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comparison mayachemtools/docs/modules/html/code/Molecule.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:Molecule.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-Molecule-"></a> 1 <span class="k">package </span><span class="i">Molecule</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: Molecule.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span> | |
| 18 5 <span class="c"># $Revision: 1.59 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">Storable</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">MathUtil</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">PeriodicTable</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> | |
| 51 38 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> | |
| 52 39 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> | |
| 53 40 <span class="k">use</span> <span class="w">Graph</span><span class="sc">;</span> | |
| 54 41 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> | |
| 55 42 <span class="k">use</span> <span class="w">Bond</span><span class="sc">;</span> | |
| 56 43 <span class="k">use</span> <span class="w">MolecularFormula</span><span class="sc">;</span> | |
| 57 44 | |
| 58 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> | |
| 59 46 | |
| 60 47 <span class="i">@ISA</span> = <span class="q">qw(Graph ObjectProperty Exporter)</span><span class="sc">;</span> | |
| 61 48 <span class="i">@EXPORT</span> = <span class="q">qw(IsMolecule)</span><span class="sc">;</span> | |
| 62 49 <span class="i">@EXPORT_OK</span> = <span class="q">qw(FormatElementalCompositionInformation GetSupportedAromaticityModels IsSupportedAromaticityModel)</span><span class="sc">;</span> | |
| 63 50 | |
| 64 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> | |
| 65 52 | |
| 66 53 <span class="c"># Setup class variables...</span> | |
| 67 54 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">$ObjectID</span><span class="cm">,</span> <span class="i">%AromaticityModelsDataMap</span><span class="cm">,</span> <span class="i">%CanonicalAromaticityModelNamesMap</span><span class="s">)</span><span class="sc">;</span> | |
| 68 55 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 69 56 | |
| 70 57 <span class="c"># Overload Perl functions...</span> | |
| 71 58 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyMolecule'</span><span class="sc">;</span> | |
| 72 59 | |
| 73 60 <span class="c"># Class constructor...</span> | |
| 74 <a name="new-"></a> 61 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 75 62 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 76 63 | |
| 77 64 <span class="c"># Initialize object...</span> | |
| 78 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> | |
| 79 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">$Class</span><span class="sc">;</span> | |
| 80 67 <span class="i">$This</span><span class="i">->_InitializeMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 81 68 | |
| 82 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">$This</span><span class="i">->_InitializeMoleculeProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> <span class="s">}</span> | |
| 83 70 | |
| 84 71 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 85 72 <span class="s">}</span> | |
| 86 73 | |
| 87 74 <span class="c"># Initialize object data...</span> | |
| 88 <a name="_InitializeMolecule-"></a> 75 <span class="k">sub </span><span class="m">_InitializeMolecule</span> <span class="s">{</span> | |
| 89 76 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 90 77 <span class="k">my</span><span class="s">(</span><span class="i">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 91 78 | |
| 92 79 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> | |
| 93 80 <span class="c"># are implemented on-demand using ObjectProperty class.</span> | |
| 94 81 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span> | |
| 95 82 <span class="i">$This</span>->{<span class="w">Name</span>} = <span class="q">"Molecule ${ObjectID}"</span><span class="sc">;</span> | |
| 96 83 <span class="s">}</span> | |
| 97 84 | |
| 98 85 <span class="c"># Initialize molecule properties...</span> | |
| 99 <a name="_InitializeMoleculeProperties-"></a> 86 <span class="k">sub </span><span class="m">_InitializeMoleculeProperties</span> <span class="s">{</span> | |
| 100 87 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 101 88 | |
| 102 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">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
| 103 90 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
| 104 91 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 105 92 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 106 93 <span class="s">}</span> | |
| 107 94 <span class="s">}</span> | |
| 108 95 | |
| 109 96 <span class="c"># Initialize class ...</span> | |
| 110 <a name="_InitializeClass-"></a> 97 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 111 98 <span class="c">#Class name...</span> | |
| 112 99 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 113 100 | |
| 114 101 <span class="c"># ID to keep track of objects...</span> | |
| 115 102 <span class="i">$ObjectID</span> = <span class="n">0</span><span class="sc">;</span> | |
| 116 103 | |
| 117 104 <span class="c"># Load molecule class data...</span> | |
| 118 105 <span class="i">_LoadMoleculeClassData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 119 106 <span class="s">}</span> | |
| 120 107 | |
| 121 108 <span class="c"># Setup an explicit SetID method to block setting of ID by AUTOLOAD function...</span> | |
| 122 <a name="SetID-"></a> 109 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span> | |
| 123 110 <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> | |
| 124 111 | |
| 125 112 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> | |
| 126 113 | |
| 127 114 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 128 115 <span class="s">}</span> | |
| 129 116 | |
| 130 117 <span class="c"># Add an atom...</span> | |
| 131 <a name="AddAtom-"></a> 118 <span class="k">sub </span><span class="m">AddAtom</span> <span class="s">{</span> | |
| 132 119 <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> | |
| 133 120 | |
| 134 121 <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> | |
| 135 122 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddAtom: No atom added: Atom must be specified..."</span><span class="sc">;</span> | |
| 136 123 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 137 124 <span class="s">}</span> | |
| 138 125 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 139 126 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddAtom: No atom added: Atom already exists..."</span><span class="sc">;</span> | |
| 140 127 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 141 128 <span class="s">}</span> | |
| 142 129 <span class="k">return</span> <span class="i">$This</span><span class="i">->_AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 143 130 <span class="s">}</span> | |
| 144 131 | |
| 145 132 <span class="c"># Add an atom...</span> | |
| 146 <a name="_AddAtom-"></a> 133 <span class="k">sub </span><span class="m">_AddAtom</span> <span class="s">{</span> | |
| 147 134 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 148 135 | |
| 149 136 <span class="c"># Assign atom to this molecule...</span> | |
| 150 137 <span class="i">$Atom</span><span class="i">->_SetMolecule</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 151 138 | |
| 152 139 <span class="c"># Add it to the graph as a vertex...</span> | |
| 153 140 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 154 141 <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> | |
| 155 142 <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> | |
| 156 143 <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">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 157 144 | |
| 158 145 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 159 146 <span class="s">}</span> | |
| 160 147 | |
| 161 148 <span class="c"># Add atoms...</span> | |
| 162 <a name="AddAtoms-"></a> 149 <span class="k">sub </span><span class="m">AddAtoms</span> <span class="s">{</span> | |
| 163 150 <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> | |
| 164 151 | |
| 165 152 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 166 153 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddAtoms: No atoms added: Atoms list must be specified..."</span><span class="sc">;</span> | |
| 167 154 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 168 155 <span class="s">}</span> | |
| 169 156 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 170 157 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 171 158 <span class="i">$This</span><span class="i">->AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 172 159 <span class="s">}</span> | |
| 173 160 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 174 161 <span class="s">}</span> | |
| 175 162 | |
| 176 163 <span class="c"># Create an atom and add it to molecule...</span> | |
| 177 <a name="NewAtom-"></a> 164 <span class="k">sub </span><span class="m">NewAtom</span> <span class="s">{</span> | |
| 178 165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 179 166 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 180 167 | |
| 181 168 <span class="i">$Atom</span> = <span class="i">new</span> <span class="i">Atom</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 182 169 <span class="i">$This</span><span class="i">->AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 183 170 | |
| 184 171 <span class="k">return</span> <span class="i">$Atom</span><span class="sc">;</span> | |
| 185 172 <span class="s">}</span> | |
| 186 173 | |
| 187 174 <span class="c"># Delete an atom...</span> | |
| 188 <a name="DeleteAtom-"></a> 175 <span class="k">sub </span><span class="m">DeleteAtom</span> <span class="s">{</span> | |
| 189 176 <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> | |
| 190 177 | |
| 191 178 <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> | |
| 192 179 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteAtom: No atom deleted: Atom must be specified..."</span><span class="sc">;</span> | |
| 193 180 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 194 181 <span class="s">}</span> | |
| 195 182 <span class="c"># Does the atom exist in molecule?</span> | |
| 196 183 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 197 184 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteAtom: No atom deleted: Atom doesn't exist..."</span><span class="sc">;</span> | |
| 198 185 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 199 186 <span class="s">}</span> | |
| 200 187 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 201 188 <span class="s">}</span> | |
| 202 189 | |
| 203 190 <span class="c"># Delete atom...</span> | |
| 204 <a name="_DeleteAtom-"></a> 191 <span class="k">sub </span><span class="m">_DeleteAtom</span> <span class="s">{</span> | |
| 205 192 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 206 193 | |
| 207 194 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 208 195 <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> | |
| 209 196 <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> | |
| 210 197 | |
| 211 198 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 212 199 <span class="s">}</span> | |
| 213 200 | |
| 214 201 <span class="c"># Delete atoms...</span> | |
| 215 <a name="DeleteAtoms-"></a> 202 <span class="k">sub </span><span class="m">DeleteAtoms</span> <span class="s">{</span> | |
| 216 203 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 217 204 | |
| 218 205 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 219 206 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteAtoms: No atoms added: Atoms list must be specified..."</span><span class="sc">;</span> | |
| 220 207 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 221 208 <span class="s">}</span> | |
| 222 209 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 223 210 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 224 211 <span class="i">$This</span><span class="i">->DeleteAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 225 212 <span class="s">}</span> | |
| 226 213 | |
| 227 214 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 228 215 <span class="s">}</span> | |
| 229 216 | |
| 230 217 <span class="c"># Is this atom present?</span> | |
| 231 <a name="HasAtom-"></a> 218 <span class="k">sub </span><span class="m">HasAtom</span> <span class="s">{</span> | |
| 232 219 <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> | |
| 233 220 | |
| 234 221 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Atom</span><span class="s">)</span> <span class="s">{</span> | |
| 235 222 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 236 223 <span class="s">}</span> | |
| 237 224 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 238 225 <span class="c"># It's not in molecule...</span> | |
| 239 226 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 240 227 <span class="s">}</span> | |
| 241 228 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 242 229 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 243 230 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 244 231 <span class="c"># It's not in molecule...</span> | |
| 245 232 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 246 233 <span class="s">}</span> | |
| 247 234 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 248 235 <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> | |
| 249 236 | |
| 250 237 <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> | |
| 251 238 <span class="s">}</span> | |
| 252 239 | |
| 253 240 <span class="c"># Return an array of atoms. In scalar context, it returns number of atoms. Additionally,</span> | |
| 254 241 <span class="c"># atoms array can be filtered by any user specifiable Atom class method...</span> | |
| 255 242 <span class="c">#</span> | |
| 256 <a name="GetAtoms-"></a> 243 <span class="k">sub </span><span class="m">GetAtoms</span> <span class="s">{</span> | |
| 257 244 <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">$NegateMethodResult</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 258 245 <span class="k">my</span><span class="s">(</span><span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 259 246 | |
| 260 247 <span class="i">@Atoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 261 248 | |
| 262 249 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 263 250 <span class="k">if</span> <span class="s">(</span>!<span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 264 251 <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> | |
| 265 252 <span class="s">}</span> | |
| 266 253 | |
| 267 254 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetVerticesProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 268 255 | |
| 269 256 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$AtomCheckMethodName</span><span class="s">)</span> <span class="s">{</span> | |
| 270 257 <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> | |
| 271 258 <span class="s">}</span> | |
| 272 259 <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">$NegateMethodResult</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 273 260 | |
| 274 261 <span class="c"># Filter out atoms...</span> | |
| 275 262 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$KeepAtom</span><span class="cm">,</span> <span class="i">@FilteredAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 276 263 <span class="i">@FilteredAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 277 264 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 278 265 <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> | |
| 279 266 <span class="k">if</span> <span class="s">(</span><span class="i">$KeepAtom</span><span class="s">)</span> <span class="s">{</span> | |
| 280 267 <span class="k">push</span> <span class="i">@FilteredAtoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="sc">;</span> | |
| 281 268 <span class="s">}</span> | |
| 282 269 <span class="s">}</span> | |
| 283 270 <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> | |
| 284 271 <span class="s">}</span> | |
| 285 272 | |
| 286 273 <span class="c"># Return an array of bonds. In scalar context, it returns number of bonds...</span> | |
| 287 <a name="GetBonds-"></a> 274 <span class="k">sub </span><span class="m">GetBonds</span> <span class="s">{</span> | |
| 288 275 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 289 276 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="cm">,</span> <span class="i">@EdgesAtomsIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 290 277 | |
| 291 278 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@EdgesAtomsIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 292 279 | |
| 293 280 <span class="i">@EdgesAtomsIDs</span> = <span class="i">$This</span><span class="i">->GetEdges</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 294 281 <span class="k">if</span> <span class="s">(</span><span class="i">@EdgesAtomsIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 295 282 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetEdgesProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">@EdgesAtomsIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 296 283 <span class="s">}</span> | |
| 297 284 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@Bonds</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@Bonds</span><span class="sc">;</span> | |
| 298 285 <span class="s">}</span> | |
| 299 286 | |
| 300 287 <span class="c"># Get number of atoms in molecule...</span> | |
| 301 <a name="GetNumOfAtoms-"></a> 288 <span class="k">sub </span><span class="m">GetNumOfAtoms</span> <span class="s">{</span> | |
| 302 289 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 303 290 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 304 291 | |
| 305 292 <span class="i">$NumOfAtoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 306 293 | |
| 307 294 <span class="k">return</span> <span class="i">$NumOfAtoms</span><span class="sc">;</span> | |
| 308 295 <span class="s">}</span> | |
| 309 296 | |
| 310 297 <span class="c"># Get number of bonds in molecule...</span> | |
| 311 <a name="GetNumOfBonds-"></a> 298 <span class="k">sub </span><span class="m">GetNumOfBonds</span> <span class="s">{</span> | |
| 312 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 313 300 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 314 301 | |
| 315 302 <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> | |
| 316 303 | |
| 317 304 <span class="k">return</span> <span class="i">$NumOfBonds</span><span class="sc">;</span> | |
| 318 305 <span class="s">}</span> | |
| 319 306 | |
| 320 307 <span class="c"># Get number of heavy atoms in molecule...</span> | |
