub </span><span class="m">_CheckPotentialAromaticRingAtomForExocylicDoubleBonds</span> <span class="s">{</span> 1814 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="cm">,</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1815 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomID</span><span class="cm">,</span> <span class="i">$ExocyclicTerminalAtom</span><span class="cm">,</span> <span class="i">$RingAtomElectronegativity</span><span class="cm">,</span> <span class="i">$TerminalAtomElectronagativity</span><span class="s">)</span><span class="sc">;</span> 1816 1817 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1818 1819 <span class="c"># Is it part of an exocyclic terminal double bond?</span> 1820 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span>->{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span> 1821 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 1822 <span class="s">}</span> 1823 1824 <span class="c"># Are exocyclic terminal double bonds allowed?</span> 1825 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowExocyclicDoubleBonds</span>}<span class="s">)</span> <span class="s">{</span> 1826 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1827 <span class="s">}</span> 1828 1829 <span class="c"># Are there multiple exocyclic double bonds?</span> 1830 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ExocyclicDoubleBondsDataMapRef</span>->{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}} > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 1831 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1832 <span class="s">}</span> 1833 <span class="s">(</span><span class="i">$ExocyclicTerminalAtom</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$ExocyclicDoubleBondsDataMapRef</span>->{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}}<span class="sc">;</span> 1834 1835 <span class="c"># Are homo nuclear exocyclic terminal double bonds allowed?</span> 1836 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowHomoNuclearExocyclicDoubleBonds</span>}<span class="s">)</span> <span class="s">{</span> 1837 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span> == <span class="i">$ExocyclicTerminalAtom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1838 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1839 <span class="s">}</span> 1840 <span class="s">}</span> 1841 1842 <span class="c"># Are ring atoms with higher electronegativity allowed in exocyclic double bonds?</span> 1843 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowElectronegativeRingAtomExocyclicDoubleBonds</span>}<span class="s">)</span> <span class="s">{</span> 1844 <span class="i">$RingAtomElectronegativity</span> = <span class="i">PeriodicTable::GetElementPaulingElectronegativity</span><span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 1845 <span class="i">$TerminalAtomElectronagativity</span> = <span class="i">PeriodicTable::GetElementPaulingElectronegativity</span><span class="s">(</span><span class="i">$ExocyclicTerminalAtom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 1846 1847 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtomElectronegativity</span> && <span class="i">$TerminalAtomElectronagativity</span><span class="s">)</span> <span class="s">{</span> 1848 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtomElectronegativity</span> > <span class="i">$TerminalAtomElectronagativity</span><span class="s">)</span> <span class="s">{</span> 1849 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1850 <span class="s">}</span> 1851 <span class="s">}</span> 1852 <span class="s">}</span> 1853 1854 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 1855 <span class="s">}</span> 1856 1857 <span class="c">#</span> 1858 <span class="c"># Check for any formal charge participation into electron delocalization...</span> 1859 <span class="c">#</span> <a name="_CheckPotentialAromaticRingAtomForFormalCharge-"></a>1860 <span class="k">sub </span><span class="m">_CheckPotentialAromaticRingAtomForFormalCharge</span> <span class="s">{</span> 1861 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1862 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span> 1863 1864 <span class="c"># Does atom has any formal charge?</span> 1865 <span class="i">$FormalCharge</span> = <span class="i">$RingAtom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1866 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FormalCharge</span><span class="s">)</span> <span class="s">{</span> 1867 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 1868 <span class="s">}</span> 1869 1870 <span class="c"># Are ring atoms with formal charge allowed to participate in electron delocalization?</span> 1871 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowRingAtomFormalCharge</span>}<span class="s">)</span> <span class="s">{</span> 1872 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1873 <span class="s">}</span> 1874 1875 <span class="c"># Are hetero ring atoms with formal charge allowed to participate in electron delocalization?</span> 1876 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1877 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowHeteroRingAtomFormalCharge</span>}<span class="s">)</span> <span class="s">{</span> 1878 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1879 <span class="s">}</span> 1880 <span class="s">}</span> 1881 1882 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 1883 <span class="s">}</span> 1884 1885 <span class="c">#</span> 1886 <span class="c"># Check ring atoms for allowed hetero atoms...</span> 1887 <span class="c">#</span> <a name="_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms-"></a>1888 <span class="k">sub </span><span class="m">_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms</span> <span class="s">{</span> 1889 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1890 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomSymbol</span><span class="s">)</span><span class="sc">;</span> 1891 1892 <span class="c"># Is it a Carbon atom?</span> 1893 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1894 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 1895 <span class="s">}</span> 1896 1897 <span class="c"># Are heteroatoms allowed?</span> 1898 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowHeteroRingAtoms</span>}<span class="s">)</span> <span class="s">{</span> 1899 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1900 <span class="s">}</span> 1901 1902 <span class="c"># Is it an allowed hetero atom?</span> 1903 <span class="i">$RingAtomSymbol</span> = <span class="i">$RingAtom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1904 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AromaticityModelDataRef</span>->{<span class="w">HeteroRingAtomsListMapRef</span>}->{<span class="i">$RingAtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> 1905 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1906 <span class="s">}</span> 1907 1908 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 1909 <span class="s">}</span> 1910 1911 <span class="c"># Check for any electron pair contributions toward pi electron delocalization due to</span> 1912 <span class="c"># -ve formal charge on ring atoms which haven't been already processed and part of</span> 1913 <span class="c"># conjugated single/double bond system...</span> 1914 <span class="c">#</span> <a name="_GetElectronPairsContributionFromConjugatedRingAtoms-"></a>1915 <span class="k">sub </span><span class="m">_GetElectronPairsContributionFromConjugatedRingAtoms</span> <span class="s">{</span> 1916 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$ExcludeFreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="cm">,</span> <span class="i">$ElectronPairContributionProcessedMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1917 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$NumOfRingAtomElectronPairs</span><span class="cm">,</span> <span class="i">$RingAtomID</span><span class="s">)</span><span class="sc">;</span> 1918 1919 <span class="c"># Is formal charge allowed on ring atoms?</span> 1920 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowRingAtomFormalCharge</span>}<span class="s">)</span> <span class="s">{</span> 1921 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1922 <span class="s">}</span> 1923 1924 <span class="i">$NumOfRingAtomElectronPairs</span> = <span class="n">0</span><span class="sc">;</span> 1925 1926 <span class="c"># Process ring atoms...</span> 1927 <span class="j">RINGBOND:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span> 1928 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 1929 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 1930 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1931 1932 <span class="c"># Is is already processed?</span> 1933 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElectronPairContributionProcessedMapRef</span>->{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span> 1934 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> 1935 <span class="s">}</span> 1936 <span class="i">$ElectronPairContributionProcessedMapRef</span>->{<span class="i">$RingAtomID</span>} = <span class="i">$RingAtomID</span><span class="sc">;</span> 1937 1938 <span class="c"># Is it allowed to have any formal charge?</span> 1939 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckPotentialAromaticRingAtomForFormalCharge</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1940 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> 1941 <span class="s">}</span> 1942 1943 <span class="c"># It it an allowed hetero ring atom or a carbon atom?</span> 1944 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1945 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> 1946 <span class="s">}</span> 1947 1948 <span class="c"># It is an atom with -ve formal charge?</span> 1949 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span> >= <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 1950 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> 1951 <span class="s">}</span> 1952 1953 <span class="c"># Is it able to donate a pair for electrons towards pi electron delocalization?</span> 1954 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetValenceFreeElectrons</span><span class="s">(</span><span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> < <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 1955 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> 1956 <span class="s">}</span> 1957 <span class="i">$NumOfRingAtomElectronPairs</span> += <span class="n">1</span><span class="sc">;</span> 1958 <span class="s">}</span> 1959 1960 <span class="k">return</span> <span class="i">$NumOfRingAtomElectronPairs</span><span class="sc">;</span> 1961 <span class="s">}</span> 1962 1963 <span class="c"># Check for ring atoms involved in two single ring bonds without any available electron</span> 1964 <span class="c"># pair which are allowed to participate in aromatic system, after all other checks</span> 1965 <span class="c"># corresponding to specified aromaticity models have already been performed...</span> 1966 <span class="c">#</span> <a name="_AllowRingAtomInTwoSingleBondsWithoutElectronPair-"></a>1967 <span class="k">sub </span><span class="m">_AllowRingAtomInTwoSingleBondsWithoutElectronPair</span> <span class="s">{</span> 1968 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$PreviousRingBond</span><span class="cm">,</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="cm">,</span> <span class="i">$FusedRingBondsMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1969 1970 <span class="j">ALLOWRINGATOM:</span> <span class="s">{</span> 1971 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span>->{<span class="w">RingAtomID</span>}{<span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 1972 <span class="c"># Ring atom in an exocylic terminal double bond without any available electron pair...</span> 1973 <span class="k">last</span> <span class="j">ALLOWRINGATOM</span><span class="sc">;</span> 1974 <span class="s">}</span> 1975 1976 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span> > <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 1977 <span class="c"># Ring atom with positive formal charge without any available electron pair...</span> 1978 <span class="k">last</span> <span class="j">ALLOWRINGATOM</span><span class="sc">;</span> 1979 <span class="s">}</span> 1980 1981 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$FusedRingBondsMapRef</span> && <span class="s">(</span><span class="k">exists</span> <span class="i">$FusedRingBondsMapRef</span>->{<span class="i">$RingBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span>} || <span class="k">exists</span> <span class="i">$FusedRingBondsMapRef</span>->{<span class="i">$PreviousRingBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1982 <span class="c"># Ring atom involved in fused ring bond, which might end up being part of a conjugated</span> 1983 <span class="c"># system in another fused ring...</span> 1984 <span class="k">last</span> <span class="j">ALLOWRINGATOM</span><span class="sc">;</span> 1985 <span class="s">}</span> 1986 1987 <span class="c"># Ring atom in any other environment is not allowed...</span> 1988 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1989 <span class="s">}</span> 1990 1991 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 1992 <span class="s">}</span> 1993 1994 <span class="c"># Do pi electrons satify huckel's rule: Number of pi electrons correspond to 4n + 2 where</span> 1995 <span class="c"># n is a positive integer...</span> 1996 <span class="c">#</span> <a name="_DoPiElectronSatifyHuckelsRule-"></a>1997 <span class="k">sub </span><span class="m">_DoPiElectronSatifyHuckelsRule</span> <span class="s">{</span> 1998 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NumOfPiElectrons</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1999 2000 <span class="i">$NumOfPiElectrons</span> = <span class="i">$NumOfPiElectrons</span> - <span class="n">2</span><span class="sc">;</span> 2001 2002 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfPiElectrons</span> > <span class="n">0</span><span class="s">)</span> ? <span class="s">(</span><span class="s">(</span><span class="i">$NumOfPiElectrons</span> % <span class="n">4</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 2003 <span class="s">}</span> 2004 2005 <span class="c"># Delete aromatic property for all atoms and bonds...</span> 2006 <span class="c">#</span> <a name="_DeleteAtomsAndBondsAromaticity-"></a>2007 <span class="k">sub </span><span class="m">_DeleteAtomsAndBondsAromaticity</span> <span class="s">{</span> 2008 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2009 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> 2010 2011 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2012 <span class="i">$Atom</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2013 <span class="s">}</span> 2014 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2015 <span class="i">$Bond</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2016 <span class="s">}</span> 2017 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 2018 <span class="s">}</span> 2019 2020 <span class="c"># Kekulize marked ring and non-ring aromatic atoms in a molecule...</span> 2021 <span class="c">#</span> <a name="KekulizeAromaticAtoms-"></a>2022 <span class="k">sub </span><span class="m">KekulizeAromaticAtoms</span> <span class="s">{</span> 2023 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2024 2025 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeAromaticAtomsInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2026 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2027 <span class="s">}</span> 2028 2029 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeAromaticAtomsNotInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2030 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2031 <span class="s">}</span> 2032 2033 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2034 <span class="s">}</span> 2035 2036 <span class="c"># Kekulize marked aromatic atoms in rings and fused ring sets...</span> 2037 <span class="c">#</span> <a name="_KekulizeAromaticAtomsInRings-"></a>2038 <span class="k">sub </span><span class="m">_KekulizeAromaticAtomsInRings</span> <span class="s">{</span> 2039 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2040 2041 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2042 <span class="c"># Nothing to do...</span> 2043 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2044 <span class="s">}</span> 2045 2046 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasAromaticAtomsInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2047 <span class="c"># Nothing to do...</span> 2048 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2049 <span class="s">}</span> 2050 2051 <span class="c"># Identify fully aromatic fused and individual rings along with any partially aromatic ring components</span> 2052 <span class="c"># using marked aromatic atoms in a molecule and kekulize them as individual stes...</span> 2053 <span class="c">#</span> 2054 <span class="k">my</span><span class="s">(</span><span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> 2055 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasFusedRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2056 <span class="s">(</span><span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetFusedAndNonFusedRingsContainingAromaticAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2057 <span class="s">}</span> 2058 <span class="k">else</span> <span class="s">{</span> 2059 <span class="s">(</span><span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetIndividualRingsContainingAromaticAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2060 <span class="s">}</span> 2061 2062 <span class="k">return</span> <span class="i">$This</span><span class="i">->_KekulizeCompleteAndPartialAromaticRings</span><span class="s">(</span><span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span><span class="sc">;</span> 2063 <span class="s">}</span> 2064 2065 <span class="c"># Identify fully aromatic fused and individual rings along with any partially aromatic ring components</span> 2066 <span class="c"># using marked aromatic atoms in a molecule...</span> 2067 <span class="c">#</span> <a name="_GetFusedAndNonFusedRingsContainingAromaticAtoms-"></a>2068 <span class="k">sub </span><span class="m">_GetFusedAndNonFusedRingsContainingAromaticAtoms</span> <span class="s">{</span> 2069 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2070 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SetAtomsCount</span><span class="cm">,</span> <span class="i">$SetAromaticAtomsCount</span><span class="cm">,</span> <span class="i">$FusedRingSetRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedRingsRef</span><span class="cm">,</span> <span class="i">$IndividualRingsRef</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingAtomsCount</span><span class="cm">,</span> <span class="i">$AromaticAtomsCount</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$NonFusedFullyAromaticRingsRef</span><span class="cm">,</span> <span class="i">$NonFusedPartiallyAromaticRingComponentsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="cm">,</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> <span class="i">@PotentialFullyAromaticRings</span><span class="cm">,</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@PotentialPartiallyAromaticRings</span><span class="cm">,</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="s">)</span><span class="sc">;</span> 2071 2072 <span class="i">@FullyAromaticFusedRingSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2073 2074 <span class="i">@PotentialFullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2075 <span class="i">@FullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2076 2077 <span class="i">@PotentialPartiallyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2078 <span class="i">@PartiallyAromaticRingComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2079 2080 <span class="s">(</span><span class="i">$FusedRingSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedRingsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetFusedAndNonFusedRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2081 2082 <span class="c"># Go over fused ring sets...</span> 2083 <span class="j">RINGSET:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 2084 <span class="i">$FusedRingSetRef</span> = <span class="i">$FusedRingSetsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 2085 2086 <span class="i">$SetAtomsCount</span> = <span class="n">0</span><span class="sc">;</span> 2087 <span class="i">$SetAromaticAtomsCount</span> = <span class="n">0</span><span class="sc">;</span> 2088 2089 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span> <span class="s">{</span> 2090 <span class="i">$SetAtomsCount</span> += <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span> 2091 2092 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 2093 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2094 <span class="i">$SetAromaticAtomsCount</span> += <span class="n">1</span><span class="sc">;</span> 2095 <span class="s">}</span> 2096 <span class="s">}</span> 2097 <span class="s">}</span> 2098 2099 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$SetAtomsCount</span> && <span class="i">$SetAromaticAtomsCount</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2100 <span class="k">next</span> <span class="j">RINGSET</span><span class="sc">;</span> 2101 <span class="s">}</span> 2102 2103 <span class="k">if</span> <span class="s">(</span><span class="i">$SetAromaticAtomsCount</span> == <span class="i">$SetAtomsCount</span><span class="s">)</span> <span class="s">{</span> 2104 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> <span class="i">$FusedRingSetRef</span><span class="sc">;</span> 2105 <span class="s">}</span> 2106 <span class="k">else</span> <span class="s">{</span> 2107 <span class="c"># Identify any individual rings in partial aromatic fused ring sets which might be</span> 2108 <span class="c"># fully or partially aromatic...</span> 2109 <span class="c">#</span> 2110 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span> <span class="s">{</span> 2111 <span class="i">$RingAtomsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span> 2112 <span class="i">$AromaticAtomsCount</span> = <span class="n">0</span><span class="sc">;</span> 2113 2114 <span class="j">RINGATOM:</span> <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 2115 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2116 <span class="k">next</span> <span class="j">RINGATOM</span><span class="sc">;</span> 2117 <span class="s">}</span> 2118 <span class="i">$AromaticAtomsCount</span> += <span class="n">1</span><span class="sc">;</span> 2119 <span class="s">}</span> 2120 2121 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$RingAtomsCount</span> && <span class="i">$AromaticAtomsCount</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2122 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span> 2123 <span class="s">}</span> 2124 2125 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtomsCount</span> == <span class="i">$AromaticAtomsCount</span><span class="s">)</span> <span class="s">{</span> 2126 <span class="k">push</span> <span class="i">@PotentialFullyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span> 2127 <span class="s">}</span> 2128 <span class="k">else</span> <span class="s">{</span> 2129 <span class="c"># Track partially aromatic rings in an different list before removing them for</span> 2130 <span class="c"># any overlap with other rings and then add to fully aromatic rings...</span> 2131 <span class="k">push</span> <span class="i">@PotentialPartiallyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span> 2132 <span class="s">}</span> 2133 <span class="s">}</span> 2134 <span class="s">}</span> 2135 <span class="s">}</span> 2136 2137 <span class="k">if</span> <span class="s">(</span><span class="i">@PotentialFullyAromaticRings</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 2138 <span class="c"># Get any fully aromatic fused ring subsets from potentially fully aromatic rings...</span> 2139 <span class="k">my</span><span class="s">(</span><span class="i">$FullyAromaticFusedRingSetsRefs</span><span class="cm">,</span> <span class="i">$FullyAromaticNonFusedRingsRef</span><span class="s">)</span><span class="sc">;</span> 2140 <span class="s">(</span><span class="i">$FullyAromaticFusedRingSetsRefs</span><span class="cm">,</span> <span class="i">$FullyAromaticNonFusedRingsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetFullyAromaticFusedAndNonFusedRingsInFusedSubset</span><span class="s">(</span>\<span class="i">@PotentialFullyAromaticRings</span><span class="s">)</span><span class="sc">;</span> 2141 2142 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FullyAromaticFusedRingSetsRefs</span>}<span class="s">)</span> <span class="s">{</span> 2143 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FullyAromaticFusedRingSetsRefs</span>}<span class="sc">;</span> 2144 <span class="s">}</span> 2145 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FullyAromaticNonFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span> 2146 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FullyAromaticNonFusedRingsRef</span>}<span class="sc">;</span> 2147 <span class="s">}</span> 2148 <span class="s">}</span> 2149 <span class="k">else</span> <span class="s">{</span> 2150 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@PotentialFullyAromaticRings</span><span class="sc">;</span> 2151 <span class="s">}</span> 2152 2153 <span class="c"># Go over partial aromatic ring components...</span> 2154 <span class="k">if</span> <span class="s">(</span><span class="i">@PotentialPartiallyAromaticRings</span><span class="s">)</span> <span class="s">{</span> 2155 <span class="i">$PartiallyAromaticRingComponentsRef</span> = <span class="i">$This</span><span class="i">->_GetPartiallyAromaticRingComponents</span><span class="s">(</span>\<span class="i">@PotentialPartiallyAromaticRings</span><span class="cm">,</span> \<span class="i">@PotentialFullyAromaticRings</span><span class="s">)</span><span class="sc">;</span> 2156 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="s">)</span> <span class="s">{</span> 2157 <span class="k">push</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span> 2158 <span class="s">}</span> 2159 <span class="s">}</span> 2160 2161 <span class="c"># Go over non-fused rings...</span> 2162 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span> 2163 <span class="s">(</span><span class="i">$NonFusedFullyAromaticRingsRef</span><span class="cm">,</span> <span class="i">$NonFusedPartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetRingsContainingAromaticAtoms</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedRingsRef</span>}<span class="s">)</span><span class="sc">;</span> 2164 2165 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedFullyAromaticRingsRef</span>}<span class="s">)</span> <span class="s">{</span> 2166 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$NonFusedFullyAromaticRingsRef</span>}<span class="sc">;</span> 2167 <span class="s">}</span> 2168 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedPartiallyAromaticRingComponentsRef</span>}<span class="s">)</span> <span class="s">{</span> 2169 <span class="k">push</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$NonFusedPartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span> 2170 <span class="s">}</span> 2171 <span class="s">}</span> 2172 2173 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> \<span class="i">@FullyAromaticRings</span><span class="cm">,</span> \<span class="i">@PartiallyAromaticRingComponents</span><span class="s">)</span><span class="sc">;</span> 2174 <span class="s">}</span> 2175 2176 <span class="c"># Identify fully aromatic fused sets and non-fused rings in potentially fully aromatic</span> 2177 <span class="c"># rings in fused ring sets...</span> 2178 <span class="c">#</span> 2179 <span class="c"># Fully aromatic rings in fused ring sets might contain fully aromatic fused subsets. These</span> 2180 <span class="c"># fused subets need to be tracked and treated as fused sets.</span> 2181 <span class="c">#</span> 2182 <span class="c"># Note:</span> 2183 <span class="c"># . Fused ring sets share at least one common bond, which could be used to identify</span> 2184 <span class="c"># any multiple fully aromatic fused rings sets; absence of a shared ring bond implies</span> 2185 <span class="c"># there are no fused ring sets.