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| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/Molecule.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,4783 @@ +<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>