| 321 <a name="GetNumOfHeavyAtoms-"></a> 308 <span class="k">sub </span><span class="m">GetNumOfHeavyAtoms</span> <span class="s">{</span> | |
| 322 309 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 323 310 | |
| 324 311 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 325 312 <span class="s">}</span> | |
| 326 313 | |
| 327 314 <span class="c"># Get number of non-hydrogen atoms in molecule...</span> | |
| 328 <a name="GetNumOfNonHydrogenAtoms-"></a> 315 <span class="k">sub </span><span class="m">GetNumOfNonHydrogenAtoms</span> <span class="s">{</span> | |
| 329 316 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 330 317 <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> | |
| 331 318 | |
| 332 319 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 333 320 <span class="i">$NumOfNonHydrogenAtoms</span> = <span class="n">0</span><span class="sc">;</span> | |
| 334 321 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 335 322 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 336 323 <span class="i">$NumOfNonHydrogenAtoms</span>++<span class="sc">;</span> | |
| 337 324 <span class="s">}</span> | |
| 338 325 <span class="s">}</span> | |
| 339 326 <span class="k">return</span> <span class="i">$NumOfNonHydrogenAtoms</span><span class="sc">;</span> | |
| 340 327 <span class="s">}</span> | |
| 341 328 | |
| 342 329 <span class="c"># Get number of hydrogen atoms in molecule...</span> | |
| 343 <a name="GetNumOfHydrogenAtoms-"></a> 330 <span class="k">sub </span><span class="m">GetNumOfHydrogenAtoms</span> <span class="s">{</span> | |
| 344 331 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 345 332 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfHydrogenAtoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> | |
| 346 333 | |
| 347 334 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 348 335 <span class="i">$NumOfHydrogenAtoms</span> = <span class="n">0</span><span class="sc">;</span> | |
| 349 336 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 350 337 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 351 338 <span class="i">$NumOfHydrogenAtoms</span>++<span class="sc">;</span> | |
| 352 339 <span class="s">}</span> | |
| 353 340 <span class="s">}</span> | |
| 354 341 <span class="k">return</span> <span class="i">$NumOfHydrogenAtoms</span><span class="sc">;</span> | |
| 355 342 <span class="s">}</span> | |
| 356 343 | |
| 357 344 <span class="c"># Get number of missing hydrogen atoms in molecule...</span> | |
| 358 <a name="GetNumOfMissingHydrogenAtoms-"></a> 345 <span class="k">sub </span><span class="m">GetNumOfMissingHydrogenAtoms</span> <span class="s">{</span> | |
| 359 346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 360 347 <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> | |
| 361 348 | |
| 362 349 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 363 350 <span class="i">$NumOfMissingHydrogenAtoms</span> = <span class="n">0</span><span class="sc">;</span> | |
| 364 351 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 365 352 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 366 353 <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> | |
| 367 354 <span class="s">}</span> | |
| 368 355 <span class="s">}</span> | |
| 369 356 <span class="k">return</span> <span class="i">$NumOfMissingHydrogenAtoms</span><span class="sc">;</span> | |
| 370 357 <span class="s">}</span> | |
| 371 358 | |
| 372 359 <span class="c"># Add bond...</span> | |
| 373 <a name="AddBond-"></a> 360 <span class="k">sub </span><span class="m">AddBond</span> <span class="s">{</span> | |
| 374 361 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 375 362 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 376 363 | |
| 377 364 <span class="s">(</span><span class="i">$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> | |
| 378 365 <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> | |
| 379 366 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddBond: No bond added: Both atoms must be specified..."</span><span class="sc">;</span> | |
| 380 367 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 381 368 <span class="s">}</span> | |
| 382 369 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$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> | |
| 383 370 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddBond: No bond added: Both atoms must be present..."</span><span class="sc">;</span> | |
| 384 371 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 385 372 <span class="s">}</span> | |
| 386 373 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 387 374 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddBond: No bond added: Bond already exists..."</span><span class="sc">;</span> | |
| 388 375 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 389 376 <span class="s">}</span> | |
| 390 377 <span class="k">return</span> <span class="i">$This</span><span class="i">->_AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
| 391 378 <span class="s">}</span> | |
| 392 379 | |
| 393 380 <span class="c"># Add bond...</span> | |
| 394 <a name="_AddBond-"></a> 381 <span class="k">sub </span><span class="m">_AddBond</span> <span class="s">{</span> | |
| 395 382 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 396 383 | |
| 397 384 <span class="c"># Assign bond to this molecule...</span> | |
| 398 385 <span class="i">$Bond</span><span class="i">->_SetMolecule</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 399 386 | |
| 400 387 <span class="c"># Add it to the graph as an edge...</span> | |
| 401 388 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 402 389 <span class="s">(</span><span class="i">$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> | |
| 403 390 <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> | |
| 404 391 <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">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 405 392 <span class="i">$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">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 406 393 | |
| 407 394 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 408 395 <span class="s">}</span> | |
| 409 396 | |
| 410 397 <span class="c"># Add Bonds...</span> | |
| 411 <a name="AddBonds-"></a> 398 <span class="k">sub </span><span class="m">AddBonds</span> <span class="s">{</span> | |
| 412 399 <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> | |
| 413 400 | |
| 414 401 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> | |
| 415 402 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddBonds: No bonds added: Bonds list must be specified..."</span><span class="sc">;</span> | |
| 416 403 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 417 404 <span class="s">}</span> | |
| 418 405 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
| 419 406 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> | |
| 420 407 <span class="i">$This</span><span class="i">->AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
| 421 408 <span class="s">}</span> | |
| 422 409 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 423 410 <span class="s">}</span> | |
| 424 411 | |
| 425 412 <span class="c"># Create a bond and add it to molecule...</span> | |
| 426 <a name="NewBond-"></a> 413 <span class="k">sub </span><span class="m">NewBond</span> <span class="s">{</span> | |
| 427 414 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 428 415 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
| 429 416 | |
| 430 417 <span class="i">$Bond</span> = <span class="i">new</span> <span class="i">Bond</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 431 418 <span class="i">$This</span><span class="i">->AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
| 432 419 | |
| 433 420 <span class="k">return</span> <span class="i">$Bond</span><span class="sc">;</span> | |
| 434 421 <span class="s">}</span> | |
| 435 422 | |
| 436 423 <span class="c"># Delete a bond...</span> | |
| 437 <a name="DeleteBond-"></a> 424 <span class="k">sub </span><span class="m">DeleteBond</span> <span class="s">{</span> | |
| 438 425 <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> | |
| 439 426 | |
| 440 427 <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> | |
| 441 428 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteBond: No bond deleted: Bond must be specified..."</span><span class="sc">;</span> | |
| 442 429 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 443 430 <span class="s">}</span> | |
| 444 431 <span class="c"># Does the bond exist in molecule?</span> | |
| 445 432 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 446 433 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteBond: No bond deleted: Bond doesn't exist..."</span><span class="sc">;</span> | |
| 447 434 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 448 435 <span class="s">}</span> | |
| 449 436 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
| 450 437 <span class="s">}</span> | |
| 451 438 | |
| 452 439 <span class="c"># Delete bond...</span> | |
| 453 <a name="_DeleteBond-"></a> 440 <span class="k">sub </span><span class="m">_DeleteBond</span> <span class="s">{</span> | |
| 454 441 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 455 442 | |
| 456 443 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 457 444 <span class="s">(</span><span class="i">$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> | |
| 458 445 <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> | |
| 459 446 <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">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 460 447 | |
| 461 448 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 462 449 <span class="s">}</span> | |
| 463 450 | |
| 464 451 <span class="c"># Delete bonds...</span> | |
| 465 <a name="DeleteBonds-"></a> 452 <span class="k">sub </span><span class="m">DeleteBonds</span> <span class="s">{</span> | |
| 466 453 <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> | |
| 467 454 | |
| 468 455 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> | |
| 469 456 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteBonds: No bonds added: Bonds list must be specified..."</span><span class="sc">;</span> | |
| 470 457 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 471 458 <span class="s">}</span> | |
| 472 459 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
| 473 460 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span> | |
| 474 461 <span class="i">$This</span><span class="i">->DeleteBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
| 475 462 <span class="s">}</span> | |
| 476 463 | |
| 477 464 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 478 465 <span class="s">}</span> | |
| 479 466 | |
| 480 467 <span class="c"># Has bond...</span> | |
| 481 <a name="HasBond-"></a> 468 <span class="k">sub </span><span class="m">HasBond</span> <span class="s">{</span> | |
| 482 469 <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> | |
| 483 470 <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> | |
| 484 471 | |
| 485 472 <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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 486 473 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$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">$Atom2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 487 474 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 488 475 <span class="s">}</span> | |
| 489 476 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 490 477 <span class="c"># It's not in molecule...</span> | |
| 491 478 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 492 479 <span class="s">}</span> | |
| 493 480 <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">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
| 494 481 <span class="i">$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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 495 482 <span class="i">$Molecule</span> = <span class="i">$Bond</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 496 483 | |
| 497 484 <span class="k">return</span> <span class="s">(</span><span class="i">$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> | |
| 498 485 <span class="s">}</span> | |
| 499 486 | |
| 500 487 <span class="c"># Get atom neighbors...</span> | |
| 501 <a name="_GetAtomNeighbors-"></a> 488 <span class="k">sub </span><span class="m">_GetAtomNeighbors</span> <span class="s">{</span> | |
| 502 489 <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> | |
| 503 490 | |
| 504 491 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 505 492 | |
| 506 493 <span class="i">@Atoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 507 494 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 508 495 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 509 496 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 510 497 <span class="i">@Atoms</span> = <span class="i">$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> | |
| 511 498 <span class="s">}</span> | |
| 512 499 <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> | |
| 513 500 <span class="s">}</span> | |
| 514 501 | |
| 515 502 <span class="c"># Get atom bonds...</span> | |
| 516 <a name="_GetAtomBonds-"></a> 503 <span class="k">sub </span><span class="m">_GetAtomBonds</span> <span class="s">{</span> | |
| 517 504 <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> | |
| 518 505 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> | |
| 519 506 | |
| 520 507 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 521 508 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 522 509 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetEdges</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 523 510 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 524 511 <span class="i">@Bonds</span> = <span class="i">$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> | |
| 525 512 <span class="s">}</span> | |
| 526 513 <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> | |
| 527 514 <span class="s">}</span> | |
| 528 515 | |
| 529 516 <span class="c"># Get bond to specified atom...</span> | |
| 530 <a name="_GetBondToAtom-"></a> 517 <span class="k">sub </span><span class="m">_GetBondToAtom</span> <span class="s">{</span> | |
| 531 518 <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">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 532 519 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 533 520 | |
| 534 521 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 535 522 <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 536 523 | |
| 537 524 <span class="k">return</span> <span class="i">$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> | |
| 538 525 <span class="s">}</span> | |
| 539 526 | |
| 540 527 <span class="c"># Are two specified atoms bonded?</span> | |
| 541 <a name="_IsBondedToAtom-"></a> 528 <span class="k">sub </span><span class="m">_IsBondedToAtom</span> <span class="s">{</span> | |
| 542 529 <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">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 543 530 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 544 531 | |
| 545 532 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 546 533 <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 547 534 | |
| 548 535 <span class="k">return</span> <span class="i">$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> | |
| 549 536 <span class="s">}</span> | |
| 550 537 | |
| 551 538 <span class="c"># Add hydrogens to each atoms in molecule and return total number of hydrogens added...</span> | |
| 552 <a name="AddHydrogens-"></a> 539 <span class="k">sub </span><span class="m">AddHydrogens</span> <span class="s">{</span> | |
| 553 540 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 554 541 | |
| 555 542 <span class="k">return</span> <span class="i">$This</span><span class="i">->_AddHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 556 543 <span class="s">}</span> | |
| 557 544 | |
| 558 545 <span class="c"># Add hydrogens to polar atoms (N, O, P, S) in molecule and return total number of hydrogens added...</span> | |
| 559 <a name="AddPolarHydrogens-"></a> 546 <span class="k">sub </span><span class="m">AddPolarHydrogens</span> <span class="s">{</span> | |
| 560 547 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 561 548 <span class="k">my</span><span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> = <span class="n">1</span><span class="sc">;</span> | |
| 562 549 | |
| 563 550 <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> | |
| 564 551 <span class="s">}</span> | |
| 565 552 | |
| 566 553 <span class="c"># Add all the hydrogens or hydrogens for polar atoms only...</span> | |
| 567 554 <span class="c">#</span> | |
| 568 555 <span class="c"># Note:</span> | |
| 569 556 <span class="c"># . The current release of MayaChemTools doesn't assign any hydrogen positions.</span> | |
| 570 557 <span class="c">#</span> | |
| 571 <a name="_AddHydrogens-"></a> 558 <span class="k">sub </span><span class="m">_AddHydrogens</span> <span class="s">{</span> | |
| 572 559 <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> | |
| 573 560 <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">$HydrogenPositionsWarning</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> | |
| 574 561 | |
| 575 562 <span class="k">if</span> <span class="s">(</span>! <span class="k">defined</span> <span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 576 563 <span class="i">$PolarHydrogensOnly</span> = <span class="n">0</span><span class="sc">;</span> | |
| 577 564 <span class="s">}</span> | |
| 578 565 | |
| 579 566 <span class="i">$NumOfHydrogensAdded</span> = <span class="n">0</span><span class="sc">;</span> | |
| 580 567 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 581 568 <span class="i">$HydrogenPositionsWarning</span> = <span class="n">0</span><span class="sc">;</span> | |
| 582 569 | |
| 583 570 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 584 571 <span class="k">if</span> <span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 585 572 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsPolarAtom</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 586 573 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 587 574 <span class="s">}</span> | |
| 588 575 <span class="s">}</span> | |
| 589 576 <span class="i">$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> | |
| 590 577 <span class="s">}</span> | |
| 591 578 <span class="k">return</span> <span class="i">$NumOfHydrogensAdded</span><span class="sc">;</span> | |
| 592 579 <span class="s">}</span> | |
| 593 580 | |
| 594 581 <span class="c"># Delete all hydrogens atoms in molecule and return total number of hydrogens removed...</span> | |
| 595 <a name="DeleteHydrogens-"></a> 582 <span class="k">sub </span><span class="m">DeleteHydrogens</span> <span class="s">{</span> | |