</span> 2186 <span class="c">#</span> 2187 <span class="c">#</span> <a name="_GetFullyAromaticFusedAndNonFusedRingsInFusedSubset-"></a>2188 <span class="k">sub </span><span class="m">_GetFullyAromaticFusedAndNonFusedRingsInFusedSubset</span> <span class="s">{</span> 2189 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PotentialFullyAromaticFusedRingsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2190 <span class="k">my</span><span class="s">(</span><span class="i">$RingIndex</span><span class="cm">,</span> <span class="i">$RingIndex1</span><span class="cm">,</span> <span class="i">$RingIndex2</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingAtomID</span><span class="cm">,</span> <span class="i">$RingIsFuesd</span><span class="cm">,</span> <span class="i">$RingIndicesGraph</span><span class="cm">,</span> <span class="i">$FusedRingSetIndicesRef</span><span class="cm">,</span> <span class="i">@RingIndices</span><span class="cm">,</span> <span class="i">@FusedRingPairIndices</span><span class="cm">,</span> <span class="i">@FusedRingSetIndicesRefs</span><span class="cm">,</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">%RingIndexToAtomIDMap</span><span class="cm">,</span> <span class="i">%FullyAromaticFusedRingIndexMap</span><span class="s">)</span><span class="sc">;</span> 2191 2192 <span class="i">@FullyAromaticFusedRingSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2193 <span class="i">@FullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2194 2195 <span class="c"># Setup a ring index map for ring atoms...</span> 2196 <span class="c">#</span> 2197 <span class="i">%RingIndexToAtomIDMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2198 <span class="k">for</span> <span class="i">$RingIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span> 2199 <span class="i">%</span>{<span class="i">$RingIndexToAtomIDMap</span>{<span class="i">$RingIndex</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2200 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>->[<span class="i">$RingIndex</span>]}<span class="s">)</span> <span class="s">{</span> 2201 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2202 <span class="i">$RingIndexToAtomIDMap</span>{<span class="i">$RingIndex</span>}{<span class="i">$RingAtomID</span>} = <span class="i">$RingAtomID</span><span class="sc">;</span> 2203 <span class="s">}</span> 2204 <span class="s">}</span> 2205 2206 <span class="c"># Identify fused ring pairs...</span> 2207 <span class="c">#</span> 2208 <span class="i">@RingIndices</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2209 <span class="i">@FusedRingPairIndices</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2210 2211 <span class="k">for</span> <span class="i">$RingIndex1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span> 2212 <span class="k">push</span> <span class="i">@RingIndices</span><span class="cm">,</span> <span class="i">$RingIndex1</span><span class="sc">;</span> 2213 <span class="k">for</span> <span class="i">$RingIndex2</span> <span class="s">(</span><span class="s">(</span><span class="i">$RingIndex1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="i">$#</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span> 2214 <span class="i">$RingIsFuesd</span> = <span class="n">0</span><span class="sc">;</span> 2215 <span class="j">RINGATOM:</span> <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>->[<span class="i">$RingIndex2</span>]}<span class="s">)</span> <span class="s">{</span> 2216 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2217 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$RingIndexToAtomIDMap</span>{<span class="i">$RingIndex1</span>}{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span> 2218 <span class="i">$RingIsFuesd</span> = <span class="n">1</span><span class="sc">;</span> 2219 <span class="k">last</span> <span class="j">RINGATOM</span><span class="sc">;</span> 2220 <span class="s">}</span> 2221 <span class="s">}</span> 2222 <span class="k">if</span> <span class="s">(</span><span class="i">$RingIsFuesd</span><span class="s">)</span> <span class="s">{</span> 2223 <span class="k">push</span> <span class="i">@FusedRingPairIndices</span><span class="cm">,</span> <span class="s">(</span><span class="i">$RingIndex1</span><span class="cm">,</span> <span class="i">$RingIndex2</span><span class="s">)</span><span class="sc">;</span> 2224 <span class="s">}</span> 2225 <span class="s">}</span> 2226 <span class="s">}</span> 2227 2228 <span class="k">if</span> <span class="s">(</span>!<span class="i">@FusedRingPairIndices</span><span class="s">)</span> <span class="s">{</span> 2229 <span class="c"># No fused ring subset out there...</span> 2230 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>}<span class="sc">;</span> 2231 2232 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> \<span class="i">@FullyAromaticRings</span><span class="s">)</span><span class="sc">;</span> 2233 <span class="s">}</span> 2234 2235 <span class="c"># Identify fused ring sets...</span> 2236 <span class="c">#</span> 2237 <span class="i">$RingIndicesGraph</span> = <span class="i">new</span> <span class="i">Graph</span><span class="s">(</span><span class="i">@RingIndices</span><span class="s">)</span><span class="sc">;</span> 2238 <span class="i">$RingIndicesGraph</span><span class="i">->AddEdges</span><span class="s">(</span><span class="i">@FusedRingPairIndices</span><span class="s">)</span><span class="sc">;</span> 2239 <span class="i">@FusedRingSetIndicesRefs</span> = <span class="i">$RingIndicesGraph</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2240 2241 <span class="c"># Collect fully aromatic fused ring sets...</span> 2242 <span class="c">#</span> 2243 <span class="i">%FullyAromaticFusedRingIndexMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2244 <span class="k">for</span> <span class="i">$FusedRingSetIndicesRef</span> <span class="s">(</span><span class="i">@FusedRingSetIndicesRefs</span><span class="s">)</span> <span class="s">{</span> 2245 <span class="k">my</span><span class="s">(</span><span class="i">@FullyAromaticFusedRingSet</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2246 <span class="k">for</span> <span class="i">$RingIndex</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetIndicesRef</span>}<span class="s">)</span> <span class="s">{</span> 2247 <span class="i">$FullyAromaticFusedRingIndexMap</span>{<span class="i">$RingIndex</span>} = <span class="i">$RingIndex</span><span class="sc">;</span> 2248 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSet</span><span class="cm">,</span> <span class="i">$PotentialFullyAromaticFusedRingsRef</span>->[<span class="i">$RingIndex</span>]<span class="sc">;</span> 2249 <span class="s">}</span> 2250 <span class="k">if</span> <span class="s">(</span><span class="i">@FullyAromaticFusedRingSet</span><span class="s">)</span> <span class="s">{</span> 2251 <span class="c"># Sort rings by size with in the fused ring set...</span> 2252 <span class="i">@FullyAromaticFusedRingSet</span> = <span class="k">sort</span> <span class="s">{</span> <span class="k">scalar</span> <span class="i">@$a</span> <=> <span class="k">scalar</span> <span class="i">@$b</span> <span class="s">}</span> <span class="i">@FullyAromaticFusedRingSet</span><span class="sc">;</span> 2253 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> \<span class="i">@FullyAromaticFusedRingSet</span><span class="sc">;</span> 2254 <span class="s">}</span> 2255 <span class="s">}</span> 2256 2257 <span class="c"># Collect fully aromatic non-fused rings...</span> 2258 <span class="c">#</span> 2259 <span class="j">RINGINDEX:</span> <span class="k">for</span> <span class="i">$RingIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span> 2260 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$FullyAromaticFusedRingIndexMap</span>{<span class="i">$RingIndex</span>}<span class="s">)</span> <span class="s">{</span> 2261 <span class="k">next</span> <span class="j">RINGINDEX</span><span class="sc">;</span> 2262 <span class="s">}</span> 2263 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">$PotentialFullyAromaticFusedRingsRef</span>->[<span class="i">$RingIndex</span>]<span class="sc">;</span> 2264 <span class="s">}</span> 2265 2266 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> \<span class="i">@FullyAromaticRings</span><span class="s">)</span><span class="sc">;</span> 2267 <span class="s">}</span> 2268 2269 <span class="c"># Identify individual non-fused rings containing aromatic atoms...</span> 2270 <span class="c">#</span> <a name="_GetIndividualRingsContainingAromaticAtoms-"></a>2271 <span class="k">sub </span><span class="m">_GetIndividualRingsContainingAromaticAtoms</span> <span class="s">{</span> 2272 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2273 2274 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRingsContainingAromaticAtoms</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 2275 <span class="s">}</span> 2276 2277 <span class="c"># Identify individual non-fused rings containing aromatic atoms...</span> 2278 <span class="c">#</span> <a name="_GetRingsContainingAromaticAtoms-"></a>2279 <span class="k">sub </span><span class="m">_GetRingsContainingAromaticAtoms</span> <span class="s">{</span> 2280 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2281 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingAtomsCount</span><span class="cm">,</span> <span class="i">$AromaticAtomsCount</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="cm">,</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@PartiallyAromaticRings</span><span class="s">)</span><span class="sc">;</span> 2282 2283 <span class="i">@FullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2284 <span class="i">@PartiallyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2285 2286 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span> 2287 <span class="i">$RingAtomsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span> 2288 <span class="i">$AromaticAtomsCount</span> = <span class="n">0</span><span class="sc">;</span> 2289 2290 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 2291 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2292 <span class="i">$AromaticAtomsCount</span> += <span class="n">1</span><span class="sc">;</span> 2293 <span class="s">}</span> 2294 <span class="s">}</span> 2295 2296 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$AromaticAtomsCount</span> && <span class="i">$RingAtomsCount</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2297 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span> 2298 <span class="s">}</span> 2299 2300 <span class="k">if</span> <span class="s">(</span><span class="i">$AromaticAtomsCount</span> == <span class="i">$RingAtomsCount</span><span class="s">)</span> <span class="s">{</span> 2301 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span> 2302 <span class="s">}</span> 2303 <span class="k">else</span> <span class="s">{</span> 2304 <span class="k">push</span> <span class="i">@PartiallyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span> 2305 <span class="s">}</span> 2306 <span class="s">}</span> 2307 2308 <span class="i">$PartiallyAromaticRingComponentsRef</span> = <span class="i">$This</span><span class="i">->_GetPartiallyAromaticRingComponents</span><span class="s">(</span>\<span class="i">@PartiallyAromaticRings</span><span class="s">)</span><span class="sc">;</span> 2309 2310 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span><span class="sc">;</span> 2311 <span class="s">}</span> 2312 2313 <span class="c"># Get connected aromatic components with in partially aromatic rings...</span> 2314 <span class="c">#</span> <a name="_GetPartiallyAromaticRingComponents-"></a>2315 <span class="k">sub </span><span class="m">_GetPartiallyAromaticRingComponents</span> <span class="s">{</span> 2316 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PotentialPartiallyAromaticRingsRef</span><span class="cm">,</span> <span class="i">$FullyAromaticRingsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2317 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingAtomID</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="cm">,</span> <span class="i">%FullyAromaticRingAtomsMap</span><span class="s">)</span><span class="sc">;</span> 2318 2319 <span class="i">@PartiallyAromaticRingComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2320 2321 <span class="c"># Setup a map for atoms involve in fully aromatic rings to remove remove partial rings</span> 2322 <span class="c"># containing only those atoms which are already part of some other fully aromatic ring</span> 2323 <span class="c"># in fused ring scenarios or some other partially aromatic ring...</span> 2324 <span class="c">#</span> 2325 <span class="i">%FullyAromaticRingAtomsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2326 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$FullyAromaticRingsRef</span><span class="s">)</span> <span class="s">{</span> 2327 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FullyAromaticRingsRef</span>}<span class="s">)</span> <span class="s">{</span> 2328 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 2329 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2330 <span class="i">$FullyAromaticRingAtomsMap</span>{<span class="i">$RingAtomID</span>} = <span class="i">$RingAtomID</span><span class="sc">;</span> 2331 <span class="s">}</span> 2332 <span class="s">}</span> 2333 <span class="s">}</span> 2334 2335 <span class="c"># . Identify any connected components with in each partially aromatic ring.</span> 2336 <span class="c"># . Use ring atom indices to figure out connnected components in rings: All ring atoms</span> 2337 <span class="c"># in a connected component have sequential indices and a difference by more than</span> 2338 <span class="c"># 1 indicates a new component in the list.</span> 2339 <span class="c">#</span> 2340 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PotentialPartiallyAromaticRingsRef</span>}<span class="s">)</span> <span class="s">{</span> 2341 <span class="k">my</span><span class="s">(</span><span class="i">@AromaticRingAtoms</span><span class="cm">,</span> <span class="i">@AromaticRingAtomsIndices</span><span class="s">)</span><span class="sc">;</span> 2342 2343 <span class="i">@AromaticRingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2344 <span class="i">@AromaticRingAtomsIndices</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2345 2346 <span class="j">RINGATOM:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 2347 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 2348 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2349 2350 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$FullyAromaticRingsRef</span> && <span class="k">exists</span> <span class="i">$FullyAromaticRingAtomsMap</span>{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span> 2351 <span class="k">next</span> <span class="j">RINGATOM</span><span class="sc">;</span> 2352 <span class="s">}</span> 2353 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2354 <span class="k">next</span> <span class="j">RINGATOM</span><span class="sc">;</span> 2355 <span class="s">}</span> 2356 <span class="k">push</span> <span class="i">@AromaticRingAtoms</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="sc">;</span> 2357 <span class="k">push</span> <span class="i">@AromaticRingAtomsIndices</span><span class="cm">,</span> <span class="i">$Index</span><span class="sc">;</span> 2358 2359 <span class="s">}</span> 2360 <span class="k">if</span> <span class="s">(</span>!<span class="i">@AromaticRingAtoms</span><span class="s">)</span> <span class="s">{</span> 2361 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span> 2362 <span class="s">}</span> 2363 2364 <span class="c"># Start off with a new connected component...</span> 2365 <span class="c">#</span> 2366 <span class="k">my</span><span class="s">(</span><span class="i">$ComponentNum</span><span class="s">)</span><span class="sc">;</span> 2367 <span class="i">$ComponentNum</span> = <span class="k">scalar</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="sc">;</span> 2368 <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponents</span>[<span class="i">$ComponentNum</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2369 2370 <span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> 2371 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponents</span>[<span class="i">$ComponentNum</span>]}<span class="cm">,</span> <span class="i">$AromaticRingAtoms</span>[<span class="i">$Index</span>]<span class="sc">;</span> 2372 2373 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#AromaticRingAtoms</span><span class="s">)</span> <span class="s">{</span> 2374 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$AromaticRingAtomsIndices</span>[<span class="i">$Index</span>] - <span class="i">$AromaticRingAtomsIndices</span>[<span class="i">$Index</span> -<span class="n">1</span>]<span class="s">)</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 2375 <span class="c"># New connected component...</span> 2376 <span class="i">$ComponentNum</span> += <span class="n">1</span><span class="sc">;</span> 2377 <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponents</span>[<span class="i">$ComponentNum</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2378 <span class="s">}</span> 2379 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponents</span>[<span class="i">$ComponentNum</span>]}<span class="cm">,</span> <span class="i">$AromaticRingAtoms</span>[<span class="i">$Index</span>]<span class="sc">;</span> 2380 <span class="s">}</span> 2381 <span class="s">}</span> 2382 2383 <span class="k">return</span> <span class="s">(</span>\<span class="i">@PartiallyAromaticRingComponents</span><span class="s">)</span><span class="sc">;</span> 2384 <span class="s">}</span> 2385 2386 <span class="c"># Kekulize fully aromatic fused and individual rings along with any partially aromatic ring</span> 2387 <span class="c"># components...</span> 2388 <span class="c">#</span> <a name="_KekulizeCompleteAndPartialAromaticRings-"></a>2389 <span class="k">sub </span><span class="m">_KekulizeCompleteAndPartialAromaticRings</span> <span class="s">{</span> 2390 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2391 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$ConnectedPathsAtomsSetsRef</span><span class="cm">,</span> <span class="i">$ConnectedPathsBondsSetsRef</span><span class="cm">,</span> <span class="i">$ConnectdPathsSetsTypesRef</span><span class="cm">,</span> <span class="i">$PathSetIndex</span><span class="cm">,</span> <span class="i">$PathAtom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$DeleteAtomsAromaticity</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="cm">,</span> <span class="i">%PathAtomsProcessingStatusMap</span><span class="cm">,</span> <span class="i">%PathBondsProcessingStatusMap</span><span class="s">)</span><span class="sc">;</span> 2392 2393 <span class="s">(</span><span class="i">$ConnectedPathsAtomsSetsRef</span><span class="cm">,</span> <span class="i">$ConnectedPathsBondsSetsRef</span><span class="cm">,</span> <span class="i">$ConnectdPathsSetsTypesRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupCompleteAndPartialAromaticRingsForKekulizaiton</span><span class="s">(</span><span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span><span class="sc">;</span> 2394 2395 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$ConnectedPathsAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 2396 <span class="c"># Nothing to do...</span> 2397 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2398 <span class="s">}</span> 2399 2400 <span class="c"># Delete any aromaticity property set for non-ring bonds connected any two ring</span> 2401 <span class="c"># aromatic atoms...</span> 2402 <span class="c">#</span> 2403 <span class="i">$This</span><span class="i">->_ProcessNonRingAromaticBondsBetweenAromaticRingAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2404 2405 <span class="i">%PathAtomsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2406 <span class="i">%PathBondsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2407 2408 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> 2409 2410 <span class="j">PATHSET:</span> <span class="k">for</span> <span class="i">$PathSetIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ConnectedPathsAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 2411 <span class="k">my</span><span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathSetProcessingStatusRef</span><span class="s">)</span><span class="sc">;</span> 2412 2413 <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathSetProcessingStatusRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> 2414 2415 <span class="k">if</span> <span class="s">(</span><span class="i">$ConnectdPathsSetsTypesRef</span>->[<span class="i">$PathSetIndex</span>] =~ <span class="q">/^FusedAromatic$/i</span><span class="s">)</span> <span class="s">{</span> 2416 <span class="c"># Fused set of connected paths...</span> 2417 <span class="c">#</span> 2418 <span class="k">my</span><span class="s">(</span><span class="i">$FusedConnectedPathAtomsSetRef</span><span class="cm">,</span> <span class="i">$FusedConnectedPathBondsSetRef</span><span class="s">)</span><span class="sc">;</span> 2419 2420 <span class="i">$FusedConnectedPathAtomsSetRef</span> = <span class="i">$ConnectedPathsAtomsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="sc">;</span> 2421 <span class="i">$FusedConnectedPathBondsSetRef</span> = <span class="i">$ConnectedPathsBondsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="sc">;</span> 2422 2423 <span class="c"># Prepare for kekulization...</span> 2424 <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathSetProcessingStatusRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupConnectedPathSetsForKekulization</span><span class="s">(</span><span class="i">$FusedConnectedPathAtomsSetRef</span><span class="cm">,</span> <span class="i">$FusedConnectedPathBondsSetRef</span><span class="s">)</span><span class="sc">;</span> 2425 2426 <span class="c"># Perform kekulization starting with the first path set...</span> 2427 <span class="i">$PathSetProcessingStatusRef</span>->[<span class="n">0</span>] = <span class="q">'Processed'</span><span class="sc">;</span> 2428 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$FusedConnectedPathAtomsSetRef</span>->[<span class="n">0</span>]<span class="cm">,</span> <span class="i">$FusedConnectedPathBondsSetRef</span>->[<span class="n">0</span>]<span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$FusedConnectedPathAtomsSetRef</span><span class="cm">,</span> <span class="i">$FusedConnectedPathBondsSetRef</span><span class="cm">,</span> <span class="i">$PathSetProcessingStatusRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2429 <span class="c"># Kekulization failed for the current fused paths set...</span> 2430 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> 2431 <span class="s">}</span> 2432 <span class="s">}</span> 2433 <span class="k">else</span> <span class="s">{</span> 2434 <span class="c"># An individual connected path...</span> 2435 <span class="c">#</span> 2436 <span class="k">my</span><span class="s">(</span><span class="i">@ConnectedPathAtomsSet</span><span class="cm">,</span> <span class="i">@ConnectedPathBondsSet</span><span class="s">)</span><span class="sc">;</span> 2437 2438 <span class="i">@ConnectedPathAtomsSet</span> = <span class="s">(</span><span class="i">$ConnectedPathsAtomsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="s">)</span><span class="sc">;</span> 2439 <span class="i">@ConnectedPathBondsSet</span> = <span class="s">(</span><span class="i">$ConnectedPathsBondsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="s">)</span><span class="sc">;</span> 2440 2441 <span class="c"># Prepare for kekulization...</span> 2442 <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupConnectedPathSetsForKekulization</span><span class="s">(</span>\<span class="i">@ConnectedPathAtomsSet</span><span class="cm">,</span> \<span class="i">@ConnectedPathBondsSet</span><span class="s">)</span><span class="sc">;</span> 2443 2444 <span class="c"># Perform kekulization...</span> 2445 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$ConnectedPathsAtomsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="cm">,</span> <span class="i">$ConnectedPathsBondsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2446 <span class="c"># Kekulization failed for the current path...</span> 2447 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> 2448 <span class="s">}</span> 2449 <span class="s">}</span> 2450 2451 <span class="c"># Did kekulization succeed for the current path or path set?</span> 2452 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span> 2453 <span class="k">last</span> <span class="j">PATHSET</span><span class="sc">;</span> 2454 <span class="s">}</span> 2455 2456 <span class="c"># Track atom and bond processing state for final assignment after kekulization</span> 2457 <span class="c"># is successfully completed for all the paths and fused path sets...</span> 2458 <span class="c">#</span> 2459 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>}<span class="s">)</span> <span class="s">{</span> 2460 <span class="i">$PathAtomsProcessingStatusMap</span>{<span class="i">$AtomID</span>} = <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$AtomID</span>}<span class="sc">;</span> 2461 <span class="s">}</span> 2462 2463 <span class="k">for</span> <span class="i">$BondID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>}<span class="s">)</span> <span class="s">{</span> 2464 <span class="i">$PathBondsProcessingStatusMap</span>{<span class="i">$BondID</span>} = <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$BondID</span>}<span class="sc">;</span> 2465 <span class="s">}</span> 2466 <span class="s">}</span> 2467 2468 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span> 2469 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_KekulizeCompleteAndPartialAromaticRings: Couldn't perform kekulization for marked ring aromatic atoms..."</span><span class="sc">;</span> 2470 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2471 <span class="s">}</span> 2472 2473 <span class="c"># Use PathAtomsProcessingStatusMap and PathBondsProcessingStatusMap to set</span> 2474 <span class="c"># single/double bonds in the molecule after successful kekulization along with modification of</span> 2475 <span class="c"># any aromatic flags...</span> 2476 2477 <span class="k">for</span> <span class="i">$PathSetIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ConnectedPathsAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 2478 <span class="i">$DeleteAtomsAromaticity</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$DeleteBondsAromaticity</span> = <span class="n">0</span><span class="sc">;</span> 2479 2480 <span class="k">if</span> <span class="s">(</span><span class="i">$ConnectdPathsSetsTypesRef</span>->[<span class="i">$PathSetIndex</span>] =~ <span class="q">/^FusedAromatic$/i</span><span class="s">)</span> <span class="s">{</span> 2481 <span class="k">for</span> <span class="i">$PathBondsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConnectedPathsBondsSetsRef</span>->[<span class="i">$PathSetIndex</span>]}<span class="s">)</span> <span class="s">{</span> 2482 <span class="i">$This</span><span class="i">->_ProcessBondOrdersAssignedDuringSuccessfulKekulization</span><span class="s">(</span><span class="i">$PathBondsRef</span><span class="cm">,</span> \<span class="i">%PathBondsProcessingStatusMap</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="s">)</span><span class="sc">;</span> 2483 <span class="s">}</span> 2484 <span class="s">}</span> 2485 <span class="k">else</span> <span class="s">{</span> 2486 <span class="k">if</span> <span class="s">(</span><span class="i">$ConnectdPathsSetsTypesRef</span>->[<span class="i">$PathSetIndex</span>] =~ <span class="q">/^PartiallyAromatic$/i</span> <span class="s">)</span> <span class="s">{</span> 2487 <span class="i">$DeleteBondsAromaticity</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$DeleteAtomsAromaticity</span> = <span class="n">1</span><span class="sc">;</span> 2488 <span class="s">}</span> 2489 2490 <span class="k">if</span> <span class="s">(</span><span class="i">$DeleteAtomsAromaticity</span><span class="s">)</span> <span class="s">{</span> 2491 <span class="k">for</span> <span class="i">$PathAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConnectedPathsAtomsSetsRef</span>->[<span class="i">$PathSetIndex</span>]}<span class="s">)</span> <span class="s">{</span> 2492 <span class="i">$PathAtom</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2493 <span class="s">}</span> 2494 <span class="s">}</span> 2495 2496 <span class="i">$This</span><span class="i">->_ProcessBondOrdersAssignedDuringSuccessfulKekulization</span><span class="s">(</span><span class="i">$ConnectedPathsBondsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="cm">,</span> \<span class="i">%PathBondsProcessingStatusMap</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="s">)</span><span class="sc">;</span> 2497 <span class="s">}</span> 2498 <span class="s">}</span> 2499 2500 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2501 <span class="s">}</span> 2502 2503 <span class="c"># Look for any aromatic bonds outside the rings between two ring aromatic atoms</span> 2504 <span class="c"># and turn them into single non-aromatic bonds before kekulization; otherwise, kekulization</span> 2505 <span class="c"># fails.</span> 2506 <span class="c">#</span> 2507 <span class="c"># Note:</span> 2508 <span class="c"># . Two atoms marked as aromatic atoms in two different rings, such as two rings</span> 2509 <span class="c"># connected through a single bond, are still aromatic, but the bond is outside</span> 2510 <span class="c"># the ring and shouldn't be marked as aromatic. It should be set to single bond without</span> 2511 <span class="c"># any aromatic property for kekulization to succeed.</span> 2512 <span class="c">#</span> 2513 <span class="c"># For example, the molecule generated by SMILES parser for biphenyl SMILES string</span> 2514 <span class="c"># "c1ccccc1c2ccccc2" sets up an aromatic bond between the two phenyl rings, as</span> 2515 <span class="c"># it's connected to two aromatic atoms.</span> 2516 <span class="c">#</span> <a name="_ProcessNonRingAromaticBondsBetweenAromaticRingAtoms-"></a>2517 <span class="k">sub </span><span class="m">_ProcessNonRingAromaticBondsBetweenAromaticRingAtoms</span> <span class="s">{</span> 2518 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2519 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 2520 2521 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2522 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Bond</span><span class="i">->IsNotInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2523 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 2524 <span class="s">}</span> 2525 2526 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2527 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom1</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2528 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 2529 <span class="s">}</span> 2530 2531 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> 2532 <span class="i">$Bond</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2533 <span class="s">}</span> 2534 2535 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 2536 <span class="s">}</span> 2537 2538 <span class="c"># Setup completelty aromatic fused and individual rings along with partially aromatic ring</span> 2539 <span class="c"># components as sets of connected paths...</span> 2540 <span class="c">#</span> <a name="_SetupCompleteAndPartialAromaticRingsForKekulizaiton-"></a>2541 <span class="k">sub </span><span class="m">_SetupCompleteAndPartialAromaticRingsForKekulizaiton</span> <span class="s">{</span> 2542 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2543 <span class="k">my</span><span class="s">(</span><span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> <span class="i">@ConnectdPathsSetsTypes</span><span class="s">)</span><span class="sc">;</span> 2544 2545 <span class="i">@ConnectedPathsSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2546 <span class="i">@ConnectedPathsBondsSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2547 <span class="i">@ConnectdPathsSetsTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2548 2549 <span class="c"># Setup atoms and bonds for connected paths in fused aromatic ring sets...</span> 2550 <span class="c">#</span> 2551 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticFusedRingSetsRef</span> && <span class="i">@</span>{<span class="i">$AromaticFusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 2552 <span class="k">my</span><span class="s">(</span><span class="i">$RingSetIndex</span><span class="s">)</span><span class="sc">;</span> 2553 2554 <span class="k">push</span> <span class="i">@ConnectdPathsSetsTypes</span><span class="cm">,</span> <span class="s">(</span><span class="q">'FusedAromatic'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$AromaticFusedRingSetsRef</span>}<span class="sc">;</span> 2555 <span class="k">push</span> <span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AromaticFusedRingSetsRef</span>}<span class="sc">;</span> 2556 2557 <span class="k">for</span> <span class="i">$RingSetIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$AromaticFusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 2558 <span class="k">my</span><span class="s">(</span><span class="i">@AromaticFusedRingBondsSet</span><span class="s">)</span><span class="sc">;</span> 2559 2560 <span class="c"># Get ring bonds for each ring set...</span> 2561 <span class="c">#</span> 2562 <span class="i">@AromaticFusedRingBondsSet</span> = <span class="i">$This</span><span class="i">->GetRingBondsFromRings</span><span class="s">(</span><span class="i">@</span>{<span class="i">$AromaticFusedRingSetsRef</span>->[<span class="i">$RingSetIndex</span>]}<span class="s">)</span><span class="sc">;</span> 2563 <span class="k">push</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> \<span class="i">@AromaticFusedRingBondsSet</span><span class="sc">;</span> 2564 <span class="s">}</span> 2565 <span class="s">}</span> 2566 2567 <span class="c"># Set up atoms and bonds for connected paths in aromatic rings...</span> 2568 <span class="c">#</span> 2569 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticRingsRef</span> && <span class="i">@</span>{<span class="i">$AromaticRingsRef</span>}<span class="s">)</span> <span class="s">{</span> 2570 <span class="k">my</span><span class="s">(</span><span class="i">@AromaticRingBondsSets</span><span class="s">)</span><span class="sc">;</span> 2571 2572 <span class="k">push</span> <span class="i">@ConnectdPathsSetsTypes</span><span class="cm">,</span> <span class="s">(</span><span class="q">'Aromatic'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$AromaticRingsRef</span>}<span class="sc">;</span> 2573 <span class="k">push</span> <span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AromaticRingsRef</span>}<span class="sc">;</span> 2574 2575 <span class="c"># Get ring bonds for each ring...</span> 2576 <span class="i">@AromaticRingBondsSets</span> = <span class="i">$This</span><span class="i">->GetRingBondsFromRings</span><span class="s">(</span><span class="i">@</span>{<span class="i">$AromaticRingsRef</span>}<span class="s">)</span><span class="sc">;</span> 2577 <span class="k">push</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> <span class="i">@AromaticRingBondsSets</span><span class="sc">;</span> 2578 <span class="s">}</span> 2579 2580 <span class="c"># Set up atoms and bonds for connected paths in partially aromatic rings...</span> 2581 <span class="c">#</span> 2582 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$PartiallyAromaticRingComponentsRef</span> && <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="s">)</span> <span class="s">{</span> 2583 <span class="k">my</span><span class="s">(</span><span class="i">$ComponentIndex</span><span class="s">)</span><span class="sc">;</span> 2584 2585 <span class="k">push</span> <span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span> 2586 <span class="k">push</span> <span class="i">@ConnectdPathsSetsTypes</span><span class="cm">,</span> <span class="s">(</span><span class="q">'PartiallyAromatic'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span> 2587 2588 <span class="k">for</span> <span class="i">$ComponentIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="s">)</span> <span class="s">{</span> 2589 <span class="k">my</span><span class="s">(</span><span class="i">@ComponentBonds</span><span class="s">)</span><span class="sc">;</span> 2590 <span class="i">@ComponentBonds</span> = <span class="i">$This</span><span class="i">->_GetPathBonds</span><span class="s">(</span><span class="i">$This</span><span class="i">->_GetAtomsIDsFromAtoms</span><span class="s">(</span><span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>->[<span class="i">$ComponentIndex</span>]}<span class="s">)</span><span class="s">)</span><span class="sc">;</span> 2591 <span class="k">push</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> \<span class="i">@ComponentBonds</span><span class="sc">;</span> 2592 <span class="s">}</span> 2593 <span class="s">}</span> 2594 2595 <span class="k">return</span> <span class="s">(</span>\<span class="i">@ConnectedPathsSets</span><span class="cm">,</span> \<span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> \<span class="i">@ConnectdPathsSetsTypes</span><span class="s">)</span><span class="sc">;</span> 2596 <span class="s">}</span> 2597 2598 <span class="c"># Process non-ring connected atoms which are marked aromatic and set connected</span> 2599 <span class="c"># bonds as alternate single/double bonds...</span> 2600 <span class="c">#</span> 2601 <span class="c"># Notes:</span> 2602 <span class="c"># . Atom and bond aromaticity is deleted during kekulization of non-ring atoms.</span> 2603 <span class="c">#</span> <a name="_KekulizeAromaticAtomsNotInRings-"></a>2604 <span class="k">sub </span><span class="m">_KekulizeAromaticAtomsNotInRings</span> <span class="s">{</span> 2605 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2606 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$PathIndex</span><span class="cm">,</span> <span class="i">$PathAtom</span><span class="cm">,</span> <span class="i">$PathAtomID</span><span class="cm">,</span> <span class="i">$PathBondID</span><span class="cm">,</span> <span class="i">$ConnectedPathsAtomsRef</span><span class="cm">,</span> <span class="i">$ConnectedPathsBondsRef</span><span class="cm">,</span> <span class="i">$DeleteAtomsAromaticity</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="cm">,</span> <span class="i">%PathAtomsProcessingStatusMap</span><span class="cm">,</span> <span class="i">%PathBondsProcessingStatusMap</span><span class="s">)</span><span class="sc">;</span> 2607 2608 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasAromaticAtomsNotInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2609 <span class="c"># Nothing to do...</span> 2610 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2611 <span class="s">}</span> 2612 2613 <span class="c"># Identify paths for connected components containing non-ring aromatic atoms...</span> 2614 <span class="s">(</span><span class="i">$ConnectedPathsAtomsRef</span><span class="cm">,</span> <span class="i">$ConnectedPathsBondsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetConnectedComponentsPathsForNonRingAromaticAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2615 2616 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$ConnectedPathsAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 2617 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_KekulizeAromaticAtomsNotInRings: Couldn't perform kekulization for marked non-ring aromatic atoms..."</span><span class="sc">;</span> 2618 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2619 <span class="s">}</span> 2620 2621 <span class="i">%PathAtomsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2622 <span class="i">%PathBondsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2623 2624 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> 2625 2626 <span class="j">PATH:</span> <span class="k">for</span> <span class="i">$PathIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ConnectedPathsAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 2627 <span class="k">my</span><span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">@ConnectedPathAtomsSet</span><span class="cm">,</span> <span class="i">@ConnectedPathBondsSet</span><span class="s">)</span><span class="sc">;</span> 2628 2629 <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">2</span><span class="sc">;</span> 2630 2631 <span class="i">@ConnectedPathAtomsSet</span> = <span class="s">(</span><span class="i">$ConnectedPathsAtomsRef</span>->[<span class="i">$PathIndex</span>]<span class="s">)</span><span class="sc">;</span> 2632 <span class="i">@ConnectedPathBondsSet</span> = <span class="s">(</span><span class="i">$ConnectedPathsBondsRef</span>->[<span class="i">$PathIndex</span>]<span class="s">)</span><span class="sc">;</span> 2633 2634 <span class="c"># Prepare for kekulization...</span> 2635 <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupConnectedPathSetsForKekulization</span><span class="s">(</span>\<span class="i">@ConnectedPathAtomsSet</span><span class="cm">,</span> \<span class="i">@ConnectedPathBondsSet</span><span class="s">)</span><span class="sc">;</span> 2636 2637 <span class="c"># Perform kekulization...</span> 2638 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$ConnectedPathsAtomsRef</span>->[<span class="i">$PathIndex</span>]<span class="cm">,</span> <span class="i">$ConnectedPathsBondsRef</span>->[<span class="i">$PathIndex</span>]<span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2639 <span class="c"># Kekulization failed for the current path...</span> 2640 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> 2641 <span class="k">last</span> <span class="j">PATH</span><span class="sc">;</span> 2642 <span class="s">}</span> 2643 2644 <span class="c"># Track atom and bond processing state for final assignment after kekulization</span> 2645 <span class="c"># is successfully completed for all the paths and fused path sets...</span> 2646 <span class="c">#</span> 2647 <span class="k">for</span> <span class="i">$PathAtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>}<span class="s">)</span> <span class="s">{</span> 2648 <span class="i">$PathAtomsProcessingStatusMap</span>{<span class="i">$PathAtomID</span>} = <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID</span>}<span class="sc">;</span> 2649 <span class="s">}</span> 2650 2651 <span class="k">for</span> <span class="i">$PathBondID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>}<span class="s">)</span> <span class="s">{</span> 2652 <span class="i">$PathBondsProcessingStatusMap</span>{<span class="i">$PathBondID</span>} = <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>}<span class="sc">;</span> 2653 <span class="s">}</span> 2654 <span class="s">}</span> 2655 2656 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span> 2657 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_KekulizeAromaticAtomsNotInRings: Couldn't perform kekulization for marked non-ring aromatic atoms..."</span><span class="sc">;</span> 2658 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2659 <span class="s">}</span> 2660 2661 <span class="i">$DeleteAtomsAromaticity</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$DeleteBondsAromaticity</span> = <span class="n">1</span><span class="sc">;</span> 2662 <span class="k">for</span> <span class="i">$PathIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ConnectedPathsAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 2663 <span class="k">if</span> <span class="s">(</span><span class="i">$DeleteAtomsAromaticity</span><span class="s">)</span> <span class="s">{</span> 2664 <span class="k">for</span> <span class="i">$PathAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConnectedPathsAtomsRef</span>->[<span class="i">$PathIndex</span>]}<span class="s">)</span> <span class="s">{</span> 2665 <span class="i">$PathAtom</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2666 <span class="s">}</span> 2667 <span class="s">}</span> 2668 <span class="i">$This</span><span class="i">->_ProcessBondOrdersAssignedDuringSuccessfulKekulization</span><span class="s">(</span><span class="i">$ConnectedPathsBondsRef</span>->[<span class="i">$PathIndex</span>]<span class="cm">,</span> \<span class="i">%PathBondsProcessingStatusMap</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="s">)</span><span class="sc">;</span> 2669 <span class="s">}</span> 2670 2671 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2672 <span class="s">}</span> 2673 2674 <span class="c"># Collect path atoms for connected components paths containing non-ring aromatic atoms...</span> 2675 <span class="c">#</span> <a name="_GetConnectedComponentsPathsForNonRingAromaticAtoms-"></a>2676 <span class="k">sub </span><span class="m">_GetConnectedComponentsPathsForNonRingAromaticAtoms</span> <span class="s">{</span> 2677 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2678 <span class="k">my</span><span class="s">(</span><span class="i">$ComponentRef</span><span class="cm">,</span> <span class="i">$AtomIDsRef</span><span class="cm">,</span> <span class="i">$AtomIDsMapRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsAtomIDsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsAtomIDsMapRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsPathsAtomIDsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsPathsAtomsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsPathsBondsRef</span><span class="s">)</span><span class="sc">;</span> 2679 2680 <span class="c"># Retrieve information for marked aromatic atoms not in the rings...</span> 2681 <span class="s">(</span><span class="i">$AtomIDsRef</span><span class="cm">,</span> <span class="i">$AtomIDsMapRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetNonRingAromaticAtomIDs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2682 2683 <span class="c"># Identify connected components containing marked aromatic atoms not in the rings...</span> 2684 <span class="s">(</span><span class="i">$ConnectedComponentsAtomIDsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsAtomIDsMapRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetConnectedComponentsForNonRingAromaticAtoms</span><span class="s">(</span><span class="i">$AtomIDsRef</span><span class="s">)</span><span class="sc">;</span> 2685 2686 <span class="c"># Identify paths for connected components containing non-ring aromatic atoms...</span> 2687 <span class="s">(</span><span class="i">$ConnectedComponentsPathsAtomsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsPathsBondsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetConnectedComponentsPathsAtomsAndBondsForNonRingAromaticAtoms</span><span class="s">(</span><span class="i">$AtomIDsMapRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsAtomIDsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsAtomIDsMapRef</span><span class="s">)</span><span class="sc">;</span> 2688 2689 <span class="k">return</span> <span class="s">(</span><span class="i">$ConnectedComponentsPathsAtomsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsPathsBondsRef</span><span class="s">)</span><span class="sc">;</span> 2690 <span class="s">}</span> 2691 2692 <span class="c"># Collect information for marked aromatic atoms not in the rings...</span> 2693 <span class="c">#</span> <a name="_GetNonRingAromaticAtomIDs-"></a>2694 <span class="k">sub </span><span class="m">_GetNonRingAromaticAtomIDs</span> <span class="s">{</span> 2695 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2696 <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">@AtomIDs</span><span class="cm">,</span> <span class="i">%AtomIDsMap</span><span class="s">)</span><span class="sc">;</span> 2697 2698 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2699 <span class="i">%AtomIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2700 2701 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2702 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2703 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 2704 <span class="s">}</span> 2705 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2706 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 2707 <span class="s">}</span> 2708 <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> 2709 2710 <span class="k">push</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="sc">;</span> 2711 <span class="i">$AtomIDsMap</span>{<span class="i">$AtomID</span>} = <span class="i">$Atom</span><span class="sc">;</span> 2712 <span class="s">}</span> 2713 2714 <span class="k">return</span> <span class="s">(</span>\<span class="i">@AtomIDs</span><span class="cm">,</span> \<span class="i">%AtomIDsMap</span><span class="s">)</span><span class="sc">;</span> 2715 <span class="s">}</span> 2716 2717 <span class="c"># Retrieve connected non-ring atom components as a reference to an array of references</span> 2718 <span class="c"># containing atom IDs of connecnted components...</span> 2719 <span class="c">#</span> <a name="_GetConnectedComponentsForNonRingAromaticAtoms-"></a>2720 <span class="k">sub </span><span class="m">_GetConnectedComponentsForNonRingAromaticAtoms</span> <span class="s">{</span> 2721 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomIDsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2722 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIDsGraph</span><span class="cm">,</span> <span class="i">@BondedAtomPairIDs</span><span class="cm">,</span> <span class="i">@ComponentsAtomIDsRefs</span><span class="cm">,</span> <span class="i">@ComponentsAtomIDsMapRefs</span><span class="s">)</span><span class="sc">;</span> 2723 2724 <span class="i">@ComponentsAtomIDsRefs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2725 <span class="i">@ComponentsAtomIDsMapRefs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2726 2727 <span class="c"># Get bonded atom pair IDs...</span> 2728 <span class="i">@BondedAtomPairIDs</span> = <span class="i">$This</span><span class="i">->_GetBondedAtomPairAtomIDsFromAtomIDs</span><span class="s">(</span><span class="i">@</span>{<span class="i">$AtomIDsRef</span>}<span class="s">)</span><span class="sc">;</span> 2729 2730 <span class="k">if</span> <span class="s">(</span>!<span class="i">@BondedAtomPairIDs</span><span class="s">)</span> <span class="s">{</span> 2731 <span class="k">return</span> <span class="s">(</span>\<span class="i">@ComponentsAtomIDsRefs</span><span class="cm">,</span> \<span class="i">@ComponentsAtomIDsMapRefs</span><span class="s">)</span><span class="sc">;</span> 2732 <span class="s">}</span> 2733 2734 <span class="i">$AtomIDsGraph</span> = <span class="i">new</span> <span class="i">Graph</span><span class="s">(</span><span class="i">@</span>{<span class="i">$AtomIDsRef</span>}<span class="s">)</span><span class="sc">;</span> 2735 <span class="i">$AtomIDsGraph</span><span class="i">->AddEdges</span><span class="s">(</span><span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span> 2736 2737 <span class="i">@ComponentsAtomIDsRefs</span> = <span class="i">$AtomIDsGraph</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2738 2739 <span class="c"># Setup atom IDs map for each component...</span> 2740 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ComponentsAtomIDsRefs</span><span class="s">)</span> <span class="s">{</span> 2741 <span class="i">%</span>{<span class="i">$ComponentsAtomIDsMapRefs</span>[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2742 2743 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ComponentsAtomIDsRefs</span>[<span class="i">$Index</span>]}<span class="s">)</span> <span class="s">{</span> 2744 <span class="i">$ComponentsAtomIDsMapRefs</span>[<span class="i">$Index</span>]{<span class="i">$AtomID</span>} = <span class="i">$AtomID</span><span class="sc">;</span> 2745 <span class="s">}</span> 2746 <span class="s">}</span> 2747 2748 <span class="k">return</span> <span class="s">(</span>\<span class="i">@ComponentsAtomIDsRefs</span><span class="cm">,</span> \<span class="i">@ComponentsAtomIDsMapRefs</span><span class="s">)</span><span class="sc">;</span> 2749 <span class="s">}</span> 2750 2751 <span class="c"># Get linear paths for connected components starting and ending at terminal aromatic atoms,</span> 2752 <span class="c"># which are connected to only one other aromatic atom in the connected component..</span> 2753 <span class="c">#</span> <a name="_GetConnectedComponentsPathsAtomsAndBondsForNonRingAromaticAtoms-"></a>2754 <span class="k">sub </span><span class="m">_GetConnectedComponentsPathsAtomsAndBondsForNonRingAromaticAtoms</span> <span class="s">{</span> 2755 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomIDsMapRef</span><span class="cm">,</span> <span class="i">$ComponentsAtomIDsRef</span><span class="cm">,</span> <span class="i">$ComponentsAtomIDsMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2756 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomNbr</span><span class="cm">,</span> <span class="i">$AtomNbrID</span><span class="cm">,</span> <span class="i">$NumOfNonRingAromaticNbrs</span><span class="cm">,</span> <span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomIDsGraph</span><span class="cm">,</span> <span class="i">$StartTerminalAtomID</span><span class="cm">,</span> <span class="i">$EndTerminalAtomID</span><span class="cm">,</span> <span class="i">@Paths</span><span class="cm">,</span> <span class="i">@PathAtomIDs</span><span class="cm">,</span> <span class="i">@PathsAtoms</span><span class="cm">,</span> <span class="i">@PathsBonds</span><span class="cm">,</span> <span class="i">@TerminalAtomIDs</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span> 2757 2758 <span class="i">@PathsAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2759 <span class="i">@PathsBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2760 2761 <span class="i">@TerminalAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2762 2763 <span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> 2764 <span class="j">COMPONENT:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ComponentsAtomIDsRef</span>}<span class="s">)</span> <span class="s">{</span> 2765 <span class="i">@</span>{<span class="i">$TerminalAtomIDs</span>[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2766 2767 <span class="c"># Identify terminal atoms for connected components...</span> 2768 <span class="c">#</span> 2769 <span class="c"># Notes:</span> 2770 <span class="c"># . Terminal atoms are defined as atoms connected to only one marked</span> 2771 <span class="c"># aromatic atom.</span> 2772 <span class="c"># . Linear connected compoents contain only two terminal atoms.</span> 2773 <span class="c">#</span> 2774 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ComponentsAtomIDsRef</span>->[<span class="i">$Index</span>]}<span class="s">)</span> <span class="s">{</span> 2775 <span class="i">$Atom</span> = <span class="i">$AtomIDsMapRef</span>->{<span class="i">$AtomID</span>}<span class="sc">;</span> 2776 <span class="i">$NumOfNonRingAromaticNbrs</span> = <span class="n">0</span><span class="sc">;</span> 2777 2778 <span class="j">ATOMNBRID:</span> <span class="k">for</span> <span class="i">$AtomNbr</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2779 <span class="i">$AtomNbrID</span> = <span class="i">$AtomNbr</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2780 2781 <span class="c"># Is neighbor in the same connected components containing aromatic atoms?</span> 2782 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ComponentsAtomIDsMapRef</span>->[<span class="i">$Index</span>]{<span class="i">$AtomNbrID</span>}<span class="s">)</span> <span class="s">{</span> 2783 <span class="k">next</span> <span class="j">ATOMNBRID</span><span class="sc">;</span> 2784 <span class="s">}</span> 2785 <span class="i">$NumOfNonRingAromaticNbrs</span>++<span class="sc">;</span> 2786 <span class="s">}</span> 2787 2788 <span class="c"># Is it a terminal atom?</span> 2789 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNonRingAromaticNbrs</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 2790 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 2791 <span class="s">}</span> 2792 <span class="k">push</span> <span class="i">@</span>{<span class="i">$TerminalAtomIDs</span>[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">$AtomID</span><span class="sc">;</span> 2793 <span class="s">}</span> 2794 2795 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$TerminalAtomIDs</span>[<span class="i">$Index</span>]} != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 2796 <span class="k">next</span> <span class="j">COMPONENT</span><span class="sc">;</span> 2797 <span class="s">}</span> 2798 2799 <span class="c"># Setup bonded atom pair IDs for connected component...</span> 2800 <span class="c">#</span> 2801 <span class="i">@AtomIDs</span> = <span class="i">@</span>{<span class="i">$ComponentsAtomIDsRef</span>->[<span class="i">$Index</span>]}<span class="sc">;</span> 2802 <span class="i">@BondedAtomPairIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2803 2804 <span class="k">for</span> <span class="i">$AtomIndex1</span> <span class="s">(</span> <span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> <span class="s">{</span> 2805 <span class="i">$AtomID1</span> = <span class="i">$AtomIDs</span>[<span class="i">$AtomIndex1</span>]<span class="sc">;</span> 2806 <span class="i">$Atom1</span> = <span class="i">$AtomIDsMapRef</span>->{<span class="i">$AtomID1</span>}<span class="sc">;</span> 2807 2808 <span class="k">for</span> <span class="i">$AtomIndex2</span> <span class="s">(</span> <span class="s">(</span><span class="i">$AtomIndex1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> <span class="s">{</span> 2809 <span class="i">$AtomID2</span> = <span class="i">$AtomIDs</span>[<span class="i">$AtomIndex2</span>]<span class="sc">;</span> 2810 <span class="i">$Atom2</span> = <span class="i">$AtomIDsMapRef</span>->{<span class="i">$AtomID2</span>}<span class="sc">;</span> 2811 2812 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsBondedToAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2813 <span class="k">push</span> <span class="i">@BondedAtomPairIDs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 2814 <span class="s">}</span> 2815 <span class="s">}</span> 2816 <span class="s">}</span> 2817 2818 <span class="k">if</span> <span class="s">(</span>!<span class="i">@BondedAtomPairIDs</span><span class="s">)</span> <span class="s">{</span> 2819 <span class="k">next</span> <span class="j">COMPONENT</span><span class="sc">;</span> 2820 <span class="s">}</span> 2821 2822 <span class="c"># Get path for connected component...</span> 2823 <span class="i">$AtomIDsGraph</span> = <span class="i">new</span> <span class="i">Graph</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 2824 <span class="i">$AtomIDsGraph</span><span class="i">->AddEdges</span><span class="s">(</span><span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span> 2825 2826 <span class="s">(</span><span class="i">$StartTerminalAtomID</span><span class="cm">,</span> <span class="i">$EndTerminalAtomID</span><span class="s">)</span> = <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$TerminalAtomIDs</span>[<span class="i">$Index</span>]}<span class="sc">;</span> 2827 <span class="i">@Paths</span> = <span class="i">$AtomIDsGraph</span><span class="i">->GetPathsBetween</span><span class="s">(</span><span class="i">$StartTerminalAtomID</span><span class="cm">,</span> <span class="i">$EndTerminalAtomID</span><span class="s">)</span><span class="sc">;</span> 2828 2829 <span class="k">if</span> <span class="s">(</span><span class="i">@Paths</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 2830 <span class="k">next</span> <span class="j">COMPONENT</span><span class="sc">;</span> 2831 <span class="s">}</span> 2832 2833 <span class="i">@PathAtomIDs</span> = <span class="i">$Paths</span>[<span class="n">0</span>]<span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2834 2835 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> 2836 <span class="i">@PathAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span> 2837 <span class="k">push</span> <span class="i">@PathsAtoms</span><span class="cm">,</span> \<span class="i">@PathAtoms</span><span class="sc">;</span> 2838 2839 <span class="k">my</span><span class="s">(</span><span class="i">@PathBonds</span><span class="s">)</span><span class="sc">;</span> 2840 <span class="i">@PathBonds</span> = <span class="i">$This</span><span class="i">->_GetPathBonds</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span> 2841 <span class="k">push</span> <span class="i">@PathsBonds</span><span class="cm">,</span> \<span class="i">@PathBonds</span><span class="sc">;</span> 2842 2843 <span class="s">}</span> 2844 2845 <span class="k">return</span> <span class="s">(</span>\<span class="i">@PathsAtoms</span><span class="cm">,</span> \<span class="i">@PathsBonds</span><span class="s">)</span><span class="sc">;</span> 2846 <span class="s">}</span> 2847 2848 <span class="c"># Setup initial processing status of atoms and bonds involved in connected paths</span> 2849 <span class="c"># before starting kekulization...</span> 2850 <span class="c">#</span> 2851 <span class="c"># Possible atom processing status: DoubleBondPossible, DoubleBondAssigned, DoubleBondNotPossible</span> 2852 <span class="c"># Initial status: DoubleBondPossible or DoubleBondNotPossible</span> 2853 <span class="c">#</span> 2854 <span class="c"># Possible bond processing status: DoubleBondAssigned, SingleBondAssigned, NotProcessed</span> 2855 <span class="c">#</span> 2856 <span class="c"># Possible paths processing status: Processed, NotProcessed</span> 2857 <span class="c"># Initial status: NotProcessed</span> 2858 <span class="c">#</span> <a name="_SetupConnectedPathSetsForKekulization-"></a>2859 <span class="k">sub </span><span class="m">_SetupConnectedPathSetsForKekulization</span> <span class="s">{</span> 2860 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2861 <span class="k">my</span><span class="s">(</span><span class="i">$PathIndex</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">%AtomProcessingStatusMap</span><span class="cm">,</span> <span class="i">%BondProcessingStatusMap</span><span class="cm">,</span> <span class="i">@PathsProcessingStatus</span><span class="cm">,</span> <span class="i">%InitialPathBondOrderMap</span><span class="s">)</span><span class="sc">;</span> 2862 2863 <span class="c"># Possible path set status values: Processed, NotProcessed</span> 2864 <span class="c"># Initial value: NotProcessed</span> 2865 <span class="c">#</span> 2866 <span class="i">@PathsProcessingStatus</span> = <span class="s">(</span><span class="q">'NotProcessed'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsSetsRef</span>}<span class="sc">;</span> 2867 2868 <span class="c"># Collect initial bond order of path bonds before setting bond orders to 1</span> 2869 <span class="c"># and use it to set the bond order back to intial value after it has been processed for</span> 2870 <span class="c"># availability of double bonds...</span> 2871 <span class="c">#</span> 2872 <span class="i">%InitialPathBondOrderMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2873 <span class="k">for</span> <span class="i">$PathBondsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 2874 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsRef</span>}<span class="s">)</span> <span class="s">{</span> 2875 <span class="i">$BondID</span> = <span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2876 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$InitialPathBondOrderMap</span>{<span class="i">$BondID</span>}<span class="s">)</span> <span class="s">{</span> 2877 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 2878 <span class="s">}</span> 2879 <span class="i">$InitialPathBondOrderMap</span>{<span class="i">$BondID</span>} = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2880 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> 2881 <span class="s">}</span> 2882 <span class="s">}</span> 2883 2884 <span class="i">%AtomProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2885 <span class="i">%BondProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2886 2887 <span class="k">for</span> <span class="i">$PathIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PathAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 2888 2889 <span class="i">$PathAtomsRef</span> = <span class="i">$PathAtomsSetsRef</span>->[<span class="i">$PathIndex</span>]<span class="sc">;</span> 2890 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 2891 <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> 2892 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomProcessingStatusMap</span>{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span> 2893 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 2894 <span class="s">}</span> 2895 <span class="i">$AtomProcessingStatusMap</span>{<span class="i">$AtomID</span>} = <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetNumOfBondsAvailableForNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> >= <span class="n">1</span><span class="s">)</span> ? <span class="q">'DoubleBondPossible'</span> <span class="co">:</span> <span class="q">'DoubleBondNotPossible'</span><span class="sc">;</span> 2896 <span class="s">}</span> 2897 2898 <span class="i">$PathBondsRef</span> = <span class="i">$PathBondsSetsRef</span>->[<span class="i">$PathIndex</span>]<span class="sc">;</span> 2899 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsRef</span>}<span class="s">)</span> <span class="s">{</span> 2900 <span class="i">$BondID</span> = <span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2901 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$BondProcessingStatusMap</span>{<span class="i">$BondID</span>}<span class="s">)</span> <span class="s">{</span> 2902 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 2903 <span class="s">}</span> 2904 <span class="i">$BondProcessingStatusMap</span>{<span class="i">$BondID</span>} = <span class="q">'NotProcessed'</span><span class="sc">;</span> 2905 <span class="s">}</span> 2906 <span class="s">}</span> 2907 2908 <span class="c"># Set bond orders back to initial bond orders...</span> 2909 <span class="k">for</span> <span class="i">$PathIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PathAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 2910 <span class="i">$PathBondsRef</span> = <span class="i">$PathBondsSetsRef</span>->[<span class="i">$PathIndex</span>]<span class="sc">;</span> 2911 2912 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsRef</span>}<span class="s">)</span> <span class="s">{</span> 2913 <span class="i">$BondID</span> = <span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2914 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$InitialPathBondOrderMap</span>{<span class="i">$BondID</span>}<span class="s">)</span> <span class="s">{</span> 2915 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="i">$InitialPathBondOrderMap</span>{<span class="i">$BondID</span>}<span class="s">)</span><span class="sc">;</span> 2916 <span class="s">}</span> 2917 <span class="s">}</span> 2918 <span class="s">}</span> 2919 2920 <span class="k">return</span> <span class="s">(</span>\<span class="i">%AtomProcessingStatusMap</span><span class="cm">,</span> \<span class="i">%BondProcessingStatusMap</span><span class="cm">,</span> \<span class="i">@PathsProcessingStatus</span><span class="s">)</span><span class="sc">;</span> 2921 <span class="s">}</span> 2922 2923 <span class="c"># Kekulize connected path sets corresponding to fused rings, individual rings, or any other</span> 2924 <span class="c"># connected path...</span> 2925 <span class="c">#</span> 2926 <span class="c"># Note:</span> 2927 <span class="c"># . PathAtomsRef and PathBondsRef contain paths and bonds corresponding to path</span> 2928 <span class="c"># under consideration for kekulization</span> 2929 <span class="c"># . PathAtomsSetsRef and PathBondsSetsRef contain any other available paths fused</span> 2930 <span class="c"># to the path being kekulized</span> 2931 <span class="c"># . _KekulizeConnectedPathSets is invoked recursively to kekulize all available paths</span> 2932 <span class="c">#</span> <a name="_KekulizeConnectedPathSets-"></a>2933 <span class="k">sub </span><span class="m">_KekulizeConnectedPathSets</span> <span class="s">{</span> 2934 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2935 <span class="k">my</span><span class="s">(</span><span class="i">$PathBond</span><span class="s">)</span><span class="sc">;</span> 2936 2937 <span class="c"># Get next available path bond...</span> 2938 <span class="i">$PathBond</span> = <span class="i">$This</span><span class="i">->_GetNextAvailablePathBondForKekulization</span><span class="s">(</span><span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="sc">;</span> 2939 2940 <span class="k">if</span> <span class="s">(</span><span class="i">$PathBond</span><span class="s">)</span> <span class="s">{</span> 2941 <span class="k">return</span> <span class="i">$This</span><span class="i">->_ProcessNextAvailablePathBondForKekulization</span><span class="s">(</span><span class="i">$PathBond</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span><span class="sc">;</span> 2942 <span class="s">}</span> 2943 2944 <span class="c"># Did kekulization succeed for the current path bonds?</span> 2945 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_DidKekulizationSucceedForPathBonds</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 2946 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 2947 <span class="s">}</span> 2948 2949 <span class="c"># Is there any other path available for kekulization?</span> 2950 <span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetNextAvailablePathForKekulization</span><span class="s">(</span><span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="sc">;</span> 2951 2952 <span class="k">if</span> <span class="s">(</span><span class="i">$PathAtomsRef</span> && <span class="i">$PathBondsRef</span><span class="s">)</span> <span class="s">{</span> 2953 <span class="c"># Recursively call itself to kekulize next path, which could either be a new path or part</span> 2954 <span class="c"># of a fused paths corresponding to fused ring sets...</span> 2955 <span class="c">#</span> 2956 <span class="k">return</span> <span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span><span class="sc">;</span> 2957 <span class="s">}</span> 2958 2959 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 2960 <span class="s">}</span> 2961 2962 <span class="c"># Get next available path bond in a list of path bonds...</span> 2963 <span class="c">#</span> <a name="_GetNextAvailablePathBondForKekulization-"></a>2964 <span class="k">sub </span><span class="m">_GetNextAvailablePathBondForKekulization</span> <span class="s">{</span> 2965 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2966 <span class="k">my</span><span class="s">(</span><span class="i">$AvailablePathBond</span><span class="cm">,</span> <span class="i">$PathBond</span><span class="cm">,</span> <span class="i">$PathBondID</span><span class="s">)</span><span class="sc">;</span> 2967 2968 <span class="i">$AvailablePathBond</span> = <span class="k">undef</span><span class="sc">;</span> 2969 2970 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$PathBond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsRef</span>}<span class="s">)</span> <span class="s">{</span> 2971 <span class="i">$PathBondID</span> = <span class="i">$PathBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2972 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>}<span class="s">)</span> <span class="s">{</span> 2973 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 2974 <span class="s">}</span> 2975 <span class="k">if</span> <span class="s">(</span><span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} =~ <span class="q">/^NotProcessed$/i</span><span class="s">)</span> <span class="s">{</span> 2976 <span class="i">$AvailablePathBond</span> = <span class="i">$PathBond</span><span class="sc">;</span> 2977 <span class="k">last</span> <span class="j">BOND</span><span class="sc">;</span> 2978 <span class="s">}</span> 2979 <span class="s">}</span> 2980 2981 <span class="k">return</span> <span class="s">(</span><span class="i">$AvailablePathBond</span><span class="s">)</span><span class="sc">;</span> 2982 <span class="s">}</span> 2983 2984 <span class="c"># Process next available path bond for kekulizaiton...</span> 2985 <span class="c">#</span> <a name="_ProcessNextAvailablePathBondForKekulization-"></a>2986 <span class="k">sub </span><span class="m">_ProcessNextAvailablePathBondForKekulization</span> <span class="s">{</span> 2987 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathBond</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 2988 <span class="k">my</span><span class="s">(</span><span class="i">$PathBondID</span><span class="cm">,</span> <span class="i">$PathAtom1</span><span class="cm">,</span> <span class="i">$PathAtom2</span><span class="cm">,</span> <span class="i">$PathAtomID1</span><span class="cm">,</span> <span class="i">$PathAtomID2</span><span class="cm">,</span> <span class="i">%CurrentAtomProcessingStatusMap</span><span class="cm">,</span> <span class="i">%CurrentBondProcessingStatusMap</span><span class="s">)</span><span class="sc">;</span> 2989 2990 <span class="i">$PathBondID</span> = <span class="i">$PathBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2991 2992 <span class="s">(</span><span class="i">$PathAtom1</span><span class="cm">,</span> <span class="i">$PathAtom2</span><span class="s">)</span> = <span class="i">$PathBond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 2993 <span class="s">(</span><span class="i">$PathAtomID1</span><span class="cm">,</span> <span class="i">$PathAtomID2</span><span class="s">)</span> = <span class="s">(</span><span class="i">$PathAtom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$PathAtom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 2994 2995 <span class="i">%CurrentAtomProcessingStatusMap</span> = <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>}<span class="sc">;</span> 2996 <span class="i">%CurrentBondProcessingStatusMap</span> = <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>}<span class="sc">;</span> 2997 2998 <span class="c"># Is it possible to assign a double bond to the current path bond?</span> 2999 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID1</span>} =~ <span class="q">/^DoubleBondPossible$/i</span> && <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID2</span>} =~ <span class="q">/^DoubleBondPossible$/i</span> <span class="s">)</span> <span class="s">{</span> 3000 <span class="c"># Set current bond to double bond by appropriately marking atom and bond process status...</span> 3001 <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID1</span>} = <span class="q">'DoubleBondAssigned'</span><span class="sc">;</span> 3002 <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID2</span>} = <span class="q">'DoubleBondAssigned'</span><span class="sc">;</span> 3003 3004 <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} = <span class="q">'DoubleBondAssigned'</span><span class="sc">;</span> 3005 3006 <span class="c"># Recursively call _KekulizeConnectedPathSets to kekulize next available bond...</span> 3007 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3008 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3009 <span class="s">}</span> 3010 3011 <span class="c"># Double bond at the current ring bond position didn't lead to successful kekulization...</span> 3012 <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>} = <span class="i">%CurrentAtomProcessingStatusMap</span><span class="sc">;</span> 3013 <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>} = <span class="i">%CurrentBondProcessingStatusMap</span><span class="sc">;</span> 3014 <span class="s">}</span> 3015 3016 <span class="c"># Try single bond at the current ring bond position and recursively call _KekulizeConnectedPathSets to kekulize</span> 3017 <span class="c"># rest of the ring bonds...</span> 3018 <span class="c">#</span> 3019 <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} = <span class="q">'SingleBondAssigned'</span><span class="sc">;</span> 3020 3021 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3022 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3023 <span class="s">}</span> 3024 3025 <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>} = <span class="i">%CurrentAtomProcessingStatusMap</span><span class="sc">;</span> 3026 <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>} = <span class="i">%CurrentBondProcessingStatusMap</span><span class="sc">;</span> 3027 3028 <span class="c"># Kekulization didn't work out for path bonds...</span> 3029 3030 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3031 3032 <span class="s">}</span> 3033 3034 <span class="c"># Get next available path for kekulization from a set of fused ring paths...</span> 3035 <span class="c">#</span> <a name="_GetNextAvailablePathForKekulization-"></a>3036 <span class="k">sub </span><span class="m">_GetNextAvailablePathForKekulization</span> <span class="s">{</span> 3037 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3038 <span class="k">my</span><span class="s">(</span><span class="i">$PathIndex</span><span class="cm">,</span> <span class="i">$AvailablePathIndex</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$PathBond</span><span class="cm">,</span> <span class="i">$PathBondID</span><span class="cm">,</span> <span class="i">$MaxNumOfPathBondsProcessed</span><span class="cm">,</span> <span class="i">$NumOfPathBondsProcessed</span><span class="s">)</span><span class="sc">;</span> 3039 3040 <span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AvailablePathIndex</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> 3041 3042 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$PathAtomsSetsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$PathBondsSetsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$PathsProcessingStatusRef</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3043 <span class="k">return</span> <span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="s">)</span><span class="sc">;</span> 3044 <span class="s">}</span> 3045 3046 <span class="i">$MaxNumOfPathBondsProcessed</span> = <span class="n">-999</span><span class="sc">;</span> 3047 <span class="i">$AvailablePathIndex</span> = <span class="k">undef</span><span class="sc">;</span> 3048 3049 <span class="j">PATHINDEX:</span> <span class="k">for</span> <span class="i">$PathIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PathsProcessingStatusRef</span>}<span class="s">)</span> <span class="s">{</span> 3050 <span class="k">if</span> <span class="s">(</span><span class="i">$PathsProcessingStatusRef</span>->[<span class="i">$PathIndex</span>] =~ <span class="q">/^Processed$/i</span><span class="s">)</span> <span class="s">{</span> 3051 <span class="k">next</span> <span class="j">PATHINDEX</span><span class="sc">;</span> 3052 <span class="s">}</span> 3053 3054 <span class="c"># Count of already processed bonds in an unprocessed path bonds through</span> 3055 <span class="c"># their participation in any fused bonds sets...</span> 3056 <span class="c">#</span> 3057 <span class="i">$NumOfPathBondsProcessed</span> = <span class="n">0</span><span class="sc">;</span> 3058 <span class="j">PATHBOND:</span> <span class="k">for</span> <span class="i">$PathBond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsSetsRef</span>->[<span class="i">$PathIndex</span>]}<span class="s">)</span> <span class="s">{</span> 3059 <span class="i">$PathBondID</span> = <span class="i">$PathBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3060 <span class="k">if</span> <span class="s">(</span><span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} =~ <span class="q">/^NotProcessed$/i</span><span class="s">)</span> <span class="s">{</span> 3061 <span class="k">next</span> <span class="j">PATHBOND</span><span class="sc">;</span> 3062 <span class="s">}</span> 3063 <span class="i">$NumOfPathBondsProcessed</span>++<span class="sc">;</span> 3064 <span class="s">}</span> 3065 3066 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfPathBondsProcessed</span> > <span class="i">$MaxNumOfPathBondsProcessed</span><span class="s">)</span> <span class="s">{</span> 3067 <span class="i">$AvailablePathIndex</span> = <span class="i">$PathIndex</span><span class="sc">;</span> 3068 <span class="i">$MaxNumOfPathBondsProcessed</span> = <span class="i">$NumOfPathBondsProcessed</span><span class="sc">;</span> 3069 <span class="s">}</span> 3070 3071 <span class="s">}</span> 3072 3073 <span class="c"># Is any path available?</span> 3074 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AvailablePathIndex</span><span class="s">)</span> <span class="s">{</span> 3075 <span class="k">return</span> <span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="s">)</span><span class="sc">;</span> 3076 <span class="s">}</span> 3077 3078 <span class="i">$PathsProcessingStatusRef</span>->[<span class="i">$AvailablePathIndex</span>] = <span class="q">'Processed'</span><span class="sc">;</span> 3079 3080 <span class="i">$PathAtomsRef</span> = <span class="i">$PathAtomsSetsRef</span>->[<span class="i">$AvailablePathIndex</span>]<span class="sc">;</span> 3081 <span class="i">$PathBondsRef</span> = <span class="i">$PathBondsSetsRef</span>->[<span class="i">$AvailablePathIndex</span>]<span class="sc">;</span> 3082 3083 <span class="k">return</span> <span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="s">)</span><span class="sc">;</span> 3084 <span class="s">}</span> 3085 3086 <span class="c"># Check for kekulization in a specific set of path bonds. For successful kekulization, all</span> 3087 <span class="c"># all path atoms marked with DoubleBondPossible must be involved in a path double bond...</span> 3088 <span class="c">#</span> <a name="_DidKekulizationSucceedForPathBonds-"></a>3089 <span class="k">sub </span><span class="m">_DidKekulizationSucceedForPathBonds</span> <span class="s">{</span> 3090 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3091 <span class="k">my</span><span class="s">(</span><span class="i">$PathAtom</span><span class="cm">,</span> <span class="i">$PathAtomID</span><span class="s">)</span><span class="sc">;</span> 3092 3093 <span class="k">for</span> <span class="i">$PathAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> 3094 <span class="i">$PathAtomID</span> = <span class="i">$PathAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3095 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID</span>} && <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID</span>} =~ <span class="q">/^DoubleBondPossible$/i</span><span class="s">)</span> <span class="s">{</span> 3096 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3097 <span class="s">}</span> 3098 <span class="s">}</span> 3099 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3100 <span class="s">}</span> 3101 3102 <span class="c"># Assign bond orders to the bonds in a molecule which have been successfully</span> 3103 <span class="c"># kekulized along with optional clearing of aromaticty property...</span> 3104 <span class="c">#</span> <a name="_ProcessBondOrdersAssignedDuringSuccessfulKekulization-"></a>3105 <span class="k">sub </span><span class="m">_ProcessBondOrdersAssignedDuringSuccessfulKekulization</span> <span class="s">{</span> 3106 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondsRef</span><span class="cm">,</span> <span class="i">$BondsProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3107 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="s">)</span><span class="sc">;</span> 3108 3109 <span class="i">$DeleteBondsAromaticity</span> = <span class="k">defined</span> <span class="i">$DeleteBondsAromaticity</span> ? <span class="i">$DeleteBondsAromaticity</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3110 3111 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$BondsRef</span>}<span class="s">)</span> <span class="s">{</span> 3112 <span class="i">$BondID</span> = <span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3113 3114 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$BondsProcessingStatusMapRef</span>->{<span class="i">$BondID</span>}<span class="s">)</span> <span class="s">{</span> 3115 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessBondOrdersAssignedDuringSuccessfulKekulization: Couldn't process bond with bond ID, $BondID: It's not available in the list of bonds processed for kekulization..."