| 596 583 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 597 584 | |
| 598 585 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 599 586 <span class="s">}</span> | |
| 600 587 | |
| 601 588 <span class="c"># Delete hydrogens to polar atoms (N, O, P, S) in molecule and return total number of hydrogens removed...</span> | |
| 602 <a name="DeletePolarHydrogens-"></a> 589 <span class="k">sub </span><span class="m">DeletePolarHydrogens</span> <span class="s">{</span> | |
| 603 590 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 604 591 <span class="k">my</span><span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> = <span class="n">1</span><span class="sc">;</span> | |
| 605 592 | |
| 606 593 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteHydrogens</span><span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span><span class="sc">;</span> | |
| 607 594 <span class="s">}</span> | |
| 608 595 | |
| 609 596 <span class="c"># Delete all hydrogens atoms in molecule and return total number of hydrogens removed...</span> | |
| 610 <a name="_DeleteHydrogens-"></a> 597 <span class="k">sub </span><span class="m">_DeleteHydrogens</span> <span class="s">{</span> | |
| 611 598 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PolarHydrogensOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 612 599 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$NumOfHydrogensRemoved</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> | |
| 613 600 | |
| 614 601 <span class="k">if</span> <span class="s">(</span>! <span class="k">defined</span> <span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 615 602 <span class="i">$PolarHydrogensOnly</span> = <span class="n">0</span><span class="sc">;</span> | |
| 616 603 <span class="s">}</span> | |
| 617 604 | |
| 618 605 <span class="i">$NumOfHydrogensRemoved</span> = <span class="n">0</span><span class="sc">;</span> | |
| 619 606 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 620 607 | |
| 621 608 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 622 609 <span class="k">if</span> <span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span> | |
| 623 610 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsPolarHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 624 611 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 625 612 <span class="s">}</span> | |
| 626 613 <span class="s">}</span> | |
| 627 614 <span class="k">elsif</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 628 615 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 629 616 <span class="s">}</span> | |
| 630 617 <span class="i">$This</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 631 618 <span class="i">$NumOfHydrogensRemoved</span>++<span class="sc">;</span> | |
| 632 619 <span class="s">}</span> | |
| 633 620 <span class="k">return</span> <span class="i">$NumOfHydrogensRemoved</span><span class="sc">;</span> | |
| 634 621 <span class="s">}</span> | |
| 635 622 | |
| 636 623 <span class="c"># Get molecular weight by summing up atomic weights of all the atoms...</span> | |
| 637 <a name="GetMolecularWeight-"></a> 624 <span class="k">sub </span><span class="m">GetMolecularWeight</span> <span class="s">{</span> | |
| 638 625 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 639 626 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 640 627 | |
| 641 628 <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">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> | |
| 642 629 | |
| 643 630 <span class="i">$MolecularWeight</span> = <span class="n">0</span><span class="sc">;</span> | |
| 644 631 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 645 632 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 646 633 <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> | |
| 647 634 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicWeight</span><span class="s">)</span> <span class="s">{</span> | |
| 648 635 <span class="i">$MolecularWeight</span> += <span class="i">$AtomicWeight</span><span class="sc">;</span> | |
| 649 636 <span class="s">}</span> | |
| 650 637 <span class="s">}</span> | |
| 651 638 | |
| 652 639 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> | |
| 653 640 <span class="k">return</span> <span class="i">$MolecularWeight</span><span class="sc">;</span> | |
| 654 641 <span class="s">}</span> | |
| 655 642 | |
| 656 643 <span class="c"># Account for missing hydrogen atoms...</span> | |
| 657 644 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 658 645 | |
| 659 646 <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> | |
| 660 647 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 661 648 <span class="i">$MolecularWeight</span> += <span class="i">$NumOfMissingHydrogenAtoms</span> * <span class="i">PeriodicTable::GetElementAtomicWeight</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span><span class="sc">;</span> | |
| 662 649 <span class="s">}</span> | |
| 663 650 | |
| 664 651 <span class="k">return</span> <span class="i">$MolecularWeight</span><span class="sc">;</span> | |
| 665 652 <span class="s">}</span> | |
| 666 653 | |
| 667 654 <span class="c"># Get exact mass by summing up exact masses of all the atoms...</span> | |
| 668 <a name="GetExactMass-"></a> 655 <span class="k">sub </span><span class="m">GetExactMass</span> <span class="s">{</span> | |
| 669 656 <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> | |
| 670 657 <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">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 671 658 | |
| 672 659 <span class="i">$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> | |
| 673 660 | |
| 674 661 <span class="i">$ExactMass</span> = <span class="n">0</span><span class="sc">;</span> | |
| 675 662 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 676 663 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 677 664 <span class="i">$AtomicMass</span> = <span class="i">$Atom</span><span class="i">->GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 678 665 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicMass</span><span class="s">)</span> <span class="s">{</span> | |
| 679 666 <span class="i">$ExactMass</span> += <span class="i">$AtomicMass</span><span class="sc">;</span> | |
| 680 667 <span class="s">}</span> | |
| 681 668 <span class="s">}</span> | |
| 682 669 | |
| 683 670 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> | |
| 684 671 <span class="k">return</span> <span class="i">$ExactMass</span><span class="sc">;</span> | |
| 685 672 <span class="s">}</span> | |
| 686 673 | |
| 687 674 <span class="c"># Account for missing hydrogen atoms...</span> | |
| 688 675 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 689 676 | |
| 690 677 <span class="i">$NumOfMissingHydrogenAtoms</span> = <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 691 678 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 692 679 <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> | |
| 693 680 <span class="s">}</span> | |
| 694 681 | |
| 695 682 <span class="k">return</span> <span class="i">$ExactMass</span><span class="sc">;</span> | |
| 696 683 <span class="s">}</span> | |
| 697 684 | |
| 698 685 <span class="c"># Get net formal charge on the molecule using one of the following two methods:</span> | |
| 699 686 <span class="c"># . Using explicitly set FormalCharge property</span> | |
| 700 687 <span class="c"># . Adding up formal charge on each atom in the molecule</span> | |
| 701 688 <span class="c">#</span> | |
| 702 689 <span class="c"># Caveats:</span> | |
| 703 690 <span class="c"># . FormalCharge is different from Charge property of the molecule which corresponds to</span> | |
| 704 691 <span class="c"># sum of partial atomic charges explicitly set for each atom using a specific methodology.</span> | |
| 705 692 <span class="c">#</span> | |
| 706 <a name="GetFormalCharge-"></a> 693 <span class="k">sub </span><span class="m">GetFormalCharge</span> <span class="s">{</span> | |
| 707 694 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 708 695 | |
| 709 696 <span class="c"># Is FormalCharge property explicitly set?</span> | |
| 710 697 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 711 698 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="sc">;</span> | |
| 712 699 <span class="s">}</span> | |
| 713 700 <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">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 714 701 | |
| 715 702 <span class="i">$FormalCharge</span> = <span class="n">0</span><span class="sc">;</span> | |
| 716 703 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 717 704 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 718 705 <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> | |
| 719 706 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicFormalCharge</span><span class="s">)</span> <span class="s">{</span> | |
| 720 707 <span class="i">$FormalCharge</span> += <span class="i">$AtomicFormalCharge</span><span class="sc">;</span> | |
| 721 708 <span class="s">}</span> | |
| 722 709 <span class="s">}</span> | |
| 723 710 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span> | |
| 724 711 <span class="s">}</span> | |
| 725 712 | |
| 726 713 <span class="c"># Get net charge on the molecule using one of the following two methods:</span> | |
| 727 714 <span class="c"># . Using explicitly set Charge property</span> | |
| 728 715 <span class="c"># . Adding up charge on each atom in the molecule</span> | |
| 729 716 <span class="c">#</span> | |
| 730 717 <span class="c"># Caveats:</span> | |
| 731 718 <span class="c"># . FormalCharge is different from Charge property of the molecule which corresponds to</span> | |
| 732 719 <span class="c"># sum of partial atomic charges explicitly set for each atom using a specific methodology.</span> | |
| 733 720 <span class="c">#</span> | |
| 734 <a name="GetCharge-"></a> 721 <span class="k">sub </span><span class="m">GetCharge</span> <span class="s">{</span> | |
| 735 722 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 736 723 | |
| 737 724 <span class="c"># Is Charge property explicitly set?</span> | |
| 738 725 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 739 726 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Charge'</span><span class="s">)</span><span class="sc">;</span> | |
| 740 727 <span class="s">}</span> | |
| 741 728 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 742 729 | |
| 743 730 <span class="i">$Charge</span> = <span class="n">0</span><span class="sc">;</span> | |
| 744 731 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 745 732 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 746 733 <span class="i">$AtomicCharge</span> = <span class="i">$Atom</span><span class="i">->GetCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 747 734 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicCharge</span><span class="s">)</span> <span class="s">{</span> | |
| 748 735 <span class="i">$Charge</span> += <span class="i">$AtomicCharge</span><span class="sc">;</span> | |
| 749 736 <span class="s">}</span> | |
| 750 737 <span class="s">}</span> | |
| 751 738 <span class="k">return</span> <span class="i">$Charge</span><span class="sc">;</span> | |
| 752 739 <span class="s">}</span> | |
| 753 740 | |
| 754 741 <span class="c"># Get total SpinMultiplicity for the molecule using one of the following two methods:</span> | |
| 755 742 <span class="c"># . Using explicitly set SpinMultiplicity property</span> | |
| 756 743 <span class="c"># . Adding up SpinMultiplicity on each atom in the molecule</span> | |
| 757 744 <span class="c">#</span> | |
| 758 745 <span class="c">#</span> | |
| 759 <a name="GetSpinMultiplicity-"></a> 746 <span class="k">sub </span><span class="m">GetSpinMultiplicity</span> <span class="s">{</span> | |
| 760 747 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 761 748 | |
| 762 749 <span class="c"># Is SpinMultiplicity property explicitly set?</span> | |
| 763 750 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 764 751 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span> | |
| 765 752 <span class="s">}</span> | |
| 766 753 <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">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 767 754 | |
| 768 755 <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span> | |
| 769 756 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 770 757 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 771 758 <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> | |
| 772 759 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicSpinMultiplicity</span><span class="s">)</span> <span class="s">{</span> | |
| 773 760 <span class="i">$SpinMultiplicity</span> += <span class="i">$AtomicSpinMultiplicity</span><span class="sc">;</span> | |
| 774 761 <span class="s">}</span> | |
| 775 762 <span class="s">}</span> | |
| 776 763 <span class="k">return</span> <span class="i">$SpinMultiplicity</span><span class="sc">;</span> | |
| 777 764 <span class="s">}</span> | |
| 778 765 | |
| 779 766 <span class="c"># Get total FreeRadicalElectrons for the molecule using one of the following two methods:</span> | |
| 780 767 <span class="c"># . Using explicitly set FreeRadicalElectrons property</span> | |
| 781 768 <span class="c"># . Adding up FreeRadicalElectrons on each atom in the molecule</span> | |
| 782 769 <span class="c">#</span> | |
| 783 770 <span class="c">#</span> | |
| 784 <a name="GetFreeRadicalElectrons-"></a> 771 <span class="k">sub </span><span class="m">GetFreeRadicalElectrons</span> <span class="s">{</span> | |
| 785 772 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 786 773 | |
| 787 774 <span class="c"># Is FreeRadicalElectrons property explicitly set?</span> | |
| 788 775 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 789 776 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="sc">;</span> | |
| 790 777 <span class="s">}</span> | |
| 791 778 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 792 779 | |
| 793 780 <span class="i">$FreeRadicalElectrons</span> = <span class="n">0</span><span class="sc">;</span> | |
| 794 781 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 795 782 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 796 783 <span class="i">$AtomicFreeRadicalElectrons</span> = <span class="i">$Atom</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 797 784 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicFreeRadicalElectrons</span><span class="s">)</span> <span class="s">{</span> | |
| 798 785 <span class="i">$FreeRadicalElectrons</span> += <span class="i">$AtomicFreeRadicalElectrons</span><span class="sc">;</span> | |
| 799 786 <span class="s">}</span> | |
| 800 787 <span class="s">}</span> | |
| 801 788 <span class="k">return</span> <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span> | |
| 802 789 <span class="s">}</span> | |
| 803 790 | |
| 804 791 <span class="c"># Set valence model...</span> | |
| 805 792 <span class="c">#</span> | |
| 806 <a name="SetValenceModel-"></a> 793 <span class="k">sub </span><span class="m">SetValenceModel</span> <span class="s">{</span> | |
| 807 794 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ValenceModel</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 808 795 | |
| 809 796 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> !~ <span class="q">/^(MDLValenceModel|DaylightValenceModel|InternalValenceModel|MayaChemToolsValenceModel)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 810 797 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetValenceModel: The current release of MayaChemTools doesn't support the specified valence model $ValenceModel. Supported valence models: MDLValenceModel, DaylightValenceModel, InternalValenceModel or MayaChemToolsValenceModel. Using internal valence model..."</span><span class="sc">;</span> | |
| 811 798 <span class="i">$ValenceModel</span> = <span class="q">'InternalValenceModel'</span><span class="sc">;</span> | |
| 812 799 <span class="s">}</span> | |
| 813 800 | |
| 814 801 <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> | |
| 815 802 | |
| 816 803 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 817 804 <span class="s">}</span> | |
| 818 805 | |
| 819 806 <span class="c"># Get valence model...</span> | |
| 820 807 <span class="c">#</span> | |
| 821 <a name="GetValenceModel-"></a> 808 <span class="k">sub </span><span class="m">GetValenceModel</span> <span class="s">{</span> | |
| 822 809 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 823 810 | |
| 824 811 <span class="c"># Is ValenceModel property explicitly set?</span> | |
| 825 812 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ValenceModel'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 826 813 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ValenceModel'</span><span class="s">)</span><span class="sc">;</span> | |
| 827 814 <span class="s">}</span> | |
| 828 815 | |
| 829 816 <span class="c"># Used internal valence model as default model...</span> | |
| 830 817 <span class="k">return</span> <span class="q">'InternalValenceModel'</span><span class="sc">;</span> | |
| 831 818 <span class="s">}</span> | |
| 832 819 | |
| 833 820 <span class="c"># Get molecular formula by collecting information about all atoms in the molecule and</span> | |
| 834 821 <span class="c"># composing the formula using Hills ordering system:</span> | |
| 835 822 <span class="c"># . C shows up first and H follows assuming C is present</span> | |
| 836 823 <span class="c"># . All other standard elements are sorted alphanumerically</span> | |
| 837 824 <span class="c"># . All other non-stanard atom symbols are also sorted alphanumerically and follow standard elements</span> | |
| 838 825 <span class="c">#</span> | |
| 839 826 <span class="c"># Caveats:</span> | |
| 840 827 <span class="c"># . By default, missing hydrogens and nonelements are also included</span> | |
| 841 828 <span class="c"># . Elements for disconnected fragments are combined into the same formula</span> | |
| 842 829 <span class="c">#</span> | |
| 843 830 <span class="c"># Handle formula generation for disconnected structures. e.g: molecule generated by</span> | |
| 844 831 <span class="c"># [Na+].[O-]c1ccccc1</span> | |
| 845 832 <span class="c">#</span> | |
| 846 <a name="GetMolecularFormula-"></a> 833 <span class="k">sub </span><span class="m">GetMolecularFormula</span> <span class="s">{</span> | |
| 847 834 <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">$IncludeNonElements</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 848 835 <span class="k">my</span><span class="s">(</span><span class="i">$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">$NonElementsCountRef</span><span class="s">)</span><span class="sc">;</span> | |
| 849 836 | |
| 850 837 <span class="i">$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> | |