</span><span class="sc">;</span> 3116 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> 3117 <span class="s">}</span> 3118 3119 <span class="i">$BondOrder</span> = <span class="s">(</span><span class="i">$BondsProcessingStatusMapRef</span>->{<span class="i">$BondID</span>} =~ <span class="q">/^DoubleBondAssigned$/i</span><span class="s">)</span> ? <span class="n">2</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> 3120 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="i">$BondOrder</span><span class="s">)</span><span class="sc">;</span> 3121 3122 <span class="k">if</span> <span class="s">(</span><span class="i">$DeleteBondsAromaticity</span><span class="s">)</span> <span class="s">{</span> 3123 <span class="i">$Bond</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3124 <span class="s">}</span> 3125 <span class="s">}</span> 3126 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 3127 <span class="s">}</span> 3128 3129 <span class="c"># Does molecule contains aromatic rings?</span> 3130 <span class="c">#</span> <a name="HasAromaticRings-"></a>3131 <span class="k">sub </span><span class="m">HasAromaticRings</span> <span class="s">{</span> 3132 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3133 3134 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfAromaticRings</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3135 <span class="s">}</span> 3136 3137 <span class="c"># Does molecule contains any aromatic atom in a ring?</span> 3138 <span class="c">#</span> <a name="HasAromaticAtomsInRings-"></a>3139 <span class="k">sub </span><span class="m">HasAromaticAtomsInRings</span> <span class="s">{</span> 3140 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3141 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 3142 3143 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3145 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 3146 <span class="s">}</span> 3147 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3148 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3149 <span class="s">}</span> 3150 <span class="s">}</span> 3151 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3152 <span class="s">}</span> 3153 3154 <span class="c"># Does molecule contains any aromatic atom not in a ring?</span> 3155 <span class="c">#</span> <a name="HasAromaticAtomsNotInRings-"></a>3156 <span class="k">sub </span><span class="m">HasAromaticAtomsNotInRings</span> <span class="s">{</span> 3157 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3158 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 3159 3160 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3161 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3162 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 3163 <span class="s">}</span> 3164 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsNotInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3165 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 3166 <span class="s">}</span> 3167 <span class="s">}</span> 3168 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 3169 <span class="s">}</span> 3170 3171 <span class="c"># Does molecule contains rings?</span> 3172 <span class="c">#</span> <a name="HasRings-"></a>3173 <span class="k">sub </span><span class="m">HasRings</span> <span class="s">{</span> 3174 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3175 3176 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsCyclic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3177 <span class="s">}</span> 3178 3179 <span class="c"># Does molecule contains only one ring?</span> 3180 <span class="c">#</span> <a name="HasOnlyOneRing-"></a>3181 <span class="k">sub </span><span class="m">HasOnlyOneRing</span> <span class="s">{</span> 3182 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3183 3184 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUnicyclic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3185 <span class="s">}</span> 3186 3187 <span class="c"># Does molecule contains any rings?</span> 3188 <span class="c">#</span> <a name="HasNoRings-"></a>3189 <span class="k">sub </span><span class="m">HasNoRings</span> <span class="s">{</span> 3190 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3191 3192 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsAcyclic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3193 <span class="s">}</span> 3194 3195 <span class="c"># Get size of smallest ring...</span> 3196 <span class="c">#</span> <a name="GetSizeOfSmallestRing-"></a>3197 <span class="k">sub </span><span class="m">GetSizeOfSmallestRing</span> <span class="s">{</span> 3198 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3199 3200 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfSmallestCycle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3201 <span class="s">}</span> 3202 3203 <span class="c"># Get size of largest ring...</span> 3204 <span class="c">#</span> <a name="GetSizeOfLargestRing-"></a>3205 <span class="k">sub </span><span class="m">GetSizeOfLargestRing</span> <span class="s">{</span> 3206 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3207 3208 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfLargestCycle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3209 <span class="s">}</span> 3210 3211 <span class="c"># Get number of rings...</span> 3212 <span class="c">#</span> <a name="GetNumOfRings-"></a>3213 <span class="k">sub </span><span class="m">GetNumOfRings</span> <span class="s">{</span> 3214 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3215 3216 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3217 <span class="s">}</span> 3218 3219 <span class="c"># Get number of aromatic rings...</span> 3220 <span class="c">#</span> <a name="GetNumOfAromaticRings-"></a>3221 <span class="k">sub </span><span class="m">GetNumOfAromaticRings</span> <span class="s">{</span> 3222 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3223 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfRings</span><span class="s">)</span><span class="sc">;</span> 3224 3225 <span class="i">$NumOfRings</span> = <span class="k">scalar</span> <span class="i">$This</span><span class="i">->GetAromaticRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3226 3227 <span class="k">return</span> <span class="i">$NumOfRings</span><span class="sc">;</span> 3228 <span class="s">}</span> 3229 3230 <span class="c"># Get num of rings with odd size...</span> 3231 <span class="c">#</span> <a name="GetNumOfRingsWithOddSize-"></a>3232 <span class="k">sub </span><span class="m">GetNumOfRingsWithOddSize</span> <span class="s">{</span> 3233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3234 3235 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithOddSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3236 <span class="s">}</span> 3237 3238 <span class="c"># Get num of rings with even size...</span> 3239 <span class="c">#</span> <a name="GetNumOfRingsWithEvenSize-"></a>3240 <span class="k">sub </span><span class="m">GetNumOfRingsWithEvenSize</span> <span class="s">{</span> 3241 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3242 3243 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithEvenSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3244 <span class="s">}</span> 3245 3246 <span class="c"># Get num of rings with specified size...</span> 3247 <span class="c">#</span> <a name="GetNumOfRingsWithSize-"></a>3248 <span class="k">sub </span><span class="m">GetNumOfRingsWithSize</span> <span class="s">{</span> 3249 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3250 3251 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithSize</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3252 <span class="s">}</span> 3253 3254 <span class="c"># Get num of rings with size less than a specified size...</span> 3255 <span class="c">#</span> <a name="GetNumOfRingsWithSizeLessThan-"></a>3256 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeLessThan</span> <span class="s">{</span> 3257 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3258 3259 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3260 <span class="s">}</span> 3261 3262 <span class="c"># Get num of rings with size greater than a specified size...</span> 3263 <span class="c">#</span> <a name="GetNumOfRingsWithSizeGreaterThan-"></a>3264 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeGreaterThan</span> <span class="s">{</span> 3265 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3266 3267 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3268 <span class="s">}</span> 3269 3270 <span class="c"># Get largest ring as an array containing ring atoms...</span> 3271 <span class="c">#</span> <a name="GetLargestRing-"></a>3272 <span class="k">sub </span><span class="m">GetLargestRing</span> <span class="s">{</span> 3273 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3274 3275 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetLargestCycle</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3276 <span class="s">}</span> 3277 3278 <span class="c"># Get smallest ring as an array containing ring atoms...</span> 3279 <span class="c">#</span> <a name="GetSmallestRing-"></a>3280 <span class="k">sub </span><span class="m">GetSmallestRing</span> <span class="s">{</span> 3281 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3282 3283 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetSmallestCycle</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3284 <span class="s">}</span> 3285 3286 <span class="c"># Get rings as an array containing references to arrays with ring atoms...</span> 3287 <span class="c">#</span> <a name="GetRings-"></a>3288 <span class="k">sub </span><span class="m">GetRings</span> <span class="s">{</span> 3289 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3290 3291 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCycles</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3292 <span class="s">}</span> 3293 3294 <span class="c"># Get aromatic rings as an array containing references to arrays with ring atoms...</span> 3295 <span class="c">#</span> <a name="GetAromaticRings-"></a>3296 <span class="k">sub </span><span class="m">GetAromaticRings</span> <span class="s">{</span> 3297 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3298 3299 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAromaticRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCycles</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3300 <span class="s">}</span> 3301 3302 <span class="c"># Get odd size rings as an array containing references to arrays with ring atoms...</span> 3303 <span class="c">#</span> <a name="GetRingsWithOddSize-"></a>3304 <span class="k">sub </span><span class="m">GetRingsWithOddSize</span> <span class="s">{</span> 3305 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3306 3307 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCyclesWithOddSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3308 <span class="s">}</span> 3309 3310 <span class="c"># Get even size rings as an array containing references to arrays with ring atoms...</span> 3311 <span class="c">#</span> <a name="GetRingsWithEvenSize-"></a>3312 <span class="k">sub </span><span class="m">GetRingsWithEvenSize</span> <span class="s">{</span> 3313 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3314 3315 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCyclesWithEvenSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3316 <span class="s">}</span> 3317 3318 <span class="c"># Get rings with a specific size as an array containing references to arrays with ring atoms...</span> 3319 <span class="c">#</span> <a name="GetRingsWithSize-"></a>3320 <span class="k">sub </span><span class="m">GetRingsWithSize</span> <span class="s">{</span> 3321 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3322 3323 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCyclesWithSize</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3324 <span class="s">}</span> 3325 3326 <span class="c"># Get rings with size less than a specific size as an array containing references to arrays with ring atoms...</span> 3327 <span class="c">#</span> <a name="GetRingsWithSizeLessThan-"></a>3328 <span class="k">sub </span><span class="m">GetRingsWithSizeLessThan</span> <span class="s">{</span> 3329 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3330 3331 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3332 <span class="s">}</span> 3333 3334 <span class="c"># Get rings with size greater than a specific size as an array containing references to arrays with ring atoms...</span> 3335 <span class="c">#</span> <a name="GetRingsWithSizeGreaterThan-"></a>3336 <span class="k">sub </span><span class="m">GetRingsWithSizeGreaterThan</span> <span class="s">{</span> 3337 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3338 3339 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3340 <span class="s">}</span> 3341 3342 <span class="c"># Generate an array of bond objects for an array of ring atoms and return an array</span> 3343 <span class="c"># of bond objects...</span> 3344 <span class="c">#</span> <a name="GetRingBonds-"></a>3345 <span class="k">sub </span><span class="m">GetRingBonds</span> <span class="s">{</span> 3346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3347 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> 3348 3349 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3350 <span class="k">if</span> <span class="s">(</span>!<span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span> 3351 <span class="c"># Return an empty ring bonds list...</span> 3352 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span> 3353 <span class="s">}</span> 3354 3355 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtomIDs</span><span class="s">)</span><span class="sc">;</span> 3356 3357 <span class="i">@RingAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3358 <span class="i">@RingAtomIDs</span> = <span class="i">$This</span><span class="i">->_GetAtomsIDsFromAtoms</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span> 3359 <span class="k">if</span> <span class="s">(</span>!<span class="i">@RingAtomIDs</span><span class="s">)</span> <span class="s">{</span> 3360 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetRingBonds: No ring bonds retrieved: Atom IDs couldn't be retrieved for specified atoms..."</span><span class="sc">;</span> 3361 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span> 3362 <span class="s">}</span> 3363 3364 <span class="c"># Add start atom to the end to make it a cyclic path for ring: It's taken out during conversion</span> 3365 <span class="c"># of cyclic path to a ring...</span> 3366 <span class="k">push</span> <span class="i">@RingAtomIDs</span><span class="cm">,</span> <span class="i">$RingAtomIDs</span>[<span class="n">0</span>]<span class="sc">;</span> 3367 3368 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPathBonds</span><span class="s">(</span><span class="i">@RingAtomIDs</span><span class="s">)</span><span class="sc">;</span> 3369 <span class="s">}</span> 3370 3371 <span class="c"># Generate an array containing references to arrays of ring bond objects for rings specified</span> 3372 <span class="c"># in an array of references to ring atoms...</span> 3373 <span class="c">#</span> <a name="GetRingBondsFromRings-"></a>3374 <span class="k">sub </span><span class="m">GetRingBondsFromRings</span> <span class="s">{</span> 3375 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtomsSets</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3376 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">@RingBondsSets</span><span class="s">)</span><span class="sc">;</span> 3377 3378 <span class="i">@RingBondsSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3379 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@RingAtomsSets</span><span class="s">)</span> <span class="s">{</span> 3380 <span class="k">my</span><span class="s">(</span><span class="i">@RingBonds</span><span class="s">)</span><span class="sc">;</span> 3381 <span class="i">@RingBonds</span> = <span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="sc">;</span> 3382 3383 <span class="k">push</span> <span class="i">@RingBondsSets</span><span class="cm">,</span> \<span class="i">@RingBonds</span><span class="sc">;</span> 3384 <span class="s">}</span> 3385 3386 <span class="k">return</span> <span class="i">@RingBondsSets</span><span class="sc">;</span> 3387 <span class="s">}</span> 3388 3389 <span class="c"># Does molecule has any fused rings?</span> 3390 <span class="c">#</span> <a name="HasFusedRings-"></a>3391 <span class="k">sub </span><span class="m">HasFusedRings</span> <span class="s">{</span> 3392 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3393 3394 <span class="k">return</span> <span class="i">$This</span><span class="i">->HasFusedCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3395 <span class="s">}</span> 3396 3397 <span class="c"># Get references to array of fused ring sets and non-fused rings. Fused ring sets array reference</span> 3398 <span class="c"># contains refernces to arrays of rings; Non-fused rings array reference contains references to</span> 3399 <span class="c"># arrays of ring atoms...</span> 3400 <span class="c"># rings.</span> 3401 <span class="c">#</span> <a name="GetFusedAndNonFusedRings-"></a>3402 <span class="k">sub </span><span class="m">GetFusedAndNonFusedRings</span> <span class="s">{</span> 3403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3404 <span class="k">my</span><span class="s">(</span><span class="i">$FusedCyclesSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedCyclesRef</span><span class="cm">,</span> <span class="i">@FusedRingSets</span><span class="cm">,</span> <span class="i">@NonFusedRings</span><span class="s">)</span><span class="sc">;</span> 3405 3406 <span class="i">@FusedRingSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@NonFusedRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3407 <span class="s">(</span><span class="i">$FusedCyclesSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedCyclesRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetFusedAndNonFusedCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3408 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FusedCyclesSetsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$NonFusedCyclesRef</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3409 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FusedRingSets</span><span class="cm">,</span> \<span class="i">@NonFusedRings</span><span class="s">)</span><span class="sc">;</span> 3410 <span class="s">}</span> 3411 <span class="k">my</span><span class="s">(</span><span class="i">$FusedCyclesSetRef</span><span class="s">)</span><span class="sc">;</span> 3412 3413 <span class="k">for</span> <span class="i">$FusedCyclesSetRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedCyclesSetsRef</span>}<span class="s">)</span> <span class="s">{</span> 3414 <span class="k">my</span><span class="s">(</span><span class="i">@FusedRingSet</span><span class="s">)</span><span class="sc">;</span> 3415 <span class="i">@FusedRingSet</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3416 <span class="i">@FusedRingSet</span> = <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">@</span>{<span class="i">$FusedCyclesSetRef</span>}<span class="s">)</span><span class="sc">;</span> 3417 <span class="k">push</span> <span class="i">@FusedRingSets</span><span class="cm">,</span> \<span class="i">@FusedRingSet</span><span class="sc">;</span> 3418 <span class="s">}</span> 3419 3420 <span class="i">@NonFusedRings</span> = <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedCyclesRef</span>}<span class="s">)</span><span class="sc">;</span> 3421 3422 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FusedRingSets</span><span class="cm">,</span> \<span class="i">@NonFusedRings</span><span class="s">)</span><span class="sc">;</span> 3423 <span class="s">}</span> 3424 3425 <span class="c"># Get rings as an array containing references to arrays with ring atoms...</span> 3426 <span class="c">#</span> <a name="_GetRings-"></a>3427 <span class="k">sub </span><span class="m">_GetRings</span> <span class="s">{</span> 3428 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@CyclicPaths</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3429 <span class="k">my</span><span class="s">(</span><span class="i">$CyclicPath</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span><span class="sc">;</span> 3430 3431 <span class="i">@Rings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3432 <span class="k">if</span> <span class="s">(</span>!<span class="i">@CyclicPaths</span><span class="s">)</span> <span class="s">{</span> 3433 <span class="k">return</span> <span class="i">@Rings</span><span class="sc">;</span> 3434 <span class="s">}</span> 3435 <span class="k">if</span> <span class="s">(</span>!<span class="i">@CyclicPaths</span><span class="s">)</span> <span class="s">{</span> 3436 <span class="c"># Return an empty ring list...</span> 3437 <span class="k">return</span> <span class="i">@Rings</span><span class="sc">;</span> 3438 <span class="s">}</span> 3439 3440 <span class="k">for</span> <span class="i">$CyclicPath</span> <span class="s">(</span><span class="i">@CyclicPaths</span><span class="s">)</span> <span class="s">{</span> 3441 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span> 3442 <span class="i">@RingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3443 <span class="k">push</span> <span class="i">@RingAtoms</span><span class="cm">,</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$CyclicPath</span><span class="s">)</span><span class="sc">;</span> 3444 3445 <span class="k">push</span> <span class="i">@Rings</span><span class="cm">,</span> \<span class="i">@RingAtoms</span><span class="sc">;</span> 3446 <span class="s">}</span> 3447 <span class="k">return</span> <span class="i">@Rings</span><span class="sc">;</span> 3448 <span class="s">}</span> 3449 3450 <span class="c"># Get aromatic rings as an array containing references to arrays with ring atoms...</span> 3451 <span class="c">#</span> <a name="_GetAromaticRings-"></a>3452 <span class="k">sub </span><span class="m">_GetAromaticRings</span> <span class="s">{</span> 3453 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@CyclicPaths</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3454 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">@Rings</span><span class="cm">,</span> <span class="i">@AromaticRings</span><span class="s">)</span><span class="sc">;</span> 3455 3456 <span class="i">@AromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3457 <span class="i">@Rings</span> = <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">@CyclicPaths</span><span class="s">)</span><span class="sc">;</span> 3458 3459 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span> 3460 <span class="k">return</span> <span class="i">@AromaticRings</span><span class="sc">;</span> 3461 <span class="s">}</span> 3462 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span> 3463 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsRingAromatic</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3464 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span> 3465 <span class="s">}</span> 3466 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span> 3467 <span class="i">@RingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3468 <span class="k">push</span> <span class="i">@RingAtoms</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span> 3469 3470 <span class="k">push</span> <span class="i">@AromaticRings</span><span class="cm">,</span> \<span class="i">@RingAtoms</span><span class="sc">;</span> 3471 <span class="s">}</span> 3472 <span class="k">return</span> <span class="i">@AromaticRings</span><span class="sc">;</span> 3473 <span class="s">}</span> 3474 3475 <span class="c"># Map atom IDs in cyclic path to atoms and return a reference to an array containing ring atoms...</span> 3476 <span class="c">#</span> 3477 <span class="c"># Note:</span> 3478 <span class="c"># . Start and end vertex is same for cyclic paths. So end atom is removed before</span> 3479 <span class="c"># returning atoms array as ring atoms...</span> 3480 <span class="c">#</span> <a name="_GetRing-"></a>3481 <span class="k">sub </span><span class="m">_GetRing</span> <span class="s">{</span> 3482 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$CyclicPath</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3483 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span> 3484 3485 <span class="i">@RingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3486 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$CyclicPath</span><span class="s">)</span> <span class="s">{</span> 3487 <span class="c"># Return an empty atoms list...</span> 3488 <span class="k">return</span> <span class="i">@RingAtoms</span><span class="sc">;</span> 3489 <span class="s">}</span> 3490 3491 <span class="i">@RingAtoms</span> = <span class="i">$This</span><span class="i">->_GetPathAtoms</span><span class="s">(</span><span class="i">$CyclicPath</span><span class="s">)</span><span class="sc">;</span> 3492 <span class="k">if</span> <span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span> 3493 <span class="k">pop</span> <span class="i">@RingAtoms</span><span class="sc">;</span> 3494 <span class="s">}</span> 3495 <span class="k">return</span> <span class="i">@RingAtoms</span><span class="sc">;</span> 3496 <span class="s">}</span> 3497 3498 <span class="c"># Map atom IDs to atoms and return a reference to an array containing these atoms...</span> 3499 <span class="c">#</span> <a name="_GetPathAtoms-"></a>3500 <span class="k">sub </span><span class="m">_GetPathAtoms</span> <span class="s">{</span> 3501 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Path</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3502 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> 3503 3504 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3505 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Path</span><span class="s">)</span> <span class="s">{</span> 3506 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetPathAtoms: No path atoms retrieved: Path must be defined..."</span><span class="sc">;</span> 3507 <span class="k">return</span> <span class="i">@PathAtoms</span><span class="sc">;</span> 3508 <span class="s">}</span> 3509 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 3510 3511 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3512 <span class="i">@AtomIDs</span> = <span class="i">$Path</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3513 3514 <span class="i">@PathAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 3515 3516 <span class="k">return</span> <span class="i">@PathAtoms</span><span class="sc">;</span> 3517 <span class="s">}</span> 3518 3519 <span class="c"># Get bonds for a path specified by atom IDs...</span> 3520 <span class="c">#</span> <a name="_GetPathBonds-"></a>3521 <span class="k">sub </span><span class="m">_GetPathBonds</span> <span class="s">{</span> 3522 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3523 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="cm">,</span> <span class="i">@EdgesAtomIDs</span><span class="s">)</span><span class="sc">;</span> 3524 3525 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@EdgesAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3526 3527 <span class="k">if</span> <span class="s">(</span>!<span class="i">@AtomIDs</span> || <span class="i">@AtomIDs</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 3528 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span> 3529 <span class="s">}</span> 3530 3531 <span class="c"># Setup edges...</span> 3532 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$#AtomIDs</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> 3533 <span class="i">$AtomID1</span> = <span class="i">$AtomIDs</span>[<span class="i">$Index</span>]<span class="sc">;</span> 3534 <span class="i">$AtomID2</span> = <span class="i">$AtomIDs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> 3535 <span class="k">push</span> <span class="i">@EdgesAtomIDs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 3536 <span class="s">}</span> 3537 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetEdgesProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">@EdgesAtomIDs</span><span class="s">)</span><span class="sc">;</span> 3538 3539 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span> 3540 <span class="s">}</span> 3541 3542 <span class="c"># Map atom ID to an atom...</span> 3543 <span class="c">#</span> <a name="_GetAtomFromAtomID-"></a>3544 <span class="k">sub </span><span class="m">_GetAtomFromAtomID</span> <span class="s">{</span> 3545 <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="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3546 3547 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetVertexProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 3548 <span class="s">}</span> 3549 3550 <span class="c"># Map atom IDs to atoms and return an array containing these atoms...