| 851 838 <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">$IncludeNonElements</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> | |
| 852 839 | |
| 853 840 <span class="c"># Get elements count and setup molecular formula...</span> | |
| 854 841 <span class="s">(</span><span class="i">$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">$IncludeMissingHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
| 855 842 <span class="i">$MolecularFormula</span> = <span class="q">''</span><span class="sc">;</span> | |
| 856 843 | |
| 857 844 <span class="c"># Count C and H first...</span> | |
| 858 845 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCountRef</span>->{<span class="w">C</span>} <span class="s">)</span> <span class="s">{</span> | |
| 859 846 <span class="i">$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> | |
| 860 847 <span class="k">delete</span> <span class="i">$ElementsCountRef</span>->{<span class="w">C</span>}<span class="sc">;</span> | |
| 861 848 | |
| 862 849 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCountRef</span>->{<span class="w">H</span>} <span class="s">)</span> <span class="s">{</span> | |
| 863 850 <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">$ElementsCountRef</span>->{<span class="w">H</span>} <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span> | |
| 864 851 <span class="k">delete</span> <span class="i">$ElementsCountRef</span>->{<span class="w">H</span>}<span class="sc">;</span> | |
| 865 852 <span class="s">}</span> | |
| 866 853 <span class="s">}</span> | |
| 867 854 | |
| 868 855 <span class="c"># Sort elements...</span> | |
| 869 856 <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> | |
| 870 857 <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> | |
| 871 858 <span class="s">}</span> | |
| 872 859 | |
| 873 860 <span class="c"># Sort non-elements...</span> | |
| 874 861 <span class="k">if</span> <span class="s">(</span><span class="i">$IncludeNonElements</span><span class="s">)</span> <span class="s">{</span> | |
| 875 862 <span class="k">for</span> <span class="i">$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">$NonElementsCountRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 876 863 <span class="i">$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">$AtomSymbol</span>} <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span> | |
| 877 864 <span class="s">}</span> | |
| 878 865 <span class="s">}</span> | |
| 879 866 | |
| 880 867 <span class="c"># Check formal charge...</span> | |
| 881 868 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span> | |
| 882 869 <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> | |
| 883 870 <span class="k">if</span> <span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> <span class="s">{</span> | |
| 884 871 <span class="c"># Setup formal charge string...</span> | |
| 885 872 <span class="k">my</span><span class="s">(</span><span class="i">$FormalChargeString</span><span class="s">)</span><span class="sc">;</span> | |
| 886 873 <span class="k">if</span> <span class="s">(</span><span class="i">$FormalCharge</span> == <span class="n">1</span> <span class="s">)</span> <span class="s">{</span> | |
| 887 874 <span class="i">$FormalChargeString</span> = <span class="q">"+"</span><span class="sc">;</span> | |
| 888 875 <span class="s">}</span> | |
| 889 876 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FormalCharge</span> == <span class="n">-1</span> <span class="s">)</span> <span class="s">{</span> | |
| 890 877 <span class="i">$FormalChargeString</span> = <span class="q">"-"</span><span class="sc">;</span> | |
| 891 878 <span class="s">}</span> | |
| 892 879 <span class="k">else</span> <span class="s">{</span> | |
| 893 880 <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> | |
| 894 881 <span class="s">}</span> | |
| 895 882 <span class="i">$MolecularFormula</span> = <span class="q">"${MolecularFormula}${FormalChargeString}"</span><span class="sc">;</span> | |
| 896 883 <span class="s">}</span> | |
| 897 884 | |
| 898 885 <span class="k">return</span> <span class="i">$MolecularFormula</span><span class="sc">;</span> | |
| 899 886 <span class="s">}</span> | |
| 900 887 | |
| 901 888 <span class="c"># Count elements and non-elements in molecule and return references to hashes</span> | |
| 902 889 <span class="c"># containing count of elements and non-elements respectively. By default, missing</span> | |
| 903 890 <span class="c"># hydrogens are not added to the element hash.</span> | |
| 904 891 <span class="c">#</span> | |
| 905 892 <span class="c">#</span> | |
| 906 <a name="GetElementsAndNonElements-"></a> 893 <span class="k">sub </span><span class="m">GetElementsAndNonElements</span> <span class="s">{</span> | |
| 907 894 <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> | |
| 908 895 <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> | |
| 909 896 | |
| 910 897 <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">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 911 898 | |
| 912 899 <span class="i">%ElementsCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">%NonElementsCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 913 900 <span class="i">$NumOfMissingHydrogens</span> = <span class="n">0</span><span class="sc">;</span> | |
| 914 901 | |
| 915 902 <span class="c"># Count elements and non elements...</span> | |
| 916 903 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 917 904 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 918 905 <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> | |
| 919 906 <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> | |
| 920 907 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 921 908 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> | |
| 922 909 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 923 910 <span class="s">}</span> | |
| 924 911 <span class="k">else</span> <span class="s">{</span> | |
| 925 912 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 926 913 <span class="s">}</span> | |
| 927 914 <span class="k">if</span> <span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> | |
| 928 915 <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> | |
| 929 916 <span class="s">}</span> | |
| 930 917 <span class="s">}</span> | |
| 931 918 <span class="k">else</span> <span class="s">{</span> | |
| 932 919 <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> | |
| 933 920 <span class="i">$NonElementsCount</span>{<span class="i">$AtomSymbol</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 934 921 <span class="s">}</span> | |
| 935 922 <span class="k">else</span> <span class="s">{</span> | |
| 936 923 <span class="i">$NonElementsCount</span>{<span class="i">$AtomSymbol</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 937 924 <span class="s">}</span> | |
| 938 925 <span class="s">}</span> | |
| 939 926 <span class="s">}</span> | |
| 940 927 <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> | |
| 941 928 <span class="i">$AtomSymbol</span> = <span class="q">'H'</span><span class="sc">;</span> | |
| 942 929 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> | |
| 943 930 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} += <span class="i">$NumOfMissingHydrogens</span><span class="sc">;</span> | |
| 944 931 <span class="s">}</span> | |
| 945 932 <span class="k">else</span> <span class="s">{</span> | |
| 946 933 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} = <span class="i">$NumOfMissingHydrogens</span><span class="sc">;</span> | |
| 947 934 <span class="s">}</span> | |
| 948 935 <span class="s">}</span> | |
| 949 936 | |
| 950 937 <span class="k">return</span> <span class="s">(</span>\<span class="i">%ElementsCount</span><span class="cm">,</span> \<span class="i">%NonElementsCount</span><span class="s">)</span><span class="sc">;</span> | |
| 951 938 <span class="s">}</span> | |
| 952 939 | |
| 953 940 <span class="c"># Get number of element and non-elements in molecule. By default, missing</span> | |
| 954 941 <span class="c"># hydrogens are not added to element count.</span> | |
| 955 942 <span class="c">#</span> | |
| 956 <a name="GetNumOfElementsAndNonElements-"></a> 943 <span class="k">sub </span><span class="m">GetNumOfElementsAndNonElements</span> <span class="s">{</span> | |
| 957 944 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 958 945 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 959 946 | |
| 960 947 <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">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 961 948 | |
| 962 949 <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> | |
| 963 950 | |
| 964 951 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 965 952 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 966 953 <span class="i">$NonElementCount</span>++<span class="sc">;</span> | |
| 967 954 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 968 955 <span class="s">}</span> | |
| 969 956 <span class="c"># Process element...</span> | |
| 970 957 <span class="i">$ElementCount</span>++<span class="sc">;</span> | |
| 971 958 <span class="k">if</span> <span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> | |
| 972 959 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 973 960 <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> | |
| 974 961 <span class="s">}</span> | |
| 975 962 <span class="s">}</span> | |
| 976 963 <span class="s">}</span> | |
| 977 964 | |
| 978 965 <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> | |
| 979 966 <span class="s">}</span> | |
| 980 967 | |
| 981 968 <span class="c"># Calculate elemental composition and return reference to arrays</span> | |
| 982 969 <span class="c"># containing elements and their percent composition.</span> | |
| 983 970 <span class="c">#</span> | |
| 984 971 <span class="c"># Caveats:</span> | |
| 985 972 <span class="c"># . By default, missing hydrogens are included</span> | |
| 986 973 <span class="c"># . Non elemnents are ignored</span> | |
| 987 974 <span class="c"># . Mass number are ignored</span> | |
| 988 975 <span class="c">#</span> | |
| 989 <a name="GetElementalComposition-"></a> 976 <span class="k">sub </span><span class="m">GetElementalComposition</span> <span class="s">{</span> | |
| 990 977 <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> | |
| 991 978 <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> | |
| 992 979 | |
| 993 980 <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">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> | |
| 994 981 | |
| 995 982 <span class="i">$IncludeNonElements</span> = <span class="n">0</span><span class="sc">;</span> | |
| 996 983 <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> | |
| 997 984 | |
| 998 985 <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> | |
| 999 986 | |
| 1000 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">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span> | |
| 1001 988 | |
| 1002 989 <span class="k">return</span> <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="s">)</span><span class="sc">;</span> | |
| 1003 990 <span class="s">}</span> | |
| 1004 991 | |
| 1005 992 <span class="c"># Using refernece to element and its composition arrays, format composition information</span> | |
| 1006 993 <span class="c"># as: Element: Composition;...</span> | |
| 1007 994 <span class="c">#</span> | |
| 1008 <a name="FormatElementalCompositionInformation-"></a> 995 <span class="k">sub </span><span class="m">FormatElementalCompositionInformation</span> <span class="s">{</span> | |
| 1009 996 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FourthParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1010 997 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Precision</span><span class="s">)</span><span class="sc">;</span> | |
| 1011 998 | |
| 1012 999 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecule</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1013 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> | |
| 1014 1001 <span class="s">}</span> | |
| 1015 1002 <span class="k">else</span> <span class="s">{</span> | |
| 1016 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> | |
| 1017 1004 <span class="s">}</span> | |
| 1018 1005 <span class="k">my</span><span class="s">(</span><span class="i">$FormattedInfo</span><span class="s">)</span> = <span class="q">''</span><span class="sc">;</span> | |
| 1019 1006 | |
| 1020 1007 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$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> | |
| 1021 1008 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->FormatElementalCompositionInformation: Elements list is not defined or empty..."</span><span class="sc">;</span> | |
| 1022 1009 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1023 1010 <span class="s">}</span> | |
| 1024 1011 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$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> | |
| 1025 1012 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->FormatElementalCompositionInformation: Elements composition list is not defined or empty..."</span><span class="sc">;</span> | |
| 1026 1013 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1027 1014 <span class="s">}</span> | |
| 1028 1015 | |
| 1029 1016 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Precision</span><span class="s">)</span> <span class="s">{</span> | |
| 1030 1017 <span class="i">$Precision</span> = <span class="n">2</span><span class="sc">;</span> | |
| 1031 1018 <span class="s">}</span> | |
| 1032 1019 | |
| 1033 1020 <span class="i">$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">$Precision</span><span class="s">)</span><span class="sc">;</span> | |
| 1034 1021 | |
| 1035 1022 <span class="k">return</span> <span class="i">$FormattedInfo</span><span class="sc">;</span> | |
| 1036 1023 <span class="s">}</span> | |
| 1037 1024 | |
| 1038 1025 <span class="c"># Copy molecule and its associated data using Storable::dclone and update:</span> | |
| 1039 1026 <span class="c">#</span> | |
| 1040 1027 <span class="c"># o Atom references corresponding atoms and bonds objects</span> | |
| 1041 1028 <span class="c"># o Bond object references</span> | |
| 1042 1029 <span class="c">#</span> | |
| 1043 1030 <span class="c"># Object IDs for Atoms and Bonds don't get changed. So there is no need to clear</span> | |
| 1044 1031 <span class="c"># up any exisiting ring data attached to molecule via graph as vertex IDs.</span> | |
| 1045 1032 <span class="c">#</span> | |
| 1046 <a name="Copy-"></a>1033 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span> | |
| 1047 1034 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1048 1035 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomID</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">%AtomsIDsToNewAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 1049 1036 | |
| 1050 1037 <span class="i">$NewMolecule</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 1051 1038 | |
| 1052 1039 <span class="c"># Update atom references stored as vertex property...</span> | |
| 1053 1040 | |
| 1054 1041 <span class="i">@Atoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1055 1042 <span class="i">%AtomsIDsToNewAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1056 1043 | |
| 1057 1044 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1058 1045 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 1059 1046 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetVerticesProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 1060 1047 <span class="s">}</span> | |
| 1061 1048 | |
| 1062 1049 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 1063 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> | |
| 1064 1051 | |
| 1065 1052 <span class="c"># Setup a reference to copied atom object...</span> | |
| 1066 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> | |
| 1067 1054 <span class="i">$AtomsIDsToNewAtoms</span>{<span class="i">$AtomID</span>} = <span class="i">$NewAtom</span><span class="sc">;</span> | |
| 1068 1055 | |
| 1069 1056 <span class="c"># Update atom reference to new atom object...</span> | |
| 1070 1057 <span class="i">$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> | |
| 1071 1058 <span class="s">}</span> | |
| 1072 1059 | |
| 1073 1060 <span class="c"># Update bond object and bond atom references stored as edge property...</span> | |
| 1074 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">$NewAtom2</span><span class="cm">,</span> <span class="i">@EdgesAtomsIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 1075 1062 <span class="i">@EdgesAtomsIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1076 1063 <span class="i">@EdgesAtomsIDs</span> = <span class="i">$This</span><span class="i">->GetEdges</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1077 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> | |
| 1078 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> | |
| 1079 1066 | |
| 1080 1067 <span class="c"># Get reference to bond object...</span> | |
| 1081 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> | |
| 1082 1069 | |
| 1083 1070 <span class="c"># Make a new bond object and update its atom references...</span> | |
| 1084 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> | |
| 1085 1072 <span class="i">$NewAtom1</span> = <span class="i">$AtomsIDsToNewAtoms</span>{<span class="i">$AtomID1</span>}<span class="sc">;</span> | |
| 1086 1073 <span class="i">$NewAtom2</span> = <span class="i">$AtomsIDsToNewAtoms</span>{<span class="i">$AtomID2</span>}<span class="sc">;</span> | |
| 1087 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">$NewAtom2</span><span class="s">)</span><span class="sc">;</span> | |
| 1088 1075 | |
| 1089 1076 <span class="c"># Update bond object reference in the new molecule...</span> | |
| 1090 1077 <span class="i">$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">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 1091 1078 <span class="s">}</span> | |
| 1092 1079 | |
| 1093 1080 <span class="k">return</span> <span class="i">$NewMolecule</span><span class="sc">;</span> | |
| 1094 1081 <span class="s">}</span> | |
| 1095 1082 | |
| 1096 1083 <span class="c"># Get number of connected components...</span> | |
| 1097 1084 <span class="c">#</span> | |
| 1098 <a name="GetNumOfConnectedComponents-"></a>1085 <span class="k">sub </span><span class="m">GetNumOfConnectedComponents</span> <span class="s">{</span> | |
| 1099 1086 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1100 1087 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfComponents</span><span class="s">)</span><span class="sc">;</span> | |
| 1101 1088 | |
| 1102 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> | |
| 1103 1090 | |
| 1104 1091 <span class="k">return</span> <span class="i">$NumOfComponents</span><span class="sc">;</span> | |
| 1105 1092 <span class="s">}</span> | |
| 1106 1093 | |
| 1107 1094 <span class="c"># Return a reference to an array containing molecules corresponding</span> | |
| 1108 1095 <span class="c"># to connected components sorted in decreasing order of component size...</span> | |
| 1109 1096 <span class="c">#</span> | |
| 1110 <a name="GetConnectedComponents-"></a>1097 <span class="k">sub </span><span class="m">GetConnectedComponents</span> <span class="s">{</span> | |
| 1111 1098 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1112 1099 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">@ComponentMolecules</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span> | |
| 1113 1100 | |
| 1114 1101 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1115 1102 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1116 1103 <span class="i">@ComponentMolecules</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1117 1104 | |
| 1118 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> | |
| 1119 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> | |
| 1120 1107 <span class="s">}</span> | |
| 1121 1108 <span class="k">return</span> <span class="i">@ComponentMolecules</span><span class="sc">;</span> | |
| 1122 1109 <span class="s">}</span> | |
| 1123 1110 | |
| 1124 1111 <span class="c"># Return a reference to largest connected component as a molecule object...</span> | |
| 1125 1112 <span class="c">#</span> | |
| 1126 <a name="GetLargestConnectedComponent-"></a>1113 <span class="k">sub </span><span class="m">GetLargestConnectedComponent</span> <span class="s">{</span> | |
| 1127 1114 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1128 1115 <span class="k">my</span><span class="s">(</span><span class="i">$LargestComponentIndex</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span> | |
| 1129 1116 | |
| 1130 1117 <span class="i">$LargestComponentIndex</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1131 1118 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1132 1119 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1133 1120 | |
| 1134 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> | |
| 1135 1122 <span class="s">}</span> | |
| 1136 1123 | |
| 1137 1124 <span class="c"># Return connected component as a molecule...</span> | |
| 1138 1125 <span class="c">#</span> | |
| 1139 <a name="_GetConnectedComponent-"></a>1126 <span class="k">sub </span><span class="m">_GetConnectedComponent</span> <span class="s">{</span> | |
| 1140 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">$ComponentIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1141 1128 <span class="k">my</span><span class="s">(</span><span class="i">$ComponentMolecule</span><span class="s">)</span><span class="sc">;</span> | |
| 1142 1129 | |
| 1143 1130 <span class="c"># Copy existing molecule...</span> | |
| 1144 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> | |
| 1145 1132 | |
| 1146 1133 <span class="c"># Delete all atoms besides the ones in specified component...</span> | |
| 1147 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">$ComponentIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 1148 1135 | |
| 1149 1136 <span class="c"># Clear any deteced rings...</span> | |
| 1150 1137 <span class="k">if</span> <span class="s">(</span><span class="i">$ComponentMolecule</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1151 1138 <span class="i">$ComponentMolecule</span><span class="i">->ClearRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1152 1139 <span class="s">}</span> | |
| 1153 1140 <span class="k">return</span> <span class="i">$ComponentMolecule</span><span class="sc">;</span> | |
| 1154 1141 <span class="s">}</span> | |
| 1155 1142 | |
| 1156 1143 <span class="c"># Delete atoms corresponding to all connected components except the one specified...</span> | |
| 1157 1144 <span class="c">#</span> | |
| 1158 <a name="_DeleteConnectedComponents-"></a>1145 <span class="k">sub </span><span class="m">_DeleteConnectedComponents</span> <span class="s">{</span> | |
| 1159 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">$KeepComponentIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1160 1147 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 1161 1148 | |
| 1162 1149 <span class="j">INDEX:</span> <span class="k">for</span> <span class="i">$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> | |
| 1163 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> | |
| 1164 1151 <span class="k">next</span> <span class="j">INDEX</span><span class="sc">;</span> | |
| 1165 1152 <span class="s">}</span> | |
| 1166 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">$Index</span>]}<span class="s">)</span> <span class="s">{</span> | |
| 1167 1154 <span class="i">$This</span><span class="i">->DeleteVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 1168 1155 <span class="s">}</span> | |
| 1169 1156 <span class="s">}</span> | |
| 1170 1157 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1171 1158 <span class="s">}</span> | |
| 1172 1159 | |
| 1173 1160 <span class="c"># Return an array containing references to atom arrays corresponding to atoms of</span> | |
| 1174 1161 <span class="c"># connected components sorted in order of their decreasing size...</span> | |
| 1175 1162 <span class="c">#</span> | |
| 1176 <a name="GetConnectedComponentsAtoms-"></a>1163 <span class="k">sub </span><span class="m">GetConnectedComponentsAtoms</span> <span class="s">{</span> | |
| 1177 1164 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1178 1165 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1179 1166 | |
| 1180 1167 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1181 1168 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1182 1169 | |
| 1183 1170 <span class="i">@ComponentsAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1184 1171 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ConnectedComponents</span><span class="s">)</span> <span class="s">{</span> | |
| 1185 1172 <span class="k">my</span><span class="s">(</span><span class="i">@ComponentAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 1186 1173 | |
| 1187 1174 <span class="i">@ComponentAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1188 1175 <span class="i">@ComponentAtoms</span> = <span class="i">$This</span><span class="i">->_GetConnectedComponentAtoms</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span> | |
| 1189 1176 <span class="k">push</span> <span class="i">@ComponentsAtoms</span><span class="cm">,</span> \<span class="i">@ComponentAtoms</span><span class="sc">;</span> | |
| 1190 1177 <span class="s">}</span> | |
| 1191 1178 <span class="k">return</span> <span class="i">@ComponentsAtoms</span><span class="sc">;</span> | |
| 1192 1179 <span class="s">}</span> | |
| 1193 1180 | |
| 1194 1181 <span class="c"># Return an array containing atoms correspondig to largest connected component...</span> | |
| 1195 1182 <span class="c">#</span> | |
| 1196 <a name="GetLargestConnectedComponentAtoms-"></a>1183 <span class="k">sub </span><span class="m">GetLargestConnectedComponentAtoms</span> <span class="s">{</span> | |
| 1197 1184 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1198 1185 <span class="k">my</span><span class="s">(</span><span class="i">$LargestComponentIndex</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span> | |
| 1199 1186 | |
| 1200 1187 <span class="i">$LargestComponentIndex</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1201 1188 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1202 1189 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1203 1190 | |
| 1204 1191 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetConnectedComponentAtoms</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$LargestComponentIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 1205 1192 <span class="s">}</span> | |
| 1206 1193 | |
| 1207 1194 <span class="c"># Return an array containing atoms corresponding to specified connected component...</span> | |
| 1208 1195 <span class="c">#</span> | |
| 1209 <a name="_GetConnectedComponentAtoms-"></a>1196 <span class="k">sub </span><span class="m">_GetConnectedComponentAtoms</span> <span class="s">{</span> | |
| 1210 1197 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1211 1198 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">@ComponentAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 1212 1199 | |
| 1213 1200 <span class="i">@ComponentAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1214 1201 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1215 1202 | |
| 1216 1203 <span class="k">for</span> <span class="i">$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> | |
| 1217 1204 <span class="k">push</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="sc">;</span> | |
| 1218 1205 <span class="s">}</span> | |
| 1219 1206 <span class="i">@ComponentAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 1220 1207 | |
| 1221 1208 <span class="k">return</span> <span class="i">@ComponentAtoms</span><span class="sc">;</span> | |
| 1222 1209 <span class="s">}</span> | |
| 1223 1210 | |
| 1224 1211 <span class="c"># Except for the largest connected component, delete atoms corresponding to all other</span> | |
| 1225 1212 <span class="c"># connected components...</span> | |
| 1226 1213 <span class="c">#</span> | |
| 1227 <a name="KeepLargestComponent-"></a>1214 <span class="k">sub </span><span class="m">KeepLargestComponent</span> <span class="s">{</span> | |
| 1228 1215 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1229 1216 <span class="k">my</span><span class="s">(</span><span class="i">$LargestComponentIndex</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span> | |
| 1230 1217 | |
| 1231 1218 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1232 1219 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1233 1220 <span class="k">if</span> <span class="s">(</span><span class="i">@ConnectedComponents</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 1234 1221 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1235 1222 <span class="s">}</span> | |
| 1236 1223 <span class="i">$LargestComponentIndex</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1237 1224 <span class="i">$This</span><span class="i">->_DeleteConnectedComponents</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$LargestComponentIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 1238 1225 | |
| 1239 1226 <span class="c"># Clear any deteced rings...</span> | |
| 1240 1227 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1241 1228 <span class="i">$This</span><span class="i">->ClearRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1242 1229 <span class="s">}</span> | |
| 1243 1230 | |
| 1244 1231 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1245 1232 <span class="s">}</span> | |
| 1246 1233 | |
| 1247 1234 <span class="c"># Get an array of topologically sorted atoms starting from a specified atom or</span> | |
| 1248 1235 <span class="c"># an arbitrary atom in the molecule...</span> | |
| 1249 1236 <span class="c">#</span> | |
| 1250 <a name="GetTopologicallySortedAtoms-"></a>1237 <span class="k">sub </span><span class="m">GetTopologicallySortedAtoms</span> <span class="s">{</span> | |
| 1251 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> | |
| 1252 1239 <span class="k">my</span><span class="s">(</span><span class="i">@SortedAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 1253 1240 | |
| 1254 1241 <span class="i">@SortedAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1255 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> | |
| 1256 1243 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetTopologicallySortedAtoms: No atoms retrieved: Start atom doesn't exist..."</span><span class="sc">;</span> | |
| 1257 1244 <span class="k">return</span> <span class="i">@SortedAtoms</span><span class="sc">;</span> | |
| 1258 1245 <span class="s">}</span> | |
| 1259 1246 <span class="k">my</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 1260 1247 | |
| 1261 1248 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1262 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">$StartAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1263 1250 | |
| 1264 1251 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetTopologicallySortedVertices</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 1265 1252 <span class="i">@SortedAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 1266 1253 | |
| 1267 1254 <span class="k">return</span> <span class="i">@SortedAtoms</span><span class="sc">;</span> | |
| 1268 1255 <span class="s">}</span> | |
| 1269 1256 | |
| 1270 1257 <span class="c"># Detect rings in molecule...</span> | |
| 1271 1258 <span class="c">#</span> | |
| 1272 <a name="DetectRings-"></a>1259 <span class="k">sub </span><span class="m">DetectRings</span> <span class="s">{</span> | |
| 1273 1260 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1274 1261 | |
| 1275 1262 <span class="c"># Use graph method to detect all cycles and associate 'em to graph as graph</span> | |
| 1276 1263 <span class="c"># and vertex properties...</span> | |
| 1277 1264 <span class="k">return</span> <span class="i">$This</span><span class="i">->DetectCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1278 1265 <span class="s">}</span> | |
| 1279 1266 | |
| 1280 1267 <span class="c"># Clear rings in molecule...</span> | |
| 1281 1268 <span class="c">#</span> | |
| 1282 <a name="ClearRings-"></a>1269 <span class="k">sub </span><span class="m">ClearRings</span> <span class="s">{</span> | |
| 1283 1270 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1284 1271 | |
| 1285 1272 <span class="c"># Use graph method to clear all cycles...</span> | |
| 1286 1273 <span class="i">$This</span><span class="i">->ClearCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1287 1274 | |
| 1288 1275 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1289 1276 <span class="s">}</span> | |
| 1290 1277 | |
| 1291 1278 <span class="c"># Setup rings type paths to use during all ring related methods. Possible values:</span> | |
| 1292 1279 <span class="c"># Independent or All. Default is to use Independent rings.</span> | |
| 1293 1280 <span class="c">#</span> | |
| 1294 <a name="SetActiveRings-"></a>1281 <span class="k">sub </span><span class="m">SetActiveRings</span> <span class="s">{</span> | |
| 1295 1282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1296 1283 | |
| 1297 1284 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$This</span><span class="i">->SetActiveCyclicPaths</span><span class="s">(</span><span class="i">$RingsType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1298 1285 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 1299 1286 <span class="s">}</span> | |
| 1300 1287 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1301 1288 <span class="s">}</span> | |
| 1302 1289 | |
| 1303 1290 <span class="c"># Is it a supported aromaticity model?</span> | |
| 1304 1291 <span class="c">#</span> | |
| 1305 <a name="IsSupportedAromaticityModel-"></a>1292 <span class="k">sub </span><span class="m">IsSupportedAromaticityModel</span> <span class="s">{</span> | |
| 1306 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> | |
| 1307 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> | |
| 1308 1295 | |
| 1309 1296 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecule</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1310 1297 <span class="s">(</span><span class="i">$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">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
| 1311 1298 <span class="s">}</span> | |
| 1312 1299 <span class="k">else</span> <span class="s">{</span> | |
| 1313 1300 <span class="s">(</span><span class="i">$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> | |
| 1314 1301 <span class="s">}</span> | |
| 1315 1302 | |
| 1316 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> | |
| 1317 1304 <span class="s">}</span> | |
| 1318 1305 | |
| 1319 1306 <span class="c"># Get a list of supported aromaticity model names...</span> | |
| 1320 1307 <span class="c">#</span> | |
| 1321 <a name="GetSupportedAromaticityModels-"></a>1308 <span class="k">sub </span><span class="m">GetSupportedAromaticityModels</span> <span class="s">{</span> | |
| 1322 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> | |
| 1323 1310 <span class="s">}</span> | |
| 1324 1311 | |
| 1325 1312 <span class="c"># Set aromaticity model...</span> | |
| 1326 1313 <span class="c">#</span> | |
| 1327 <a name="SetAromaticityModel-"></a>1314 <span class="k">sub </span><span class="m">SetAromaticityModel</span> <span class="s">{</span> | |
| 1328 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> | |
| 1329 1316 | |
| 1330 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> | |
| 1331 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> | |
| 1332 1319 | |
| 1333 1320 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAromaticityModel: The current release of MayaChemTools doesn't support the specified aromaticity model $AromaticityModel. Supported aromaticity models defined in AromaticityModelsData.csv file are: @SupportedModels . Using MayaChemToolsAromaticityModel..."</span><span class="sc">;</span> | |
| 1334 1321 <span class="i">$AromaticityModel</span> = <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span> | |
| 1335 1322 <span class="s">}</span> | |
| 1336 1323 | |
| 1337 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> | |
| 1338 1325 | |
| 1339 1326 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1340 1327 <span class="s">}</span> | |
| 1341 1328 | |
| 1342 1329 <span class="c"># Get aromaticity model...</span> | |
| 1343 1330 <span class="c">#</span> | |
| 1344 <a name="GetAromaticityModel-"></a>1331 <span class="k">sub </span><span class="m">GetAromaticityModel</span> <span class="s">{</span> | |
| 1345 1332 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1346 1333 | |
| 1347 1334 <span class="c"># Is ValenceModel property explicitly set?</span> | |
| 1348 1335 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'AromaticityModel'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1349 1336 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'AromaticityModel'</span><span class="s">)</span><span class="sc">;</span> | |
| 1350 1337 <span class="s">}</span> | |
| 1351 1338 | |
| 1352 1339 <span class="c"># Used internal aromaticity model as default model...</span> | |
| 1353 1340 <span class="k">return</span> <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span> | |
| 1354 1341 <span class="s">}</span> | |
| 1355 1342 | |
| 1356 1343 <span class="c"># Identify aromatic rings and ring systems in a molecule and set aromaticity for</span> | |
| 1357 1344 <span class="c"># corresponding atoms and bonds.</span> | |
| 1358 1345 <span class="c">#</span> | |