</span> 3551 <span class="c">#</span> <a name="_GetAtomsFromAtomIDs-"></a>3552 <span class="k">sub </span><span class="m">_GetAtomsFromAtomIDs</span> <span class="s">{</span> 3553 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3554 3555 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetVerticesProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 3556 <span class="s">}</span> 3557 3558 <span class="c"># Map atoms to atom IDs and return an array containing these atoms...</span> 3559 <span class="c">#</span> <a name="_GetAtomsIDsFromAtoms-"></a>3560 <span class="k">sub </span><span class="m">_GetAtomsIDsFromAtoms</span> <span class="s">{</span> 3561 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3562 3563 <span class="k">return</span> <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@Atoms</span><span class="sc">;</span> 3564 <span class="s">}</span> 3565 3566 <span class="c"># Get bonded atom pair atom IDs for specified list of atom IDs...</span> 3567 <span class="c">#</span> <a name="_GetBondedAtomPairAtomIDsFromAtomIDs-"></a>3568 <span class="k">sub </span><span class="m">_GetBondedAtomPairAtomIDsFromAtomIDs</span> <span class="s">{</span> 3569 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3570 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span> 3571 3572 <span class="i">@BondedAtomPairIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3573 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> 3574 3575 <span class="k">for</span> <span class="i">$AtomIndex1</span> <span class="s">(</span> <span class="n">0</span> .. <span class="i">$#Atoms</span><span class="s">)</span> <span class="s">{</span> 3576 <span class="i">$Atom1</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex1</span>]<span class="sc">;</span> 3577 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3578 3579 <span class="j">ATOMINDEX2:</span> <span class="k">for</span> <span class="i">$AtomIndex2</span> <span class="s">(</span> <span class="s">(</span><span class="i">$AtomIndex1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="i">$#Atoms</span><span class="s">)</span> <span class="s">{</span> 3580 <span class="i">$Atom2</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex2</span>]<span class="sc">;</span> 3581 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom1</span><span class="i">->IsBondedToAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3582 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span> 3583 <span class="s">}</span> 3584 <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3585 3586 <span class="k">push</span> <span class="i">@BondedAtomPairIDs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> 3587 <span class="s">}</span> 3588 <span class="s">}</span> 3589 3590 <span class="k">return</span> <span class="i">@BondedAtomPairIDs</span><span class="sc">;</span> 3591 <span class="s">}</span> 3592 3593 <span class="c"># Get bonded atom pair atoms for specified list of atoms...</span> 3594 <span class="c">#</span> <a name="_GetBondedAtomPairAtomsFromAtoms-"></a>3595 <span class="k">sub </span><span class="m">_GetBondedAtomPairAtomsFromAtoms</span> <span class="s">{</span> 3596 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3597 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">@BondedAtomPairAtoms</span><span class="s">)</span><span class="sc">;</span> 3598 3599 <span class="i">@BondedAtomPairAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3600 3601 <span class="k">for</span> <span class="i">$AtomIndex1</span> <span class="s">(</span> <span class="n">0</span> .. <span class="i">$#Atoms</span><span class="s">)</span> <span class="s">{</span> 3602 <span class="i">$Atom1</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex1</span>]<span class="sc">;</span> 3603 3604 <span class="j">ATOMINDEX2:</span> <span class="k">for</span> <span class="i">$AtomIndex2</span> <span class="s">(</span> <span class="s">(</span><span class="i">$AtomIndex1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="i">$#Atoms</span><span class="s">)</span> <span class="s">{</span> 3605 <span class="i">$Atom2</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex2</span>]<span class="sc">;</span> 3606 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsBondedToAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 3607 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span> 3608 <span class="s">}</span> 3609 3610 <span class="k">push</span> <span class="i">@BondedAtomPairAtoms</span><span class="cm">,</span> <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3611 <span class="s">}</span> 3612 <span class="s">}</span> 3613 3614 <span class="k">return</span> <span class="i">@BondedAtomPairAtoms</span><span class="sc">;</span> 3615 <span class="s">}</span> 3616 3617 <span class="c"># Is atom in a ring?</span> 3618 <span class="c">#</span> <a name="_IsAtomInRing-"></a>3619 <span class="k">sub </span><span class="m">_IsAtomInRing</span> <span class="s">{</span> 3620 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3621 3622 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsCyclicVertex</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3623 <span class="s">}</span> 3624 3625 <span class="c"># Is atom not in a ring?</span> 3626 <span class="c">#</span> <a name="_IsAtomNotInRing-"></a>3627 <span class="k">sub </span><span class="m">_IsAtomNotInRing</span> <span class="s">{</span> 3628 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3629 3630 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsAcyclicVertex</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3631 <span class="s">}</span> 3632 3633 <span class="c"># Is atom only in one ring?</span> 3634 <span class="c">#</span> <a name="_IsAtomInOnlyOneRing-"></a>3635 <span class="k">sub </span><span class="m">_IsAtomInOnlyOneRing</span> <span class="s">{</span> 3636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3637 3638 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUnicyclicVertex</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3639 <span class="s">}</span> 3640 3641 <span class="c"># Is atom in a ring of specified size?</span> 3642 <span class="c">#</span> <a name="_IsAtomInRingOfSize-"></a>3643 <span class="k">sub </span><span class="m">_IsAtomInRingOfSize</span> <span class="s">{</span> 3644 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3645 3646 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3647 <span class="s">}</span> 3648 3649 <span class="c"># Get size of smallest ring containing specified atom...</span> 3650 <span class="c">#</span> <a name="_GetSizeOfSmallestAtomRing-"></a>3651 <span class="k">sub </span><span class="m">_GetSizeOfSmallestAtomRing</span> <span class="s">{</span> 3652 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3653 3654 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfSmallestVertexCycle</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3655 <span class="s">}</span> 3656 3657 <span class="c"># Get size of largest ring containing specified atom...</span> 3658 <span class="c">#</span> <a name="_GetSizeOfLargestAtomRing-"></a>3659 <span class="k">sub </span><span class="m">_GetSizeOfLargestAtomRing</span> <span class="s">{</span> 3660 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3661 3662 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfLargestVertexCycle</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3663 <span class="s">}</span> 3664 3665 <span class="c"># Get number of rings containing specified atom...</span> 3666 <span class="c">#</span> <a name="_GetNumOfAtomRings-"></a>3667 <span class="k">sub </span><span class="m">_GetNumOfAtomRings</span> <span class="s">{</span> 3668 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3669 3670 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCycles</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3671 <span class="s">}</span> 3672 3673 <span class="c"># Get number of rings with odd size containing specified atom...</span> 3674 <span class="c">#</span> <a name="_GetNumOfAtomRingsWithOddSize-"></a>3675 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithOddSize</span> <span class="s">{</span> 3676 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3677 3678 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithOddSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3679 <span class="s">}</span> 3680 3681 <span class="c"># Get number of rings with even size containing specified atom...</span> 3682 <span class="c">#</span> <a name="_GetNumOfAtomRingsWithEvenSize-"></a>3683 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithEvenSize</span> <span class="s">{</span> 3684 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3685 3686 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithEvenSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3687 <span class="s">}</span> 3688 3689 <span class="c"># Get number of rings with specified size containing specified atom...</span> 3690 <span class="c">#</span> <a name="_GetNumOfAtomRingsWithSize-"></a>3691 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithSize</span> <span class="s">{</span> 3692 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3693 3694 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3695 <span class="s">}</span> 3696 3697 <span class="c"># Get number of rings with size less than specified containing specified atom...</span> 3698 <span class="c">#</span> <a name="_GetNumOfAtomRingsWithSizeLessThan-"></a>3699 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithSizeLessThan</span> <span class="s">{</span> 3700 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3701 3702 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3703 <span class="s">}</span> 3704 3705 <span class="c"># Get number of rings with size greater than specified containing specified atom...</span> 3706 <span class="c">#</span> <a name="_GetNumOfAtomRingsWithSizeGreaterThan-"></a>3707 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithSizeGreaterThan</span> <span class="s">{</span> 3708 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3709 3710 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3711 <span class="s">}</span> 3712 3713 <span class="c"># Get smallest ring as an array containing ring atoms...</span> 3714 <span class="c">#</span> <a name="_GetSmallestAtomRing-"></a>3715 <span class="k">sub </span><span class="m">_GetSmallestAtomRing</span> <span class="s">{</span> 3716 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3717 3718 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetSmallestVertexCycle</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3719 <span class="s">}</span> 3720 3721 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> 3722 <span class="c">#</span> <a name="_GetLargestAtomRing-"></a>3723 <span class="k">sub </span><span class="m">_GetLargestAtomRing</span> <span class="s">{</span> 3724 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3725 3726 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetLargestVertexCycle</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3727 <span class="s">}</span> 3728 3729 <span class="c"># Get all rings an array of references to arrays containing ring atoms...</span> 3730 <span class="c">#</span> <a name="_GetAtomRings-"></a>3731 <span class="k">sub </span><span class="m">_GetAtomRings</span> <span class="s">{</span> 3732 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3733 3734 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCycles</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3735 <span class="s">}</span> 3736 3737 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> 3738 <span class="c">#</span> <a name="_GetAtomRingsWithOddSize-"></a>3739 <span class="k">sub </span><span class="m">_GetAtomRingsWithOddSize</span> <span class="s">{</span> 3740 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3741 3742 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCyclesWithOddSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3743 <span class="s">}</span> 3744 3745 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span> 3746 <span class="c">#</span> <a name="_GetAtomRingsWithEvenSize-"></a>3747 <span class="k">sub </span><span class="m">_GetAtomRingsWithEvenSize</span> <span class="s">{</span> 3748 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3749 3750 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCyclesWithEvenSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3751 <span class="s">}</span> 3752 3753 <span class="c"># Get rings with specified size an array of references to arrays containing ring atoms...</span> 3754 <span class="c">#</span> <a name="_GetAtomRingsWithSize-"></a>3755 <span class="k">sub </span><span class="m">_GetAtomRingsWithSize</span> <span class="s">{</span> 3756 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3757 3758 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCyclesWithSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3759 <span class="s">}</span> 3760 3761 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> 3762 <span class="c">#</span> <a name="_GetAtomRingsWithSizeLessThan-"></a>3763 <span class="k">sub </span><span class="m">_GetAtomRingsWithSizeLessThan</span> <span class="s">{</span> 3764 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3765 3766 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3767 <span class="s">}</span> 3768 3769 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> 3770 <span class="c">#</span> <a name="_GetAtomRingsWithSizeGreaterThan-"></a>3771 <span class="k">sub </span><span class="m">_GetAtomRingsWithSizeGreaterThan</span> <span class="s">{</span> 3772 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3773 3774 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3775 <span class="s">}</span> 3776 3777 <span class="c"># Is bond in a ring?</span> 3778 <span class="c">#</span> <a name="_IsBondInRing-"></a>3779 <span class="k">sub </span><span class="m">_IsBondInRing</span> <span class="s">{</span> 3780 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3781 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3782 3783 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3784 3785 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsCyclicEdge</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3786 <span class="s">}</span> 3787 3788 <span class="c"># Is bond not in a ring?</span> 3789 <span class="c">#</span> <a name="_IsBondNotInRing-"></a>3790 <span class="k">sub </span><span class="m">_IsBondNotInRing</span> <span class="s">{</span> 3791 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3792 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3793 3794 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3795 3796 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsAcyclicEdge</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3797 <span class="s">}</span> 3798 3799 <span class="c"># Is bond only in one ring?</span> 3800 <span class="c">#</span> <a name="_IsBondInOnlyOneRing-"></a>3801 <span class="k">sub </span><span class="m">_IsBondInOnlyOneRing</span> <span class="s">{</span> 3802 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3803 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3804 3805 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3806 3807 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUnicyclicEdge</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3808 <span class="s">}</span> 3809 3810 <span class="c"># Is bond in a ring of specified size?</span> 3811 <span class="c">#</span> <a name="_IsBondInRingOfSize-"></a>3812 <span class="k">sub </span><span class="m">_IsBondInRingOfSize</span> <span class="s">{</span> 3813 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3814 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3815 3816 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3817 3818 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 3819 <span class="s">}</span> 3820 3821 <span class="c"># Get size of smallest ring containing specified bond...</span> 3822 <span class="c">#</span> <a name="_GetSizeOfSmallestBondRing-"></a>3823 <span class="k">sub </span><span class="m">_GetSizeOfSmallestBondRing</span> <span class="s">{</span> 3824 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3825 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3826 3827 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3828 3829 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfSmallestEdgeCycle</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3830 <span class="s">}</span> 3831 3832 <span class="c"># Get size of largest ring containing specified bond...</span> 3833 <span class="c">#</span> <a name="_GetSizeOfLargestBondRing-"></a>3834 <span class="k">sub </span><span class="m">_GetSizeOfLargestBondRing</span> <span class="s">{</span> 3835 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3836 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3837 3838 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3839 3840 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfLargestEdgeCycle</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3841 <span class="s">}</span> 3842 3843 <span class="c"># Get number of rings containing specified bond...</span> 3844 <span class="c">#</span> <a name="_GetNumOfBondRings-"></a>3845 <span class="k">sub </span><span class="m">_GetNumOfBondRings</span> <span class="s">{</span> 3846 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3847 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3848 3849 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3850 3851 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCycles</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3852 <span class="s">}</span> 3853 3854 <span class="c"># Get number of rings with odd size containing specified bond...</span> 3855 <span class="c">#</span> <a name="_GetNumOfBondRingsWithOddSize-"></a>3856 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithOddSize</span> <span class="s">{</span> 3857 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3858 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3859 3860 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3861 3862 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithOddSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3863 <span class="s">}</span> 3864 3865 <span class="c"># Get number of rings with even size containing specified bond...</span> 3866 <span class="c">#</span> <a name="_GetNumOfBondRingsWithEvenSize-"></a>3867 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithEvenSize</span> <span class="s">{</span> 3868 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3869 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3870 3871 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3872 3873 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithEvenSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3874 <span class="s">}</span> 3875 3876 <span class="c"># Get number of rings with specified size containing specified bond...</span> 3877 <span class="c">#</span> <a name="_GetNumOfBondRingsWithSize-"></a>3878 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithSize</span> <span class="s">{</span> 3879 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3880 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3881 3882 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3883 3884 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3885 <span class="s">}</span> 3886 3887 <span class="c"># Get number of rings with size less than specified containing specified bond...</span> 3888 <span class="c">#</span> <a name="_GetNumOfBondRingsWithSizeLessThan-"></a>3889 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithSizeLessThan</span> <span class="s">{</span> 3890 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3891 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3892 3893 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3894 3895 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3896 <span class="s">}</span> 3897 3898 <span class="c"># Get number of rings with size greater than specified containing specified bond...</span> 3899 <span class="c">#</span> <a name="_GetNumOfBondRingsWithSizeGreaterThan-"></a>3900 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithSizeGreaterThan</span> <span class="s">{</span> 3901 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3902 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3903 3904 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3905 3906 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> 3907 <span class="s">}</span> 3908 3909 <span class="c"># Get smallest ring as an array containing ring atoms...</span> 3910 <span class="c">#</span> <a name="_GetSmallestBondRing-"></a>3911 <span class="k">sub </span><span class="m">_GetSmallestBondRing</span> <span class="s">{</span> 3912 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3913 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3914 3915 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3916 3917 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetSmallestEdgeCycle</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3918 <span class="s">}</span> 3919 3920 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> 3921 <span class="c">#</span> <a name="_GetLargestBondRing-"></a>3922 <span class="k">sub </span><span class="m">_GetLargestBondRing</span> <span class="s">{</span> 3923 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3924 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3925 3926 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3927 3928 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetLargestEdgeCycle</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3929 <span class="s">}</span> 3930 3931 <span class="c"># Get all rings an array of references to arrays containing ring atoms...</span> 3932 <span class="c">#</span> <a name="_GetBondRings-"></a>3933 <span class="k">sub </span><span class="m">_GetBondRings</span> <span class="s">{</span> 3934 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3935 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3936 3937 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3938 3939 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCycles</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3940 <span class="s">}</span> 3941 3942 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> 3943 <span class="c">#</span> <a name="_GetBondRingsWithOddSize-"></a>3944 <span class="k">sub </span><span class="m">_GetBondRingsWithOddSize</span> <span class="s">{</span> 3945 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3946 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3947 3948 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3949 3950 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCyclesWithOddSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3951 <span class="s">}</span> 3952 3953 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span> 3954 <span class="c">#</span> <a name="_GetBondRingsWithEvenSize-"></a>3955 <span class="k">sub </span><span class="m">_GetBondRingsWithEvenSize</span> <span class="s">{</span> 3956 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3957 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3958 3959 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3960 3961 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCyclesWithEvenSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3962 <span class="s">}</span> 3963 3964 <span class="c"># Get rings with specified size an array of references to arrays containing ring atoms...</span> 3965 <span class="c">#</span> <a name="_GetBondRingsWithSize-"></a>3966 <span class="k">sub </span><span class="m">_GetBondRingsWithSize</span> <span class="s">{</span> 3967 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3968 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3969 3970 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3971 3972 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCyclesWithSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3973 <span class="s">}</span> 3974 3975 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> 3976 <span class="c">#</span> <a name="_GetBondRingsWithSizeLessThan-"></a>3977 <span class="k">sub </span><span class="m">_GetBondRingsWithSizeLessThan</span> <span class="s">{</span> 3978 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3979 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3980 3981 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3982 3983 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3984 <span class="s">}</span> 3985 3986 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> 3987 <span class="c">#</span> <a name="_GetBondRingsWithSizeGreaterThan-"></a>3988 <span class="k">sub </span><span class="m">_GetBondRingsWithSizeGreaterThan</span> <span class="s">{</span> 3989 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 3990 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> 3991 3992 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 3993 3994 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> 3995 <span class="s">}</span> 3996 3997 3998 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> 3999 <span class="c"># to arrays with path atoms.</span> 4000 <span class="c">#</span> 4001 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with length</span> 4002 <span class="c"># upto a specified length and sharing of bonds in paths traversed. By default, rings are</span> 4003 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4004 <span class="c">#</span> 4005 <span class="c"># Note:</span> 4006 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> 4007 <span class="c"># as GetAtomPathsStartingAtWithLengthUpto method.</span> 4008 <span class="c">#</span> <a name="GetAllAtomPathsStartingAtWithLengthUpto-"></a>4009 <span class="k">sub </span><span class="m">GetAllAtomPathsStartingAtWithLengthUpto</span> <span class="s">{</span> 4010 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4011 4012 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AllAtomPathsWithLengthUpto'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4013 <span class="s">}</span> 4014 4015 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> 4016 <span class="c"># to arrays with path atoms.</span> 4017 <span class="c">#</span> 4018 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with</span> 4019 <span class="c"># specified length and sharing of bonds in paths traversed. By default, rings are</span> 4020 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4021 <span class="c">#</span> 4022 <span class="c"># Note:</span> 4023 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> 4024 <span class="c"># as GetAtomPathsStartingAtWithLengthUpto method.</span> 4025 <span class="c">#</span> <a name="GetAllAtomPathsStartingAtWithLength-"></a>4026 <span class="k">sub </span><span class="m">GetAllAtomPathsStartingAtWithLength</span> <span class="s">{</span> 4027 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4028 4029 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AllAtomPathsWithLength'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4030 <span class="s">}</span> 4031 4032 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> 4033 <span class="c"># to arrays with path atoms.</span> 4034 <span class="c">#</span> 4035 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with all</span> 4036 <span class="c"># possible lengths and sharing of bonds in paths traversed. By default, rings are</span> 4037 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4038 <span class="c">#</span> 4039 <span class="c"># Note:</span> 4040 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> 4041 <span class="c"># as GetAtomPathsStartingAt method.</span> 4042 <span class="c">#</span> <a name="GetAllAtomPathsStartingAt-"></a>4043 <span class="k">sub </span><span class="m">GetAllAtomPathsStartingAt</span> <span class="s">{</span> 4044 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4045 4046 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AllAtomPathsWithAllLengths'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4047 <span class="s">}</span> 4048 4049 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> 4050 <span class="c"># to arrays with path atoms.</span> 4051 <span class="c">#</span> 4052 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with length</span> 4053 <span class="c"># upto a specified length and no sharing of bonds in paths traversed. By default, rings are</span> 4054 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4055 <span class="c">#</span> <a name="GetAtomPathsStartingAtWithLengthUpto-"></a>4056 <span class="k">sub </span><span class="m">GetAtomPathsStartingAtWithLengthUpto</span> <span class="s">{</span> 4057 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4058 4059 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AtomPathsWithLengthUpto'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4060 <span class="s">}</span> 4061 4062 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> 4063 <span class="c"># to arrays with path atoms.</span> 4064 <span class="c">#</span> 4065 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with</span> 4066 <span class="c"># specified length and no sharing of bonds in paths traversed. By default, rings are</span> 4067 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4068 <span class="c">#</span> <a name="GetAtomPathsStartingAtWithLength-"></a>4069 <span class="k">sub </span><span class="m">GetAtomPathsStartingAtWithLength</span> <span class="s">{</span> 4070 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4071 4072 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AtomPathsWithLength'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4073 <span class="s">}</span> 4074 4075 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> 4076 <span class="c"># to arrays with path atoms.</span> 4077 <span class="c">#</span> 4078 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with all</span> 4079 <span class="c"># possible lengths and no sharing of bonds in paths traversed. By default, rings are</span> 4080 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4081 <span class="c">#</span> 4082 <span class="c">#</span> <a name="GetAtomPathsStartingAt-"></a>4083 <span class="k">sub </span><span class="m">GetAtomPathsStartingAt</span> <span class="s">{</span> 4084 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4085 4086 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AtomPathsWithAllLengths'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4087 <span class="s">}</span> 4088 4089 <span class="c"># Get atom paths as an array containing references to arrays with path atoms...</span> 4090 <span class="c">#</span> <a name="_GetAtomPathsStartingAt-"></a>4091 <span class="k">sub </span><span class="m">_GetAtomPathsStartingAt</span> <span class="s">{</span> 4092 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4093 <span class="k">my</span><span class="s">(</span><span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span> 4094 4095 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4096 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$StartAtom</span><span class="s">)</span> <span class="s">{</span> 4097 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Start atom is not defined..."</span><span class="sc">;</span> 4098 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span> 4099 <span class="s">}</span> 4100 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4101 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Start atom doesn't exist..."</span><span class="sc">;</span> 4102 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span> 4103 <span class="s">}</span> 4104 <span class="k">my</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span> 4105 4106 <span class="i">$StartAtomID</span> = <span class="i">$StartAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4107 <span class="i">@Paths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4108 4109 <span class="c"># Collect appropriate atom paths...</span> 4110 <span class="j">MODE:</span> <span class="s">{</span> 4111 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithLengthUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetPathsStartingAtWithLengthUpto</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4112 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithLength$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetPathsStartingAtWithLength</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4113 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithAllLengths$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetPathsStartingAt</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4114 4115 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithLengthUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetAllPathsStartingAtWithLengthUpto</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4116 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithLength$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetAllPathsStartingAtWithLength</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4117 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithAllLengths$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetAllPathsStartingAt</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4118 4119 <span class="k">print</span> <span class="q">"Warn: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Mode, $Mode, is not supported..."</span><span class="sc">;</span> 4120 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span> 4121 <span class="s">}</span> 4122 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsFromPaths</span><span class="s">(</span>\<span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span> 4123 <span class="s">}</span> 4124 4125 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> 4126 <span class="c"># path atoms.</span> 4127 <span class="c">#</span> 4128 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with length</span> 4129 <span class="c"># upto a specified length and sharing of bonds in paths traversed. By default, rings are</span> 4130 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4131 <span class="c">#</span> 4132 <span class="c"># Notes:</span> 4133 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> 4134 <span class="c"># as GetAtomPathsWithLengthUpto method.</span> 4135 <span class="c">#</span> <a name="GetAllAtomPathsWithLengthUpto-"></a>4136 <span class="k">sub </span><span class="m">GetAllAtomPathsWithLengthUpto</span> <span class="s">{</span> 4137 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4138 4139 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AllAtomPathsWithLengthUpto'</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4140 <span class="s">}</span> 4141 4142 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> 4143 <span class="c"># path atoms.</span> 4144 <span class="c">#</span> 4145 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with</span> 4146 <span class="c"># a specified length and sharing of bonds in paths traversed. By default, rings are</span> 4147 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4148 <span class="c">#</span> 4149 <span class="c"># Notes:</span> 4150 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> 4151 <span class="c"># as GetAtomPathsWithLengthUpto method.</span> 4152 <span class="c">#</span> <a name="GetAllAtomPathsWithLength-"></a>4153 <span class="k">sub </span><span class="m">GetAllAtomPathsWithLength</span> <span class="s">{</span> 4154 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4155 4156 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AllAtomPathsWithLength'</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4157 <span class="s">}</span> 4158 4159 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> 4160 <span class="c"># path atoms.</span> 4161 <span class="c">#</span> 4162 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with all</span> 4163 <span class="c"># possible lengths and sharing of bonds in paths traversed. By default, rings are</span> 4164 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4165 <span class="c">#</span> 4166 <span class="c"># Notes:</span> 4167 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> 4168 <span class="c"># as GetAtomPaths method.</span> 4169 <span class="c">#</span> <a name="GetAllAtomPaths-"></a>4170 <span class="k">sub </span><span class="m">GetAllAtomPaths</span> <span class="s">{</span> 4171 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4172 4173 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AllAtomPathsWithAllLengths'</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4174 <span class="s">}</span> 4175 4176 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> 4177 <span class="c"># path atoms.</span> 4178 <span class="c">#</span> 4179 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with length</span> 4180 <span class="c"># upto a specified length and no sharing of bonds in paths traversed. By default, rings are</span> 4181 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4182 <span class="c">#</span> <a name="GetAtomPathsWithLengthUpto-"></a>4183 <span class="k">sub </span><span class="m">GetAtomPathsWithLengthUpto</span> <span class="s">{</span> 4184 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4185 4186 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AtomPathsWithLengthUpto'</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4187 <span class="s">}</span> 4188 4189 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> 4190 <span class="c"># path atoms.</span> 4191 <span class="c">#</span> 4192 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with</span> 4193 <span class="c"># a specified length and no sharing of bonds in paths traversed. By default, rings are</span> 4194 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4195 <span class="c">#</span> <a name="GetAtomPathsWithLength-"></a>4196 <span class="k">sub </span><span class="m">GetAtomPathsWithLength</span> <span class="s">{</span> 4197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4198 4199 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AtomPathsWithLength'</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4200 <span class="s">}</span> 4201 4202 4203 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> 4204 <span class="c"># path atoms.</span> 4205 <span class="c">#</span> 4206 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with all</span> 4207 <span class="c"># possible lengths and no sharing of bonds in paths traversed. By default, rings are</span> 4208 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> 4209 <span class="c">#</span> <a name="GetAtomPaths-"></a>4210 <span class="k">sub </span><span class="m">GetAtomPaths</span> <span class="s">{</span> 4211 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4212 4213 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AtomPathsWithAllLengths'</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> 4214 <span class="s">}</span> 4215 4216 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> 4217 <span class="c"># path atoms.</span> 4218 <span class="c">#</span> <a name="_GetAtomPaths-"></a>4219 <span class="k">sub </span><span class="m">_GetAtomPaths</span> <span class="s">{</span> 4220 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4221 <span class="k">my</span><span class="s">(</span><span class="i">$PathsRef</span><span class="cm">,</span> <span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span> 4222 4223 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4224 <span class="c"># Collect appropriate atom paths...</span> 4225 <span class="j">MODE:</span> <span class="s">{</span> 4226 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithLengthUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetPathsWithLengthUpto</span><span class="s">(</span><span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4227 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithLength$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetPathsWithLength</span><span class="s">(</span><span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4228 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithAllLengths$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetPaths</span><span class="s">(</span><span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4229 4230 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithLengthUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetAllPathsWithLengthUpto</span><span class="s">(</span><span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4231 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithLength$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetAllPathsWithLength</span><span class="s">(</span><span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4232 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithAllLengths$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetAllPaths</span><span class="s">(</span><span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4233 4234 <span class="k">print</span> <span class="q">"Warn: ${ClassName}->_GetAtomPaths: No atom paths retrieved: Mode, $Mode, is not supported..."</span><span class="sc">;</span> 4235 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span> 4236 <span class="s">}</span> 4237 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsFromPaths</span><span class="s">(</span><span class="i">$PathsRef</span><span class="s">)</span><span class="sc">;</span> 4238 <span class="s">}</span> 4239 4240 <span class="c"># Get atom paths as an array reference containing references to arrays with path atoms...</span> 4241 <span class="c">#</span> <a name="_GetAtomPathsFromPaths-"></a>4242 <span class="k">sub </span><span class="m">_GetAtomPathsFromPaths</span> <span class="s">{</span> 4243 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4244 <span class="k">my</span><span class="s">(</span><span class="i">$Path</span><span class="cm">,</span> <span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span> 4245 4246 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4247 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$PathsRef</span><span class="s">)</span> <span class="s">{</span> 4248 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span> 4249 <span class="s">}</span> 4250 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$PathsRef</span>}<span class="s">)</span> <span class="s">{</span> 4251 <span class="c"># Return an empty atom paths list...</span> 4252 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span> 4253 <span class="s">}</span> 4254 <span class="k">for</span> <span class="i">$Path</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathsRef</span>}<span class="s">)</span> <span class="s">{</span> 4255 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> 4256 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4257 <span class="i">@PathAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomPathFromPath</span><span class="s">(</span><span class="i">$Path</span><span class="s">)</span><span class="sc">;</span> 4258 4259 <span class="k">push</span> <span class="i">@AtomPaths</span><span class="cm">,</span> \<span class="i">@PathAtoms</span><span class="sc">;</span> 4260 <span class="s">}</span> 4261 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span> 4262 <span class="s">}</span> 4263 4264 <span class="c"># Generate an array of bond objects for an array of path atoms and return an array</span> 4265 <span class="c"># of bond objects...</span> 4266 <span class="c">#</span> <a name="GetAtomPathBonds-"></a>4267 <span class="k">sub </span><span class="m">GetAtomPathBonds</span> <span class="s">{</span> 4268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@PathAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4269 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> 4270 4271 <span class="k">if</span> <span class="s">(</span>!<span class="i">@PathAtoms</span><span class="s">)</span> <span class="s">{</span> 4272 <span class="c"># Return an empty ring bonds list...</span> 4273 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span> 4274 <span class="s">}</span> 4275 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span> 4276 4277 <span class="i">@PathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4278 <span class="i">@PathAtomIDs</span> = <span class="i">$This</span><span class="i">->_GetAtomsIDsFromAtoms</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> 4279 4280 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPathBonds</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span> 4281 <span class="s">}</span> 4282 4283 <span class="c"># Map atom IDs in path to atoms and return a reference to an array containing ring atoms...</span> 4284 <span class="c">#</span> <a name="_GetAtomPathFromPath-"></a>4285 <span class="k">sub </span><span class="m">_GetAtomPathFromPath</span> <span class="s">{</span> 4286 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Path</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4287 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> 4288 4289 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4290 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Path</span><span class="s">)</span> <span class="s">{</span> 4291 <span class="c"># Return an empty atoms list...</span> 4292 <span class="k">return</span> <span class="i">@PathAtoms</span><span class="sc">;</span> 4293 <span class="s">}</span> 4294 4295 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPathAtoms</span><span class="s">(</span><span class="i">$Path</span><span class="s">)</span><span class="sc">;</span> 4296 <span class="s">}</span> 4297 4298 <span class="c"># Get atom paths between two specified atoms as a reference to an array containing references</span> 4299 <span class="c"># to arrays with path atoms. For molecules with rings, atom paths array contains may contain</span> 4300 <span class="c"># two paths.</span> 4301 <span class="c">#</span> <a name="GetAtomPathsBetween-"></a>4302 <span class="k">sub </span><span class="m">GetAtomPathsBetween</span> <span class="s">{</span> 4303 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$EndAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4304 <span class="k">my</span><span class="s">(</span><span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span> 4305 4306 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4307 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4308 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsBetween: No atom paths retrieved: Start atom is not defined or it doesn't exist..."</span><span class="sc">;</span> 4309 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span> 4310 <span class="s">}</span> 4311 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$EndAtom</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$EndAtom</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4312 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsBetween: No atom paths retrieved: End atom is not defined or it doesn't exist..."</span><span class="sc">;</span> 4313 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span> 4314 <span class="s">}</span> 4315 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsBetween</span><span class="s">(</span><span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$EndAtom</span><span class="s">)</span><span class="sc">;</span> 4316 <span class="s">}</span> 4317 4318 <span class="c"># Get atom paths between two specified atoms as a reference to an array containing references</span> 4319 <span class="c"># to arrays with path atoms.</span> 4320 <span class="c">#</span> <a name="_GetAtomPathsBetween-"></a>4321 <span class="k">sub </span><span class="m">_GetAtomPathsBetween</span> <span class="s">{</span> 4322 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$EndAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4323 <span class="k">my</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$EndAtomID</span><span class="cm">,</span> <span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span> 4324 4325 <span class="i">$StartAtomID</span> = <span class="i">$StartAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4326 <span class="i">$EndAtomID</span> = <span class="i">$EndAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4327 4328 <span class="i">@Paths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4329 <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetPathsBetween</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$EndAtomID</span><span class="s">)</span><span class="sc">;</span> 4330 4331 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsFromPaths</span><span class="s">(</span>\<span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span> 4332 <span class="s">}</span> 4333 4334 <span class="c"># Get atom neighborhoods around a specified atom as an array containing references</span> 4335 <span class="c"># to arrays with neighborhood atoms at different radii upto specified radius...</span> 4336 <span class="c">#</span> <a name="GetAtomNeighborhoodsWithRadiusUpto-"></a>4337 <span class="k">sub </span><span class="m">GetAtomNeighborhoodsWithRadiusUpto</span> <span class="s">{</span> 4338 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4339 4340 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="q">'RadiusUpto'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="sc">;</span> 4341 <span class="s">}</span> 4342 4343 <span class="c"># Get atom neighborhoods around a specified atom as an array containing references</span> 4344 <span class="c"># to arrays with neighborhood atoms at possible radii...</span> 4345 <span class="c">#</span> <a name="GetAtomNeighborhoods-"></a>4346 <span class="k">sub </span><span class="m">GetAtomNeighborhoods</span> <span class="s">{</span> 4347 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4348 4349 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="q">'AllRadii'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> 4350 <span class="s">}</span> 4351 4352 <span class="c"># Get atom neighborhood around a specified atom, along with their successor connected atoms, collected</span> 4353 <span class="c"># with in a specified radius as a list containing references to lists with first value corresponding to neighborhood</span> 4354 <span class="c"># atom at a specific radius and second value as reference to a list containing its successor connected atoms.</span> 4355 <span class="c">#</span> 4356 <span class="c"># For a neighborhood atom at each radius level, the successor connected atoms correspond to the</span> 4357 <span class="c"># neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last</span> 4358 <span class="c"># radius level don't contain any successor atoms which fall outside the range of specified radius.</span> 4359 <span class="c">#</span> <a name="GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto-"></a>4360 <span class="k">sub </span><span class="m">GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto</span> <span class="s">{</span> 4361 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4362 4363 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="q">'WithSuccessorsAndRadiusUpto'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="sc">;</span> 4364 <span class="s">}</span> 4365 4366 <span class="c"># Get atom neighborhood around a specified atom, along with their successor connected atoms, collected</span> 4367 <span class="c"># at all radii as a list containing references to lists with first value corresponding to neighborhood</span> 4368 <span class="c"># atom at a specific radius and second value as reference to a list containing its successor connected atoms.</span> 4369 <span class="c">#</span> 4370 <span class="c"># For a neighborhood atom at each radius level, the successor connected atoms correspond to the</span> 4371 <span class="c"># neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last</span> 4372 <span class="c"># radius level don't contain any successor atoms which fall outside the range of specified radius.</span> 4373 <span class="c">#</span> 4374 <span class="c">#</span> <a name="GetAtomNeighborhoodsWithSuccessorAtoms-"></a>4375 <span class="k">sub </span><span class="m">GetAtomNeighborhoodsWithSuccessorAtoms</span> <span class="s">{</span> 4376 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4377 4378 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="q">'WithSuccessorsAndAllRadii'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> 4379 <span class="s">}</span> 4380 4381 <span class="c"># Get atom neighborhoods...</span> 4382 <span class="c">#</span> <a name="_GetAtomNeighborhoods-"></a>4383 <span class="k">sub </span><span class="m">_GetAtomNeighborhoods</span> <span class="s">{</span> 4384 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4385 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighborhoods</span><span class="s">)</span><span class="sc">;</span> 4386 4387 <span class="i">@AtomNeighborhoods</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4388 4389 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4390 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomNeighborhoods: No atom neighborhoods retrieved: Start atom is not defined or it doesn't exist..."</span><span class="sc">;</span> 4391 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> 4392 <span class="s">}</span> 4393 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(RadiusUpto|WithSuccessorsAndRadiusUpto)$/i</span><span class="s">)</span> <span class="s">{</span> 4394 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Radius</span><span class="s">)</span> && <span class="i">$Radius</span> > <span class="n">0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4395 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomNeighborhoods: No atom neighborhoods retrieved: Radius is not defined or it's <= 0 ..."</span><span class="sc">;</span> 4396 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> 4397 <span class="s">}</span> 4398 <span class="s">}</span> 4399 4400 <span class="c"># Collect neighborhood atom IDs...</span> 4401 <span class="k">my</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">@NeighborhoodAtomIDs</span><span class="cm">,</span> <span class="i">@NeighborhoodAtomIDsWithSuccessors</span><span class="s">)</span><span class="sc">;</span> 4402 4403 <span class="i">@NeighborhoodAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@NeighborhoodAtomIDsWithSuccessors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4404 <span class="i">$StartAtomID</span> = <span class="i">$StartAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4405 4406 <span class="j">MODE:</span> <span class="s">{</span> 4407 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RadiusUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@NeighborhoodAtomIDs</span> = <span class="i">$This</span><span class="i">->GetNeighborhoodVerticesWithRadiusUpto</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4408 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllRadii$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@NeighborhoodAtomIDs</span> = <span class="i">$This</span><span class="i">->GetNeighborhoodVertices</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4409 4410 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^WithSuccessorsAndRadiusUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@NeighborhoodAtomIDsWithSuccessors</span> = <span class="i">$This</span><span class="i">->GetNeighborhoodVerticesWithSuccessorsAndRadiusUpto</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4411 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^WithSuccessorsAndAllRadii$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@NeighborhoodAtomIDsWithSuccessors</span> = <span class="i">$This</span><span class="i">->GetNeighborhoodVerticesWithSuccessors</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 4412 4413 <span class="k">print</span> <span class="q">"Warn: ${ClassName}->_GetAtomNeighborhood: No atom neighborhoods retrieved: Mode, $Mode, is not supported..."</span><span class="sc">;</span> 4414 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> 4415 <span class="s">}</span> 4416 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(RadiusUpto|AllRadii)$/i</span><span class="s">)</span> <span class="s">{</span> 4417 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNeighborhoodAtomsFromAtomIDs</span><span class="s">(</span>\<span class="i">@NeighborhoodAtomIDs</span><span class="s">)</span><span class="sc">;</span> 4418 <span class="s">}</span> 4419 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(WithSuccessorsAndRadiusUpto|WithSuccessorsAndAllRadii)$/i</span><span class="s">)</span> <span class="s">{</span> 4420 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNeighborhoodAtomsWithSuccessorsFromAtomIDs</span><span class="s">(</span>\<span class="i">@NeighborhoodAtomIDsWithSuccessors</span><span class="s">)</span><span class="sc">;</span> 4421 <span class="s">}</span> 4422 4423 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> 4424 <span class="s">}</span> 4425 4426 <span class="c"># Map neighborhood atom IDs to atoms...