| 1359 1346 <span class="c"># What is aromaticity? [ Ref 124 ] It's in the code of the implementer, did you</span> | |
| 1360 1347 <span class="c"># say? Agree. The implementation of aromaticity varies widely across different</span> | |
| 1361 1348 <span class="c"># packages [ Ref 125 ]; additionally, the implementation details are not always</span> | |
| 1362 1349 <span class="c"># completely available, and it's not possible to figure out the exact implementation</span> | |
| 1363 1350 <span class="c"># of aromaticity across various packages. Using the publicly available information,</span> | |
| 1364 1351 <span class="c"># however, one can try to reproduce the available results to the extent possible,</span> | |
| 1365 1352 <span class="c"># along with parameterizing all the control parameters used to implement different</span> | |
| 1366 1353 <span class="c"># aromaticity models, and that's exactly what the current release of MayaChemTools</span> | |
| 1367 1354 <span class="c"># does.</span> | |
| 1368 1355 <span class="c">#</span> | |
| 1369 1356 <span class="c"># The implementation of aromaticity corresponding to various aromaticity models in</span> | |
| 1370 1357 <span class="c"># MayaChemTools package is driven by an external CSV file AromaticityModelsData.csv,</span> | |
| 1371 1358 <span class="c"># which is distributed with the package and is available in lib/data directory. The CSV</span> | |
| 1372 1359 <span class="c"># files contains names of supported aromaticity models, along with various control</span> | |
| 1373 1360 <span class="c"># parameters and their values. This file is loaded and processed during instantiation</span> | |
| 1374 1361 <span class="c"># of Molecule class and data corresponding to specific aromaticity model are used</span> | |
| 1375 1362 <span class="c"># to detect aromaticity for that model. Any new aromaticity model added to the</span> | |
| 1376 1363 <span class="c"># aromaticity data file, using different combinations of values for existing control</span> | |
| 1377 1364 <span class="c"># parameters would work without any changes to the code; the addition of any new</span> | |
| 1378 1365 <span class="c"># control parameters, however, requires its implementation in the code used to</span> | |
| 1379 1366 <span class="c"># calculate number of pi electrons available towards delocalization in a ring or ring</span> | |
| 1380 1367 <span class="c"># systems.</span> | |
| 1381 1368 <span class="c">#</span> | |
| 1382 1369 <span class="c"># The current release of MayaChemTools package supports these aromaticity</span> | |
| 1383 1370 <span class="c"># models: MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,</span> | |
| 1384 1371 <span class="c"># ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,</span> | |
| 1385 1372 <span class="c"># DaylightAromaticityModel, MayaChemToolsAromaticityModel.</span> | |
| 1386 1373 <span class="c">#</span> | |
| 1387 1374 <span class="c"># The current list of control parameters available to detect aromaticity corresponding</span> | |
| 1388 1375 <span class="c"># to different aromaticity models are: AllowHeteroRingAtoms, HeteroRingAtomsList,</span> | |
| 1389 1376 <span class="c"># AllowExocyclicDoubleBonds, AllowHomoNuclearExocyclicDoubleBonds,</span> | |
| 1390 1377 <span class="c"># AllowElectronegativeRingAtomExocyclicDoubleBonds, AllowRingAtomFormalCharge,</span> | |
| 1391 1378 <span class="c"># AllowHeteroRingAtomFormalCharge, MinimumRingSize. The values for these control</span> | |
| 1392 1379 <span class="c"># parameters are specified in AromaticityModelsData.csv file.</span> | |
| 1393 1380 <span class="c">#</span> | |
| 1394 1381 <span class="c"># Although definition of aromaticity differs across various aromaticity models, a ring</span> | |
| 1395 1382 <span class="c"># or a ring system containing 4n + 2 pi electrons (Huckel's rule) corresponding to</span> | |
| 1396 1383 <span class="c"># alternate single and double bonds, in general, is considered aromatic.</span> | |
| 1397 1384 <span class="c">#</span> | |
| 1398 1385 <span class="c"># The available valence free electrons on heterocyclic ring atoms, involved in two single</span> | |
| 1399 1386 <span class="c"># ring bonds, are also allowed to participate in pi electron delocalizaiton for most of</span> | |
| 1400 1387 <span class="c"># the supported aromaticity models.</span> | |
| 1401 1388 <span class="c">#</span> | |
| 1402 1389 <span class="c"># The presence of exocyclic terminal double bond on ring atoms involved in pi electron</span> | |
| 1403 1390 <span class="c"># delocalization is only allowed for some of the aromaticity models. Additionally, the type</span> | |
| 1404 1391 <span class="c"># atoms involved in exocyclic terminal double bonds may result in making a ring or ring</span> | |
| 1405 1392 <span class="c"># system non-aromatic.</span> | |
| 1406 1393 <span class="c">#</span> | |
| 1407 <a name="DetectAromaticity-"></a>1394 <span class="k">sub </span><span class="m">DetectAromaticity</span> <span class="s">{</span> | |
| 1408 1395 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1409 1396 | |
| 1410 1397 <span class="c"># Delete aromaticity property for atoms and bonds...</span> | |
| 1411 1398 <span class="i">$This</span><span class="i">->DeleteAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1412 1399 | |
| 1413 1400 <span class="c"># Any ring out there...</span> | |
| 1414 1401 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1415 1402 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1416 1403 <span class="s">}</span> | |
| 1417 1404 | |
| 1418 1405 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasFusedRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1419 1406 <span class="i">$This</span><span class="i">->_DetectAromaticityUsingFusedRingSets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1420 1407 <span class="s">}</span> | |
| 1421 1408 <span class="k">else</span> <span class="s">{</span> | |
| 1422 1409 <span class="i">$This</span><span class="i">->_DetectAromaticityUsingIndividualRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1423 1410 <span class="s">}</span> | |
| 1424 1411 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1425 1412 <span class="s">}</span> | |
| 1426 1413 | |
| 1427 1414 <span class="c"># Go over all rings and set aromaticity property for corresponding ring atoms</span> | |
| 1428 1415 <span class="c"># and bonds involved in aromatic rings...</span> | |
| 1429 1416 <span class="c">#</span> | |
| 1430 <a name="_DetectAromaticityUsingIndividualRings-"></a>1417 <span class="k">sub </span><span class="m">_DetectAromaticityUsingIndividualRings</span> <span class="s">{</span> | |
| 1431 1418 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1432 1419 | |
| 1433 1420 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DetectRingsAromaticity</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 1434 1421 <span class="s">}</span> | |
| 1435 1422 | |
| 1436 1423 <span class="c"># For each fused ring set, detect aromaticity by treating all of its ring as one aromatic</span> | |
| 1437 1424 <span class="c"># system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in</span> | |
| 1438 1425 <span class="c"># fused set are treated individually for aromaticity detection. Additionally, non-fused</span> | |
| 1439 1426 <span class="c"># rings are handled on their own during aromaticity detection.</span> | |
| 1440 1427 <span class="c">#</span> | |
| 1441 1428 <span class="c"># Note:</span> | |
| 1442 1429 <span class="c"># . pi electrons in common bonds involved in fused ring sets are only counted once.</span> | |
| 1443 1430 <span class="c">#</span> | |
| 1444 1431 <span class="c">#</span> | |
| 1445 <a name="_DetectAromaticityUsingFusedRingSets-"></a>1432 <span class="k">sub </span><span class="m">_DetectAromaticityUsingFusedRingSets</span> <span class="s">{</span> | |
| 1446 1433 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1447 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">$NonFusedRingsRef</span><span class="cm">,</span> <span class="i">@FusedRingSetIsAromatic</span><span class="s">)</span><span class="sc">;</span> | |
| 1448 1435 | |
| 1449 1436 <span class="s">(</span><span class="i">$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> | |
| 1450 1437 | |
| 1451 1438 <span class="i">@FusedRingSetIsAromatic</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1452 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">$FusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1453 1440 <span class="i">$FusedRingSetRef</span> = <span class="i">$FusedRingSetsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 1454 1441 <span class="i">$FusedRingSetIsAromatic</span>[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> | |
| 1455 1442 | |
| 1456 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> | |
| 1457 1444 | |
| 1458 1445 <span class="i">$NumOfPiElectronsInRingSet</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1459 1446 | |
| 1460 1447 <span class="i">%FusedRingSetsBondsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1461 1448 <span class="i">%FusedRingSetsBondsVisitedMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1462 1449 <span class="i">%FusedRingBondsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1463 1450 | |
| 1464 1451 <span class="c"># Setup a bond ID map for all bonds in fused ring set and another one</span> | |
| 1465 1452 <span class="c"># for bonds involved in more than one ring...</span> | |
| 1466 1453 <span class="c">#</span> | |
| 1467 1454 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1468 1455 <span class="k">for</span> <span class="i">$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> | |
| 1469 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> | |
| 1470 1457 <span class="i">$FusedRingSetsBondsMap</span>{<span class="i">$BondID</span>} = <span class="i">$BondID</span><span class="sc">;</span> | |
| 1471 1458 | |
| 1472 1459 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 1473 1460 <span class="i">$FusedRingBondsMap</span>{<span class="i">$BondID</span>} = <span class="i">$BondID</span><span class="sc">;</span> | |
| 1474 1461 <span class="s">}</span> | |
| 1475 1462 <span class="s">}</span> | |
| 1476 1463 <span class="s">}</span> | |
| 1477 1464 | |
| 1478 1465 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1479 1466 <span class="k">my</span><span class="s">(</span><span class="i">@RingBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 1480 1467 | |
| 1481 1468 <span class="i">@RingBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1482 1469 <span class="i">@RingBonds</span> = <span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="sc">;</span> | |
| 1483 1470 <span class="i">$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> | |
| 1484 1471 | |
| 1485 1472 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfPiElectronsInRing</span><span class="s">)</span> <span class="s">{</span> | |
| 1486 1473 <span class="k">next</span> <span class="j">RINGSET</span><span class="sc">;</span> | |
| 1487 1474 <span class="s">}</span> | |
| 1488 1475 <span class="i">$NumOfPiElectronsInRingSet</span> += <span class="i">$NumOfPiElectronsInRing</span><span class="sc">;</span> | |
| 1489 1476 <span class="s">}</span> | |
| 1490 1477 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->_DoPiElectronSatifyHuckelsRule</span><span class="s">(</span><span class="i">$NumOfPiElectronsInRingSet</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1491 1478 <span class="i">$FusedRingSetIsAromatic</span>[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> | |
| 1492 1479 <span class="s">}</span> | |
| 1493 1480 <span class="s">}</span> | |
| 1494 1481 | |
| 1495 1482 <span class="c"># Set atom and bond aromatic flags for ring sets whose pi electrons satisfy Huckel's rule; otherwise,</span> | |
| 1496 1483 <span class="c"># treat rings in a ring set as individual rings for detecting aromaticity...</span> | |
| 1497 1484 <span class="k">for</span> <span class="i">$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> | |
| 1498 1485 <span class="i">$FusedRingSetRef</span> = <span class="i">$FusedRingSetsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 1499 1486 <span class="k">if</span> <span class="s">(</span><span class="i">$FusedRingSetIsAromatic</span>[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span> | |
| 1500 1487 <span class="i">$This</span><span class="i">->_SetRingsAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span><span class="sc">;</span> | |
| 1501 1488 <span class="s">}</span> | |
| 1502 1489 <span class="k">else</span> <span class="s">{</span> | |
| 1503 1490 <span class="i">$This</span><span class="i">->_DetectRingsAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span><span class="sc">;</span> | |
| 1504 1491 <span class="s">}</span> | |
| 1505 1492 <span class="s">}</span> | |
| 1506 1493 | |
| 1507 1494 <span class="i">$This</span><span class="i">->_DetectRingsAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedRingsRef</span>}<span class="s">)</span><span class="sc">;</span> | |
| 1508 1495 | |
| 1509 1496 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1510 1497 <span class="s">}</span> | |
| 1511 1498 | |
| 1512 1499 <span class="c"># Detect and set aromaticity for rings...</span> | |
| 1513 1500 <span class="c">#</span> | |
| 1514 <a name="_DetectRingsAromaticity-"></a>1501 <span class="k">sub </span><span class="m">_DetectRingsAromaticity</span> <span class="s">{</span> | |
| 1515 1502 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1516 1503 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1517 1504 | |
| 1518 1505 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span> | |
| 1519 1506 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckRingAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1520 1507 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span> | |
| 1521 1508 <span class="s">}</span> | |
| 1522 1509 <span class="i">$This</span><span class="i">->_SetRingAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="sc">;</span> | |
| 1523 1510 <span class="s">}</span> | |
| 1524 1511 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1525 1512 <span class="s">}</span> | |
| 1526 1513 | |
| 1527 1514 <span class="c"># Set aromatic property for all all atoms and bonds involved in all specified rings..</span> | |
| 1528 1515 <span class="c">#</span> | |
| 1529 <a name="_SetRingsAromaticity-"></a>1516 <span class="k">sub </span><span class="m">_SetRingsAromaticity</span> <span class="s">{</span> | |
| 1530 1517 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1531 1518 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomsRef</span> <span class="s">)</span><span class="sc">;</span> | |
| 1532 1519 | |
| 1533 1520 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span> | |
| 1534 1521 <span class="i">$This</span><span class="i">->_SetRingAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="sc">;</span> | |
| 1535 1522 <span class="s">}</span> | |
| 1536 1523 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1537 1524 <span class="s">}</span> | |
| 1538 1525 | |
| 1539 1526 <span class="c"># Set aromatic property for all all atoms and bonds involved in ring..</span> | |
| 1540 1527 <span class="c">#</span> | |
| 1541 <a name="_SetRingAromaticity-"></a>1528 <span class="k">sub </span><span class="m">_SetRingAromaticity</span> <span class="s">{</span> | |
| 1542 1529 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1543 1530 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="s">)</span><span class="sc">;</span> | |
| 1544 1531 | |
| 1545 1532 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 1546 1533 <span class="i">$RingAtom</span><span class="i">->SetAromatic</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 1547 1534 <span class="s">}</span> | |
| 1548 1535 <span class="k">for</span> <span class="i">$RingBond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1549 1536 <span class="i">$RingBond</span><span class="i">->SetAromatic</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 1550 1537 <span class="s">}</span> | |
| 1551 1538 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 1552 1539 <span class="s">}</span> | |
| 1553 1540 | |
| 1554 1541 | |
| 1555 1542 <span class="c"># For a ring to be an aromatic ring, all of its atoms must have aromatic property</span> | |
| 1556 1543 <span class="c"># set.</span> | |
| 1557 1544 <span class="c">#</span> | |
| 1558 <a name="IsRingAromatic-"></a>1545 <span class="k">sub </span><span class="m">IsRingAromatic</span> <span class="s">{</span> | |
| 1559 1546 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1560 1547 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtom</span><span class="s">)</span><span class="sc">;</span> | |
| 1561 1548 | |
| 1562 1549 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 1563 1550 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1564 1551 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1565 1552 <span class="s">}</span> | |
| 1566 1553 <span class="s">}</span> | |
| 1567 1554 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 1568 1555 <span class="s">}</span> | |
| 1569 1556 | |
| 1570 1557 <span class="c"># Delete aromatic property for all atoms and bonds...</span> | |
| 1571 1558 <span class="c">#</span> | |
| 1572 <a name="DeleteAromaticity-"></a>1559 <span class="k">sub </span><span class="m">DeleteAromaticity</span> <span class="s">{</span> | |
| 1573 1560 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1574 1561 | |
| 1575 1562 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteAtomsAndBondsAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1576 1563 <span class="s">}</span> | |
| 1577 1564 | |
| 1578 1565 <span class="c"># Check ring aromaticity...</span> | |
| 1579 1566 <span class="c">#</span> | |
| 1580 <a name="_CheckRingAromaticity-"></a>1567 <span class="k">sub </span><span class="m">_CheckRingAromaticity</span> <span class="s">{</span> | |
| 1581 1568 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1582 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> | |
| 1583 1570 | |
| 1584 1571 <span class="i">@RingBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1585 1572 <span class="i">@RingBonds</span> = <span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 1586 1573 | |
| 1587 1574 <span class="i">$NumOfPiElectrons</span> = <span class="i">$This</span><span class="i">->_GetNumOfPiElectronsAvailableForDelocalization</span><span class="s">(</span>\<span class="i">@RingAtoms</span><span class="cm">,</span> \<span class="i">@RingBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 1588 1575 | |
| 1589 1576 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DoPiElectronSatifyHuckelsRule</span><span class="s">(</span><span class="i">$NumOfPiElectrons</span><span class="s">)</span><span class="sc">;</span> | |