</span> 4427 <span class="c">#</span> <a name="_GetNeighborhoodAtomsFromAtomIDs-"></a>4428 <span class="k">sub </span><span class="m">_GetNeighborhoodAtomsFromAtomIDs</span> <span class="s">{</span> 4429 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NeighborhoodsAtomIDsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4430 <span class="k">my</span><span class="s">(</span><span class="i">$NeighborhoodAtomIDsRef</span><span class="cm">,</span> <span class="i">@AtomNeighborhoods</span><span class="s">)</span><span class="sc">;</span> 4431 4432 <span class="i">@AtomNeighborhoods</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4433 <span class="k">for</span> <span class="i">$NeighborhoodAtomIDsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodsAtomIDsRef</span>}<span class="s">)</span> <span class="s">{</span> 4434 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighborhood</span><span class="s">)</span><span class="sc">;</span> 4435 4436 <span class="i">@AtomNeighborhood</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4437 <span class="i">@AtomNeighborhood</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomIDsRef</span>}<span class="s">)</span><span class="sc">;</span> 4438 <span class="k">push</span> <span class="i">@AtomNeighborhoods</span><span class="cm">,</span> \<span class="i">@AtomNeighborhood</span><span class="sc">;</span> 4439 <span class="s">}</span> 4440 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> 4441 <span class="s">}</span> 4442 4443 <span class="c"># Map neighborhood atom IDs with successors to atoms...</span> 4444 <span class="c">#</span> <a name="_GetNeighborhoodAtomsWithSuccessorsFromAtomIDs-"></a>4445 <span class="k">sub </span><span class="m">_GetNeighborhoodAtomsWithSuccessorsFromAtomIDs</span> <span class="s">{</span> 4446 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NeighborhoodsAtomIDsWithSuccessorsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4447 <span class="k">my</span><span class="s">(</span><span class="i">$Depth</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomIDsWithSuccessorsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomIDWithSuccessorsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorsIDsRef</span><span class="cm">,</span> <span class="i">@AtomNeighborhoods</span><span class="s">)</span><span class="sc">;</span> 4448 4449 <span class="i">$Depth</span> = <span class="n">0</span><span class="sc">;</span> 4450 <span class="i">@AtomNeighborhoods</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4451 4452 <span class="c"># Go over neighborhoods at each level...</span> 4453 <span class="k">for</span> <span class="i">$NeighborhoodAtomIDsWithSuccessorsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodsAtomIDsWithSuccessorsRef</span>}<span class="s">)</span> <span class="s">{</span> 4454 <span class="i">@</span>{<span class="i">$AtomNeighborhoods</span>[<span class="i">$Depth</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4455 4456 <span class="c"># Go over the neighborhood atoms and their successors at a specific level..</span> 4457 <span class="k">for</span> <span class="i">$NeighborhoodAtomIDWithSuccessorsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomIDsWithSuccessorsRef</span>}<span class="s">)</span> <span class="s">{</span> 4458 <span class="k">my</span><span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">@NeighborhoodAtomWithSuccessors</span><span class="cm">,</span> <span class="i">@NeighborhoodAtomSuccessorAtoms</span><span class="s">)</span><span class="sc">;</span> 4459 4460 <span class="i">@NeighborhoodAtomWithSuccessors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@NeighborhoodAtomSuccessorAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4461 <span class="s">(</span><span class="i">$NeighborhoodAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorsIDsRef</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$NeighborhoodAtomIDWithSuccessorsRef</span>}<span class="sc">;</span> 4462 4463 <span class="c"># Map atom IDs to atoms...</span> 4464 <span class="i">$NeighborhoodAtom</span> = <span class="i">$This</span><span class="i">->_GetAtomFromAtomID</span><span class="s">(</span><span class="i">$NeighborhoodAtomID</span><span class="s">)</span><span class="sc">;</span> 4465 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorsIDsRef</span>}<span class="s">)</span> <span class="s">{</span> 4466 <span class="i">@NeighborhoodAtomSuccessorAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorsIDsRef</span>}<span class="s">)</span><span class="sc">;</span> 4467 <span class="s">}</span> 4468 4469 <span class="c"># Store an atom and its successors at each level in an array...</span> 4470 <span class="k">push</span> <span class="i">@NeighborhoodAtomWithSuccessors</span><span class="cm">,</span> <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> \<span class="i">@NeighborhoodAtomSuccessorAtoms</span><span class="s">)</span><span class="sc">;</span> 4471 4472 <span class="k">push</span> <span class="i">@</span>{<span class="i">$AtomNeighborhoods</span>[<span class="i">$Depth</span>]} <span class="cm">,</span> \<span class="i">@NeighborhoodAtomWithSuccessors</span><span class="sc">;</span> 4473 <span class="s">}</span> 4474 <span class="i">$Depth</span>++<span class="sc">;</span> 4475 <span class="s">}</span> 4476 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> 4477 <span class="s">}</span> 4478 4479 <span class="c"># Get next object ID...</span> <a name="_GetNewObjectID-"></a>4480 <span class="k">sub </span><span class="m">_GetNewObjectID</span> <span class="s">{</span> 4481 <span class="i">$ObjectID</span>++<span class="sc">;</span> 4482 <span class="k">return</span> <span class="i">$ObjectID</span><span class="sc">;</span> 4483 <span class="s">}</span> 4484 4485 <span class="c"># Is aromatic property set for the molecule?</span> <a name="IsAromatic-"></a>4486 <span class="k">sub </span><span class="m">IsAromatic</span> <span class="s">{</span> 4487 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4488 <span class="k">my</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span><span class="sc">;</span> 4489 4490 <span class="i">$Aromatic</span> = <span class="i">$This</span><span class="i">->GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4491 4492 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span> && <span class="i">$Aromatic</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 4493 <span class="s">}</span> 4494 4495 <span class="c"># Does molecule contains any atoms with non-zero Z coordiantes?</span> <a name="IsThreeDimensional-"></a>4496 <span class="k">sub </span><span class="m">IsThreeDimensional</span> <span class="s">{</span> 4497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4498 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> 4499 4500 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4501 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 4502 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetZ</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 4503 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 4504 <span class="s">}</span> 4505 <span class="s">}</span> 4506 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 4507 <span class="s">}</span> 4508 4509 <span class="c"># Does molecule contains any atoms with non-zero X or Y coordinates</span> 4510 <span class="c"># and only zero Z-coordinates?</span> <a name="IsTwoDimensional-"></a>4511 <span class="k">sub </span><span class="m">IsTwoDimensional</span> <span class="s">{</span> 4512 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4513 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> 4514 4515 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4516 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 4517 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetZ</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 4518 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 4519 <span class="s">}</span> 4520 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetX</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span> || <span class="i">$Atom</span><span class="i">->GetY</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 4521 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 4522 <span class="s">}</span> 4523 <span class="s">}</span> 4524 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 4525 <span class="s">}</span> 4526 4527 <span class="c"># Get dimensionality of the molecule using one of the following two methods:</span> 4528 <span class="c"># . Using explicitly set Dimensionality</span> 4529 <span class="c"># . Going over atomic coordinates</span> 4530 <span class="c">#</span> 4531 <span class="c"># The valid dimensionality values are:</span> 4532 <span class="c"># . 3D - Three dimensional: One of X, Y or Z coordinate is non-zero</span> 4533 <span class="c"># . 2D - Two dimensional: One of X or Y coordinate is non-zero; All Z coordinates are zero</span> 4534 <span class="c"># . 0D - Zero dimensional: All atomic coordinates are zero</span> 4535 <span class="c">#</span> <a name="GetDimensionality-"></a>4536 <span class="k">sub </span><span class="m">GetDimensionality</span> <span class="s">{</span> 4537 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4538 4539 <span class="c"># Is Dimensionality property explicitly set?</span> 4540 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Dimensionality'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4541 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Dimensionality'</span><span class="s">)</span><span class="sc">;</span> 4542 <span class="s">}</span> 4543 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> 4544 4545 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4546 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> 4547 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetZ</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 4548 <span class="k">return</span> <span class="q">'3D'</span><span class="sc">;</span> 4549 <span class="s">}</span> 4550 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetX</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span> || <span class="i">$Atom</span><span class="i">->GetY</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> 4551 <span class="k">return</span> <span class="q">'2D'</span><span class="sc">;</span> 4552 <span class="s">}</span> 4553 <span class="s">}</span> 4554 <span class="k">return</span> <span class="q">'0D'</span><span class="sc">;</span> 4555 <span class="s">}</span> 4556 4557 <span class="c"># Is it a molecule object?</span> <a name="IsMolecule-"></a>4558 <span class="k">sub </span><span class="m">IsMolecule ($)</span> <span class="s">{</span> 4559 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4560 4561 <span class="k">return</span> <span class="i">_IsMolecule</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span><span class="sc">;</span> 4562 <span class="s">}</span> 4563 4564 <span class="c"># Return a string containing vertices, edges and other properties...</span> <a name="StringifyMolecule-"></a>4565 <span class="k">sub </span><span class="m">StringifyMolecule</span> <span class="s">{</span> 4566 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4567 <span class="k">my</span><span class="s">(</span><span class="i">$MoleculeString</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$NumOfAtoms</span><span class="cm">,</span> <span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$MolecularFormula</span><span class="cm">,</span> <span class="i">$NumOfRings</span><span class="cm">,</span> <span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="i">$ExactMass</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$SpinMultiplicity</span><span class="cm">,</span> <span class="i">$FreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="cm">,</span> <span class="i">$ElementalComposition</span><span class="s">)</span><span class="sc">;</span> 4568 4569 <span class="i">$ID</span> = <span class="i">$This</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4570 <span class="i">$Name</span> = <span class="i">$This</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4571 <span class="i">$NumOfAtoms</span> = <span class="i">$This</span><span class="i">->GetNumOfAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4572 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4573 4574 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4575 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NumOfRings</span><span class="s">)</span> <span class="s">{</span> 4576 <span class="i">$NumOfRings</span> = <span class="q">'undefined'</span><span class="sc">;</span> 4577 <span class="s">}</span> 4578 4579 <span class="i">$MolecularFormula</span> = <span class="i">$This</span><span class="i">->GetMolecularFormula</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4580 4581 <span class="i">$MolecularWeight</span> = <span class="i">$This</span><span class="i">->GetMolecularWeight</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4582 <span class="i">$MolecularWeight</span> = <span class="i">round</span><span class="s">(</span><span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="n">4</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> 4583 4584 <span class="i">$ExactMass</span> = <span class="i">$This</span><span class="i">->GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4585 <span class="i">$ExactMass</span> = <span class="i">round</span><span class="s">(</span><span class="i">$ExactMass</span><span class="cm">,</span> <span class="n">4</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> 4586 4587 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4588 <span class="i">$Charge</span> = <span class="i">$This</span><span class="i">->GetCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4589 4590 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4591 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4592 4593 <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetElementalComposition</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4594 <span class="i">$ElementalComposition</span> = <span class="q">'None'</span><span class="sc">;</span> 4595 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ElementsRef</span>}<span class="s">)</span> <span class="s">{</span> 4596 <span class="i">$ElementalComposition</span> = <span class="q">"[ "</span> . <span class="i">FormatElementalCompositionInformation</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="s">)</span> . <span class="q">" ]"</span><span class="sc">;</span> 4597 <span class="s">}</span> 4598 4599 <span class="i">$MoleculeString</span> = <span class="q">"Molecule: ID: $ID; Name: \"$Name\"; NumOfAtoms: $NumOfAtoms; NumOfBonds: $NumOfBonds; NumOfRings: $NumOfRings; MolecularFormula: $MolecularFormula; MolecularWeight: $MolecularWeight; ExactMass: $ExactMass; FormalCharge: $FormalCharge; Charge: $Charge; SpinMultiplicity: $SpinMultiplicity; FreeRadicalElectrons: $FreeRadicalElectrons; ElementalComposition: $ElementalComposition"</span><span class="sc">;</span> 4600 4601 <span class="k">return</span> <span class="i">$MoleculeString</span><span class="sc">;</span> 4602 <span class="s">}</span> 4603 4604 <span class="c"># Load appropriate atom data files from <MayaChemTools>/lib directory used by various</span> 4605 <span class="c"># object methods in the current class...</span> 4606 <span class="c">#</span> <a name="_LoadMoleculeClassData-"></a>4607 <span class="k">sub </span><span class="m">_LoadMoleculeClassData</span> <span class="s">{</span> 4608 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span> 4609 4610 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4611 4612 <span class="c"># Load and process data for aromaticity models...</span> 4613 <span class="i">_LoadAromaticityModelsData</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span> 4614 <span class="i">_ProcessAromaticityModelsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4615 <span class="s">}</span> 4616 4617 <span class="c">#</span> 4618 <span class="c"># Load data for supported aromaticity models...</span> 4619 <span class="c">#</span> <a name="_LoadAromaticityModelsData-"></a>4620 <span class="k">sub </span><span class="m">_LoadAromaticityModelsData</span> <span class="s">{</span> 4621 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4622 <span class="k">my</span><span class="s">(</span><span class="i">$DataFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">$ModelName</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">%ParameterNames</span><span class="cm">,</span> <span class="i">%ColIndexToModelName</span><span class="cm">,</span> <span class="i">%SupportedParameterNames</span><span class="s">)</span><span class="sc">;</span> 4623 4624 <span class="i">%AromaticityModelsDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4625 <span class="i">%CanonicalAromaticityModelNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4626 4627 <span class="c"># File format:</span> 4628 <span class="c">#</span> 4629 <span class="c"># "ParameterName","MDLAromaticityModel","TriposAromaticityModel","MMFFAromaticityModel","ChemAxonBasicAromaticityModel","ChemAxonGeneralAromaticityModel","DaylightAromaticityModel","MayaChemToolsAromaticityModel"</span> 4630 <span class="c"># "AllowHeteroRingAtoms","No","No","Yes","Yes","Yes","Yes","Yes"</span> 4631 <span class="c">#</span> 4632 <span class="i">$DataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">"/data/AromaticityModelsData.csv"</span><span class="sc">;</span> 4633 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$DataFile"</span><span class="s">)</span> <span class="s">{</span> 4634 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAromaticityModelsData: MayaChemTools package file, $DataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> 4635 <span class="s">}</span> 4636 4637 <span class="c"># Setup a list of currently supported aromaticity parameters...</span> 4638 <span class="c">#</span> 4639 <span class="k">my</span><span class="s">(</span><span class="i">@KnownNames</span><span class="s">)</span><span class="sc">;</span> 4640 <span class="i">@KnownNames</span> = <span class="q">qw(AllowHeteroRingAtoms HeteroRingAtomsList AllowExocyclicDoubleBonds AllowHomoNuclearExocyclicDoubleBonds AllowElectronegativeRingAtomExocyclicDoubleBonds AllowRingAtomFormalCharge AllowHeteroRingAtomFormalCharge MinimumRingSize)</span><span class="sc">;</span> 4641 4642 <span class="i">%SupportedParameterNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4643 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="i">@KnownNames</span><span class="s">)</span> <span class="s">{</span> 4644 <span class="i">$SupportedParameterNames</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterName</span><span class="sc">;</span> 4645 <span class="s">}</span> 4646 4647 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span> 4648 <span class="k">open</span> <span class="w">DATAFILE</span><span class="cm">,</span> <span class="q">"$DataFile"</span> <span class="k">or</span> <span class="w">croak</span> <span class="q">"Couldn't open $DataFile: $! ..."</span><span class="sc">;</span> 4649 4650 <span class="c"># Skip lines up to column labels...</span> 4651 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*DATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4652 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> 4653 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> 4654 <span class="s">}</span> 4655 <span class="s">}</span> 4656 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> 4657 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span> 4658 4659 <span class="i">%ColIndexToModelName</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4660 4661 <span class="c"># Process names of aromaticity models...</span> 4662 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#ColLabels</span><span class="s">)</span> <span class="s">{</span> 4663 <span class="i">$ModelName</span> = <span class="i">$ColLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span> 4664 <span class="i">$ModelName</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 4665 4666 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}<span class="s">)</span> <span class="s">{</span> 4667 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAromaticityModelsData: The aromaticity model name, $ModelName, in $DataFile has already exists.\nLine: $Line..."</span><span class="sc">;</span> 4668 <span class="s">}</span> 4669 <span class="i">%</span>{<span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4670 4671 <span class="c"># Cannonicalize aromatic model name by converting into all lowercase...</span> 4672 <span class="i">$CanonicalAromaticityModelNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ModelName</span><span class="s">)</span>} = <span class="i">$ModelName</span><span class="sc">;</span> 4673 4674 <span class="i">$ColIndexToModelName</span>{<span class="i">$Index</span>} = <span class="i">$ModelName</span><span class="sc">;</span> 4675 <span class="s">}</span> 4676 4677 <span class="c"># Process paramater name and their values for specified aromaticity models...</span> 4678 <span class="c">#</span> 4679 <span class="i">%ParameterNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4680 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*DATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 4681 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> 4682 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> 4683 <span class="s">}</span> 4684 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4685 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> 4686 <span class="k">if</span> <span class="s">(</span><span class="i">@LineWords</span> != <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span> 4687 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAromaticityModelsData: The number of data fields, @LineWords, in $DataFile must be $NumOfCols.\nLine: $Line..."</span><span class="sc">;</span> 4688 <span class="s">}</span> 4689 4690 <span class="c"># Process parameter name and values for aromaticity models...</span> 4691 <span class="c">#</span> 4692 <span class="i">$ParameterName</span> = <span class="i">$LineWords</span>[<span class="n">0</span>]<span class="sc">;</span> 4693 4694 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$SupportedParameterNames</span>{<span class="i">$ParameterName</span>}<span class="s">)</span> <span class="s">{</span> 4695 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}::_LoadAromaticityModelsData: The current release of MayaChemTools doesn't support aromaticity model parameter name, $ParameterName, specified in $DataFile. It would be ignore during aromaticity detection.\nLine: $Line..."</span><span class="sc">;</span> 4696 <span class="s">}</span> 4697 4698 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ParameterNames</span>{<span class="i">$ParameterName</span>}<span class="s">)</span> <span class="s">{</span> 4699 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}::_LoadAromaticityModelsData: Ignoring aromaticity model data for parameter name, $ParameterName, in $DataFile. It has already been loaded.\nLine: $Line..."</span><span class="sc">;</span> 4700 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> 4701 <span class="s">}</span> 4702 <span class="i">$ParameterNames</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterName</span><span class="sc">;</span> 4703 4704 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#LineWords</span><span class="s">)</span> <span class="s">{</span> 4705 <span class="i">$ModelName</span> = <span class="i">$ColIndexToModelName</span>{<span class="i">$Index</span>}<span class="sc">;</span> 4706 <span class="i">$ParameterValue</span> = <span class="i">$LineWords</span>[<span class="i">$Index</span>]<span class="sc">;</span> 4707 <span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span> 4708 <span class="s">}</span> 4709 <span class="s">}</span> 4710 <span class="k">close</span> <span class="w">DATAFILE</span><span class="sc">;</span> 4711 <span class="s">}</span> 4712 4713 <span class="c"># Process already loaded aromaticity model data...</span> 4714 <span class="c">#</span> <a name="_ProcessAromaticityModelsData-"></a>4715 <span class="k">sub </span><span class="m">_ProcessAromaticityModelsData</span> <span class="s">{</span> 4716 <span class="k">my</span><span class="s">(</span><span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">$ModelName</span><span class="cm">,</span> <span class="i">$NewParameterValue</span><span class="s">)</span><span class="sc">;</span> 4717 4718 <span class="k">for</span> <span class="i">$ModelName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AromaticityModelsDataMap</span><span class="s">)</span> <span class="s">{</span> 4719 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}}<span class="s">)</span> <span class="s">{</span> 4720 <span class="i">$ParameterValue</span> = <span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}{<span class="i">$ParameterName</span>}<span class="sc">;</span> 4721 <span class="i">$ParameterValue</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> 4722 4723 <span class="j">VALUE:</span> <span class="s">{</span> 4724 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> <span class="s">{</span> 4725 <span class="i">$NewParameterValue</span> = <span class="n">1</span><span class="sc">;</span> 4726 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> 4727 <span class="s">}</span> 4728 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^(NA|No)$/i</span><span class="s">)</span> <span class="s">{</span> 4729 <span class="i">$NewParameterValue</span> = <span class="n">0</span><span class="sc">;</span> 4730 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> 4731 <span class="s">}</span> 4732 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> 4733 <span class="i">$NewParameterValue</span> = <span class="q">''</span><span class="sc">;</span> 4734 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> 4735 <span class="s">}</span> 4736 <span class="i">$NewParameterValue</span> = <span class="i">$ParameterValue</span><span class="sc">;</span> 4737 <span class="s">}</span> 4738 <span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}{<span class="i">$ParameterName</span>} = <span class="i">$NewParameterValue</span><span class="sc">;</span> 4739 4740 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/List/i</span><span class="s">)</span> <span class="s">{</span> 4741 <span class="c"># Setup a new parameter conatining a reference to a hash for the specified values...</span> 4742 <span class="k">my</span><span class="s">(</span><span class="i">$DataMapRefName</span><span class="cm">,</span> <span class="i">$DataValue</span><span class="cm">,</span> <span class="i">%DataMap</span><span class="s">)</span><span class="sc">;</span> 4743 4744 <span class="i">$DataMapRefName</span> = <span class="q">"${ParameterName}MapRef"</span><span class="sc">;</span> 4745 4746 <span class="i">%DataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 4747 <span class="k">for</span> <span class="i">$DataValue</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NewParameterValue</span><span class="s">)</span> <span class="s">{</span> 4748 <span class="i">$DataMap</span>{<span class="i">$DataValue</span>} = <span class="i">$DataValue</span><span class="sc">;</span> 4749 <span class="s">}</span> 4750 <span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}{<span class="i">$DataMapRefName</span>} = \<span class="i">%DataMap</span><span class="sc">;</span> 4751 <span class="s">}</span> 4752 <span class="s">}</span> 4753 <span class="s">}</span> 4754 <span class="s">}</span> 4755 4756 <span class="c"># Is it a molecule object?</span> <a name="_IsMolecule-"></a>4757 <span class="k">sub </span><span class="m">_IsMolecule</span> <span class="s">{</span> 4758 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 4759 4760 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 4761 <span class="s">}</span> 4762 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>