| 1590 1577 <span class="s">}</span> | |
| 1591 1578 | |
| 1592 1579 <span class="c"># Get number of pi electrons available for delocalizaiton in a ring or ring system...</span> | |
| 1593 1580 <span class="c">#</span> | |
| 1594 <a name="_GetNumOfPiElectronsAvailableForDelocalization-"></a>1581 <span class="k">sub </span><span class="m">_GetNumOfPiElectronsAvailableForDelocalization</span> <span class="s">{</span> | |
| 1595 1582 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FusedRingBondsMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1596 1583 <span class="k">my</span><span class="s">(</span><span class="i">$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">$ExcludeFreeRadicalElectrons</span><span class="cm">,</span> <span class="i">%ElectronPairContributionProcessedMap</span><span class="s">)</span><span class="sc">;</span> | |
| 1597 1584 | |
| 1598 1585 <span class="i">$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> | |
| 1599 1586 <span class="i">$AromaticityModelDataRef</span> = \<span class="i">%</span>{<span class="i">$AromaticityModelsDataMap</span>{<span class="i">$AromaticityModelName</span>}}<span class="sc">;</span> | |
| 1600 1587 | |
| 1601 1588 <span class="c"># Perform an intial check for potential atomatic ring atoms..</span> | |
| 1602 1589 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1603 1590 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1604 1591 <span class="s">}</span> | |
| 1605 1592 | |
| 1606 1593 <span class="i">$ExocyclicDoubleBondsDataMapRef</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 1607 1594 <span class="i">$ExcludeFreeRadicalElectrons</span> = <span class="n">1</span><span class="sc">;</span> | |
| 1608 1595 | |
| 1609 1596 <span class="i">%ElectronPairContributionProcessedMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1610 1597 | |
| 1611 1598 <span class="s">(</span><span class="i">$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> | |
| 1612 1599 | |
| 1613 1600 <span class="c"># Go over ring atoms and bonds to check their participation in aromaticity and count</span> | |
| 1614 1601 <span class="c"># pi electrons available for delocalization corresponding to various aromaticity models...</span> | |
| 1615 1602 <span class="c">#</span> | |
| 1616 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">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1617 1604 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 1618 1605 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 1619 1606 <span class="i">$BondOrder</span> = <span class="i">$RingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1620 1607 | |
| 1621 1608 <span class="c"># Is this ring bond part of a fused ring system which has been already processed?</span> | |
| 1622 1609 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FusedRingSetsBondsVisitedMapRef</span><span class="s">)</span> && <span class="i">$RingBond</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 1623 1610 <span class="i">$RingBondID</span> = <span class="i">$RingBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1624 1611 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$FusedRingSetsBondsVisitedMapRef</span>->{<span class="i">$RingBondID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1625 1612 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> | |
| 1626 1613 <span class="s">}</span> | |
| 1627 1614 <span class="i">$FusedRingSetsBondsVisitedMapRef</span>->{<span class="i">$RingBondID</span>} = <span class="i">$RingBondID</span><span class="sc">;</span> | |
| 1628 1615 <span class="s">}</span> | |
| 1629 1616 <span class="i">$NumOfRingBondsProcessed</span>++<span class="sc">;</span> | |
| 1630 1617 | |
| 1631 1618 <span class="c"># For first ring, previous ring bond corrresponds to last ring bond...</span> | |
| 1632 1619 <span class="i">$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> | |
| 1633 1620 <span class="i">$PreviousRingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$PreviousIndex</span>]<span class="sc">;</span> | |
| 1634 1621 | |
| 1635 1622 <span class="c"># Check for presence of alternate single/double bond configuration, and pesence of</span> | |
| 1636 1623 <span class="c"># hetero atoms with two single ring bonds along with any exocyclic double bonds...</span> | |
| 1637 1624 <span class="c">#</span> | |
| 1638 1625 <span class="j">BONDORDER:</span> <span class="s">{</span> | |
| 1639 1626 <span class="c"># Is current ring double bond in an alternate single/double bond configuration?</span> | |
| 1640 1627 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 1641 1628 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 1642 1629 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1643 1630 <span class="s">}</span> | |
| 1644 1631 <span class="i">$NumOfConjugatedDoubleBonds</span> += <span class="n">1</span><span class="sc">;</span> | |
| 1645 1632 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> | |
| 1646 1633 <span class="s">}</span> | |
| 1647 1634 | |
| 1648 1635 <span class="c"># Is current ring bond order correspond to an explicit aromatic bond?</span> | |
| 1649 1636 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1.5</span><span class="s">)</span> <span class="s">{</span> | |
| 1650 1637 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 1651 1638 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1652 1639 <span class="s">}</span> | |
| 1653 1640 <span class="i">$NumOfExplicitAromaticBonds</span> += <span class="n">1</span><span class="sc">;</span> | |
| 1654 1641 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> | |
| 1655 1642 <span class="s">}</span> | |
| 1656 1643 | |
| 1657 1644 <span class="c"># Check for potential hetero atoms involved in two single ring bonds along</span> | |
| 1658 1645 <span class="c"># with any terminal exocyclic bonds...</span> | |
| 1659 1646 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 1660 1647 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 1661 1648 <span class="c"># Part of a conjugated system...</span> | |
| 1662 1649 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> | |
| 1663 1650 <span class="s">}</span> | |
| 1664 1651 | |
| 1665 1652 <span class="c"># Identify any exocylic bonds on rings atoms...</span> | |
| 1666 1653 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="s">)</span> <span class="s">{</span> | |
| 1667 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">$FusedRingSetsBondsMapRef</span><span class="s">)</span><span class="sc">;</span> | |
| 1668 1655 <span class="s">}</span> | |
| 1669 1656 | |
| 1670 1657 <span class="c"># Is current ring atom part of an allowed exocyclic terminal bond?</span> | |
| 1671 1658 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">$ExocyclicDoubleBondsDataMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1672 1659 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1673 1660 <span class="s">}</span> | |
| 1674 1661 | |
| 1675 1662 <span class="c"># Is it allowed to have any formal charge?</span> | |
| 1676 1663 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 1677 1664 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1678 1665 <span class="s">}</span> | |
| 1679 1666 | |
| 1680 1667 <span class="c"># It it an allowed hetero ring atom or a carbon atom?</span> | |
| 1681 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">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1682 1669 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1683 1670 <span class="s">}</span> | |
| 1684 1671 | |
| 1685 1672 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1686 1673 <span class="i">$ElectronPairContributionProcessedMap</span>{<span class="i">$RingAtomID</span>} = <span class="i">$RingAtomID</span><span class="sc">;</span> | |
| 1687 1674 | |
| 1688 1675 <span class="c"># Is it able to donate a pair for electrons towards pi electron delocalization?</span> | |
| 1689 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> | |
| 1690 1677 <span class="c"># Possibilites:</span> | |
| 1691 1678 <span class="c"># . Hetero atom with or without formal charge and an available electron pair</span> | |
| 1692 1679 <span class="c"># . Carbon atom with -ve formal charge and with an available electron pair</span> | |
| 1693 1680 <span class="c">#</span> | |
| 1694 1681 <span class="i">$NumOfRingAtomElectronPairs</span> += <span class="n">1</span><span class="sc">;</span> | |
| 1695 1682 <span class="s">}</span> | |
| 1696 1683 <span class="k">else</span> <span class="s">{</span> | |
| 1697 1684 <span class="c"># Is ring atom involved in two single bonds without any electron pair allowed?</span> | |
| 1698 1685 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">$FusedRingBondsMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1699 1686 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1700 1687 <span class="s">}</span> | |
| 1701 1688 <span class="s">}</span> | |
| 1702 1689 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> | |
| 1703 1690 <span class="s">}</span> | |
| 1704 1691 | |
| 1705 1692 <span class="c"># Any other type of ring atom/bond is not allowed to contribute towards pi electron count</span> | |
| 1706 1693 <span class="c"># and caused loss of aromaticity...</span> | |
| 1707 1694 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1708 1695 <span class="s">}</span> | |
| 1709 1696 <span class="s">}</span> | |
| 1710 1697 | |
| 1711 1698 <span class="c"># Check for any electron pair contributions towards pi electron delocalization due to</span> | |
| 1712 1699 <span class="c"># -ve formal charge on ring atoms which haven't been already processed and part of</span> | |
| 1713 1700 <span class="c"># conjugated single/double bond system...</span> | |
| 1714 1701 <span class="c">#</span> | |
| 1715 1702 <span class="i">$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">$AromaticityModelDataRef</span><span class="cm">,</span> \<span class="i">%ElectronPairContributionProcessedMap</span><span class="s">)</span><span class="sc">;</span> | |
| 1716 1703 | |
| 1717 1704 <span class="c"># Setup pi electron count available for delocalization...</span> | |
| 1718 1705 <span class="j">COUNT:</span> <span class="s">{</span> | |
| 1719 1706 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfExplicitAromaticBonds</span> == <span class="i">$NumOfRingBondsProcessed</span><span class="s">)</span> <span class="s">{</span> | |
| 1720 1707 <span class="c"># Each aromatic bond contribute one electron towards pi electron delocalization...</span> | |
| 1721 1708 <span class="i">$NumOfPiElectrons</span> = <span class="i">$NumOfExplicitAromaticBonds</span><span class="sc">;</span> | |
| 1722 1709 <span class="k">last</span> <span class="j">COUNT</span><span class="sc">;</span> | |
| 1723 1710 <span class="s">}</span> | |
| 1724 1711 | |
| 1725 1712 <span class="c"># Each conjugated double bond contribute two electrons towards pi electron delocalization...</span> | |
| 1726 1713 <span class="i">$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> | |
| 1727 1714 <span class="s">}</span> | |
| 1728 1715 | |
| 1729 1716 <span class="k">return</span> <span class="i">$NumOfPiElectrons</span><span class="sc">;</span> | |
| 1730 1717 <span class="s">}</span> | |
| 1731 1718 | |
| 1732 1719 <span class="c"># Check ring atoms for their potential participation in aromatic systems..</span> | |
| 1733 1720 <span class="c">#</span> | |
| 1734 <a name="_CheckRingAtomsForPotentialAromaticity-"></a>1721 <span class="k">sub </span><span class="m">_CheckRingAtomsForPotentialAromaticity</span> <span class="s">{</span> | |
| 1735 1722 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AromaticityModelDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1736 1723 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1737 1724 | |
| 1738 1725 <span class="c"># Check availability of ring atoms and bonds...</span> | |
| 1739 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> | |
| 1740 1727 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1741 1728 <span class="s">}</span> | |
| 1742 1729 | |
| 1743 1730 <span class="c"># Is there any minimum ring size limit?</span> | |
| 1744 1731 <span class="k">if</span> <span class="s">(</span><span class="i">$AromaticityModelDataRef</span>->{<span class="w">MinimumRingSize</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1745 1732 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>} < <span class="i">$AromaticityModelDataRef</span>->{<span class="w">MinimumRingSize</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1746 1733 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1747 1734 <span class="s">}</span> | |
| 1748 1735 <span class="s">}</span> | |
| 1749 1736 | |
| 1750 1737 <span class="c"># Make sure ring bond order is not greater than 2 and ring atom is not connected to more</span> | |
| 1751 1738 <span class="c"># than 3 other atoms to eliminate any non sp2 carbon atoms and still allow for hetero atoms</span> | |
| 1752 1739 <span class="c"># to contrbute towards electron delocalization...</span> | |
| 1753 1740 <span class="c">#</span> | |
| 1754 1741 <span class="k">for</span> <span class="i">$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> | |
| 1755 1742 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 1756 1743 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 1757 1744 | |
| 1758 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">$RingAtom</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> > <span class="n">3</span><span class="s">)</span> <span class="s">{</span> | |
| 1759 1746 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1760 1747 <span class="s">}</span> | |
| 1761 1748 <span class="s">}</span> | |
| 1762 1749 | |
| 1763 1750 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 1764 1751 <span class="s">}</span> | |
| 1765 1752 | |
| 1766 1753 <span class="c"># Identify any exocylic double bonds on ring atoms...</span> | |
| 1767 1754 <span class="c">#</span> | |
| 1768 <a name="_IdentifyRingAtomsInvolvedInExocyclicDoubleBonds-"></a>1755 <span class="k">sub </span><span class="m">_IdentifyRingAtomsInvolvedInExocyclicDoubleBonds</span> <span class="s">{</span> | |
| 1769 1756 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FusedRingSetsBondsMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1770 1757 <span class="k">my</span><span class="s">(</span><span class="i">$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">$RingBondsMapRef</span><span class="cm">,</span> <span class="i">%RingBondsMap</span><span class="cm">,</span> <span class="i">%ExocyclicDoubleBondsDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 1771 1758 | |
| 1772 1759 <span class="c"># Setup a ring bond map to process exocyclic bonds...</span> | |
| 1773 1760 <span class="i">$RingBondsMapRef</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 1774 1761 <span class="i">%RingBondsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1775 1762 | |
| 1776 1763 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$FusedRingSetsBondsMapRef</span><span class="s">)</span> <span class="s">{</span> | |
| 1777 1764 <span class="i">$RingBondsMapRef</span> = <span class="i">$FusedRingSetsBondsMapRef</span><span class="sc">;</span> | |
| 1778 1765 <span class="s">}</span> | |
| 1779 1766 <span class="k">else</span> <span class="s">{</span> | |
| 1780 1767 <span class="k">for</span> <span class="i">$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> | |
| 1781 1768 <span class="i">$RingBondsMap</span>{<span class="i">$BondID</span>} = <span class="i">$BondID</span><span class="sc">;</span> | |
| 1782 1769 <span class="s">}</span> | |
| 1783 1770 <span class="i">$RingBondsMapRef</span> = \<span class="i">%RingBondsMap</span><span class="sc">;</span> | |
| 1784 1771 <span class="s">}</span> | |
| 1785 1772 | |
| 1786 1773 <span class="c"># Intialize exocyclic terminal double bond data...</span> | |
| 1787 1774 <span class="i">%ExocyclicDoubleBondsDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1788 1775 <span class="i">%</span>{<span class="i">$ExocyclicDoubleBondsDataMap</span>{<span class="w">RingAtomID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1789 1776 | |
| 1790 1777 <span class="k">for</span> <span class="i">$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> | |
| 1791 1778 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 1792 1779 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 1793 1780 | |
| 1794 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> | |
| 1795 1782 | |
| 1796 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> | |
| 1797 1784 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->GetBondOrder</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 1798 1785 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 1799 1786 <span class="s">}</span> | |
| 1800 1787 | |
| 1801 1788 <span class="c"># Is it part of ring or ring system under consideration?</span> | |
| 1802 1789 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$RingBondsMapRef</span>->{<span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1803 1790 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 1804 1791 <span class="s">}</span> | |
| 1805 1792 | |
| 1806 1793 <span class="c"># Is bonded atom in a ring or a non-terminal atom?</span> | |
| 1807 1794 <span class="i">$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> | |
| 1808 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> | |
| 1809 1796 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 1810 1797 <span class="s">}</span> | |
| 1811 1798 | |
| 1812 1799 <span class="c"># Track exocyclic terminal double bond information...</span> | |
| 1813 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> | |
| 1814 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> | |
| 1815 1802 <span class="s">}</span> | |
| 1816 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">$BondedAtom</span><span class="sc">;</span> | |
| 1817 1804 <span class="s">}</span> | |
| 1818 1805 <span class="s">}</span> | |
| 1819 1806 | |
| 1820 1807 <span class="k">return</span> \<span class="i">%ExocyclicDoubleBondsDataMap</span><span class="sc">;</span> | |
| 1821 1808 <span class="s">}</span> | |
| 1822 1809 | |
| 1823 1810 <span class="c"># Check to see whether ring atoms are allowed to participate in exocyclic terminal double</span> | |
| 1824 1811 <span class="c"># bonds...</span> | |
| 1825 1812 <span class="c">#</span> | |
| 1826 <a name="_CheckPotentialAromaticRingAtomForExocylicDoubleBonds-"></a>1813 <span class="k">sub </span><span class="m">_CheckPotentialAromaticRingAtomForExocylicDoubleBonds</span> <span class="s">{</span> | |
| 1827 1814 <span class="k">my</span><span class="s">(</span><span class="i">$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">$ExocyclicDoubleBondsDataMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1828 1815 <span class="k">my</span><span class="s">(</span><span class="i">$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">$TerminalAtomElectronagativity</span><span class="s">)</span><span class="sc">;</span> | |
| 1829 1816 | |
| 1830 1817 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1831 1818 | |
| 1832 1819 <span class="c"># Is it part of an exocyclic terminal double bond?</span> | |
| 1833 1820 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span>->{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1834 1821 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 1835 1822 <span class="s">}</span> | |
| 1836 1823 | |
| 1837 1824 <span class="c"># Are exocyclic terminal double bonds allowed?</span> | |
| 1838 1825 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowExocyclicDoubleBonds</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1839 1826 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1840 1827 <span class="s">}</span> | |
| 1841 1828 | |
| 1842 1829 <span class="c"># Are there multiple exocyclic double bonds?</span> | |
| 1843 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> | |
| 1844 1831 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1845 1832 <span class="s">}</span> | |
| 1846 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">$RingAtomID</span>}}<span class="sc">;</span> | |
| 1847 1834 | |
| 1848 1835 <span class="c"># Are homo nuclear exocyclic terminal double bonds allowed?</span> | |
| 1849 1836 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowHomoNuclearExocyclicDoubleBonds</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1850 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> | |
| 1851 1838 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1852 1839 <span class="s">}</span> | |
| 1853 1840 <span class="s">}</span> | |
| 1854 1841 | |
| 1855 1842 <span class="c"># Are ring atoms with higher electronegativity allowed in exocyclic double bonds?</span> | |
| 1856 1843 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowElectronegativeRingAtomExocyclicDoubleBonds</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1857 1844 <span class="i">$RingAtomElectronegativity</span> = <span class="i">PeriodicTable::GetElementPaulingElectronegativity</span><span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 1858 1845 <span class="i">$TerminalAtomElectronagativity</span> = <span class="i">PeriodicTable::GetElementPaulingElectronegativity</span><span class="s">(</span><span class="i">$ExocyclicTerminalAtom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 1859 1846 | |
| 1860 1847 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtomElectronegativity</span> && <span class="i">$TerminalAtomElectronagativity</span><span class="s">)</span> <span class="s">{</span> | |
| 1861 1848 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtomElectronegativity</span> > <span class="i">$TerminalAtomElectronagativity</span><span class="s">)</span> <span class="s">{</span> | |
| 1862 1849 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1863 1850 <span class="s">}</span> | |
| 1864 1851 <span class="s">}</span> | |
| 1865 1852 <span class="s">}</span> | |
| 1866 1853 | |
| 1867 1854 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 1868 1855 <span class="s">}</span> | |
| 1869 1856 | |
| 1870 1857 <span class="c">#</span> | |
| 1871 1858 <span class="c"># Check for any formal charge participation into electron delocalization...</span> | |
| 1872 1859 <span class="c">#</span> | |
| 1873 <a name="_CheckPotentialAromaticRingAtomForFormalCharge-"></a>1860 <span class="k">sub </span><span class="m">_CheckPotentialAromaticRingAtomForFormalCharge</span> <span class="s">{</span> | |
| 1874 1861 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1875 1862 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span> | |
| 1876 1863 | |
| 1877 1864 <span class="c"># Does atom has any formal charge?</span> | |
| 1878 1865 <span class="i">$FormalCharge</span> = <span class="i">$RingAtom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1879 1866 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FormalCharge</span><span class="s">)</span> <span class="s">{</span> | |
| 1880 1867 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 1881 1868 <span class="s">}</span> | |
| 1882 1869 | |
| 1883 1870 <span class="c"># Are ring atoms with formal charge allowed to participate in electron delocalization?</span> | |
| 1884 1871 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowRingAtomFormalCharge</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1885 1872 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1886 1873 <span class="s">}</span> | |
| 1887 1874 | |
| 1888 1875 <span class="c"># Are hetero ring atoms with formal charge allowed to participate in electron delocalization?</span> | |
| 1889 1876 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1890 1877 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowHeteroRingAtomFormalCharge</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1891 1878 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1892 1879 <span class="s">}</span> | |
| 1893 1880 <span class="s">}</span> | |
| 1894 1881 | |
| 1895 1882 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 1896 1883 <span class="s">}</span> | |
| 1897 1884 | |
| 1898 1885 <span class="c">#</span> | |
| 1899 1886 <span class="c"># Check ring atoms for allowed hetero atoms...</span> | |
| 1900 1887 <span class="c">#</span> | |
| 1901 <a name="_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms-"></a>1888 <span class="k">sub </span><span class="m">_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms</span> <span class="s">{</span> | |
| 1902 1889 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1903 1890 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomSymbol</span><span class="s">)</span><span class="sc">;</span> | |
| 1904 1891 | |
| 1905 1892 <span class="c"># Is it a Carbon atom?</span> | |
| 1906 1893 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1907 1894 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 1908 1895 <span class="s">}</span> | |
| 1909 1896 | |
| 1910 1897 <span class="c"># Are heteroatoms allowed?</span> | |
| 1911 1898 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowHeteroRingAtoms</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1912 1899 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1913 1900 <span class="s">}</span> | |
| 1914 1901 | |
| 1915 1902 <span class="c"># Is it an allowed hetero atom?</span> | |
| 1916 1903 <span class="i">$RingAtomSymbol</span> = <span class="i">$RingAtom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1917 1904 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AromaticityModelDataRef</span>->{<span class="w">HeteroRingAtomsListMapRef</span>}->{<span class="i">$RingAtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1918 1905 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1919 1906 <span class="s">}</span> | |
| 1920 1907 | |
| 1921 1908 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 1922 1909 <span class="s">}</span> | |
| 1923 1910 | |
| 1924 1911 <span class="c"># Check for any electron pair contributions toward pi electron delocalization due to</span> | |
| 1925 1912 <span class="c"># -ve formal charge on ring atoms which haven't been already processed and part of</span> | |
| 1926 1913 <span class="c"># conjugated single/double bond system...</span> | |
| 1927 1914 <span class="c">#</span> | |
| 1928 <a name="_GetElectronPairsContributionFromConjugatedRingAtoms-"></a>1915 <span class="k">sub </span><span class="m">_GetElectronPairsContributionFromConjugatedRingAtoms</span> <span class="s">{</span> | |
| 1929 1916 <span class="k">my</span><span class="s">(</span><span class="i">$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">$ElectronPairContributionProcessedMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1930 1917 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 1931 1918 | |
| 1932 1919 <span class="c"># Is formal charge allowed on ring atoms?</span> | |
| 1933 1920 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowRingAtomFormalCharge</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1934 1921 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 1935 1922 <span class="s">}</span> | |
| 1936 1923 | |
| 1937 1924 <span class="i">$NumOfRingAtomElectronPairs</span> = <span class="n">0</span><span class="sc">;</span> | |
| 1938 1925 | |
| 1939 1926 <span class="c"># Process ring atoms...</span> | |
| 1940 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">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1941 1928 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 1942 1929 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 1943 1930 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 1944 1931 | |
| 1945 1932 <span class="c"># Is is already processed?</span> | |
| 1946 1933 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElectronPairContributionProcessedMapRef</span>->{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1947 1934 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> | |
| 1948 1935 <span class="s">}</span> | |
| 1949 1936 <span class="i">$ElectronPairContributionProcessedMapRef</span>->{<span class="i">$RingAtomID</span>} = <span class="i">$RingAtomID</span><span class="sc">;</span> | |
| 1950 1937 | |
| 1951 1938 <span class="c"># Is it allowed to have any formal charge?</span> | |
| 1952 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">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1953 1940 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> | |
| 1954 1941 <span class="s">}</span> | |
| 1955 1942 | |
| 1956 1943 <span class="c"># It it an allowed hetero ring atom or a carbon atom?</span> | |
| 1957 1944 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 1958 1945 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> | |
| 1959 1946 <span class="s">}</span> | |
| 1960 1947 | |
| 1961 1948 <span class="c"># It is an atom with -ve formal charge?</span> | |
| 1962 1949 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span> >= <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 1963 1950 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> | |
| 1964 1951 <span class="s">}</span> | |
| 1965 1952 | |
| 1966 1953 <span class="c"># Is it able to donate a pair for electrons towards pi electron delocalization?</span> | |
| 1967 1954 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetValenceFreeElectrons</span><span class="s">(</span><span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> < <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 1968 1955 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span> | |
| 1969 1956 <span class="s">}</span> | |
| 1970 1957 <span class="i">$NumOfRingAtomElectronPairs</span> += <span class="n">1</span><span class="sc">;</span> | |
| 1971 1958 <span class="s">}</span> | |
| 1972 1959 | |
| 1973 1960 <span class="k">return</span> <span class="i">$NumOfRingAtomElectronPairs</span><span class="sc">;</span> | |
| 1974 1961 <span class="s">}</span> | |
| 1975 1962 | |
| 1976 1963 <span class="c"># Check for ring atoms involved in two single ring bonds without any available electron</span> | |
| 1977 1964 <span class="c"># pair which are allowed to participate in aromatic system, after all other checks</span> | |
| 1978 1965 <span class="c"># corresponding to specified aromaticity models have already been performed...</span> | |
| 1979 1966 <span class="c">#</span> | |
| 1980 <a name="_AllowRingAtomInTwoSingleBondsWithoutElectronPair-"></a>1967 <span class="k">sub </span><span class="m">_AllowRingAtomInTwoSingleBondsWithoutElectronPair</span> <span class="s">{</span> | |
| 1981 1968 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FusedRingBondsMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 1982 1969 | |
| 1983 1970 <span class="j">ALLOWRINGATOM:</span> <span class="s">{</span> | |
| 1984 1971 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span>->{<span class="w">RingAtomID</span>}{<span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> | |
| 1985 1972 <span class="c"># Ring atom in an exocylic terminal double bond without any available electron pair...</span> | |
| 1986 1973 <span class="k">last</span> <span class="j">ALLOWRINGATOM</span><span class="sc">;</span> | |
| 1987 1974 <span class="s">}</span> | |
| 1988 1975 | |
| 1989 1976 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 1990 1977 <span class="c"># Ring atom with positive formal charge without any available electron pair...</span> | |
| 1991 1978 <span class="k">last</span> <span class="j">ALLOWRINGATOM</span><span class="sc">;</span> | |
| 1992 1979 <span class="s">}</span> | |
| 1993 1980 | |
| 1994 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">$PreviousRingBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 1995 1982 <span class="c"># Ring atom involved in fused ring bond, which might end up being part of a conjugated</span> | |
| 1996 1983 <span class="c"># system in another fused ring...</span> | |
| 1997 1984 <span class="k">last</span> <span class="j">ALLOWRINGATOM</span><span class="sc">;</span> | |
| 1998 1985 <span class="s">}</span> | |
| 1999 1986 | |
| 2000 1987 <span class="c"># Ring atom in any other environment is not allowed...</span> | |
| 2001 1988 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2002 1989 <span class="s">}</span> | |
| 2003 1990 | |
| 2004 1991 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2005 1992 <span class="s">}</span> | |
| 2006 1993 | |
| 2007 1994 <span class="c"># Do pi electrons satify huckel's rule: Number of pi electrons correspond to 4n + 2 where</span> | |
| 2008 1995 <span class="c"># n is a positive integer...</span> | |
| 2009 1996 <span class="c">#</span> | |
| 2010 <a name="_DoPiElectronSatifyHuckelsRule-"></a>1997 <span class="k">sub </span><span class="m">_DoPiElectronSatifyHuckelsRule</span> <span class="s">{</span> | |
| 2011 1998 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NumOfPiElectrons</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2012 1999 | |
| 2013 2000 <span class="i">$NumOfPiElectrons</span> = <span class="i">$NumOfPiElectrons</span> - <span class="n">2</span><span class="sc">;</span> | |
| 2014 2001 | |
| 2015 2002 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfPiElectrons</span> > <span class="n">0</span><span class="s">)</span> ? <span class="s">(</span><span class="s">(</span><span class="i">$NumOfPiElectrons</span> % <span class="n">4</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 2016 2003 <span class="s">}</span> | |
| 2017 2004 | |
| 2018 2005 <span class="c"># Delete aromatic property for all atoms and bonds...</span> | |
| 2019 2006 <span class="c">#</span> | |
| 2020 <a name="_DeleteAtomsAndBondsAromaticity-"></a>2007 <span class="k">sub </span><span class="m">_DeleteAtomsAndBondsAromaticity</span> <span class="s">{</span> | |
| 2021 2008 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2022 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> | |
| 2023 2010 | |
| 2024 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> | |
| 2025 2012 <span class="i">$Atom</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2026 2013 <span class="s">}</span> | |
| 2027 2014 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2028 2015 <span class="i">$Bond</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2029 2016 <span class="s">}</span> | |
| 2030 2017 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 2031 2018 <span class="s">}</span> | |
| 2032 2019 | |
| 2033 2020 <span class="c"># Kekulize marked ring and non-ring aromatic atoms in a molecule...</span> | |
| 2034 2021 <span class="c">#</span> | |
| 2035 <a name="KekulizeAromaticAtoms-"></a>2022 <span class="k">sub </span><span class="m">KekulizeAromaticAtoms</span> <span class="s">{</span> | |
| 2036 2023 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2037 2024 | |
| 2038 2025 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeAromaticAtomsInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2039 2026 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2040 2027 <span class="s">}</span> | |
| 2041 2028 | |
| 2042 2029 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeAromaticAtomsNotInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2043 2030 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2044 2031 <span class="s">}</span> | |
| 2045 2032 | |
| 2046 2033 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2047 2034 <span class="s">}</span> | |
| 2048 2035 | |
| 2049 2036 <span class="c"># Kekulize marked aromatic atoms in rings and fused ring sets...</span> | |
| 2050 2037 <span class="c">#</span> | |
| 2051 <a name="_KekulizeAromaticAtomsInRings-"></a>2038 <span class="k">sub </span><span class="m">_KekulizeAromaticAtomsInRings</span> <span class="s">{</span> | |
| 2052 2039 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2053 2040 | |
| 2054 2041 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2055 2042 <span class="c"># Nothing to do...</span> | |
| 2056 2043 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2057 2044 <span class="s">}</span> | |
| 2058 2045 | |
| 2059 2046 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasAromaticAtomsInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2060 2047 <span class="c"># Nothing to do...</span> | |
| 2061 2048 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2062 2049 <span class="s">}</span> | |
| 2063 2050 | |
| 2064 2051 <span class="c"># Identify fully aromatic fused and individual rings along with any partially aromatic ring components</span> | |
| 2065 2052 <span class="c"># using marked aromatic atoms in a molecule and kekulize them as individual stes...</span> | |
| 2066 2053 <span class="c">#</span> | |
| 2067 2054 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 2068 2055 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasFusedRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2069 2056 <span class="s">(</span><span class="i">$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">$This</span><span class="i">->_GetFusedAndNonFusedRingsContainingAromaticAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2070 2057 <span class="s">}</span> | |
| 2071 2058 <span class="k">else</span> <span class="s">{</span> | |
| 2072 2059 <span class="s">(</span><span class="i">$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> | |
| 2073 2060 <span class="s">}</span> | |
| 2074 2061 | |
| 2075 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> | |
| 2076 2063 <span class="s">}</span> | |
| 2077 2064 | |
| 2078 2065 <span class="c"># Identify fully aromatic fused and individual rings along with any partially aromatic ring components</span> | |
| 2079 2066 <span class="c"># using marked aromatic atoms in a molecule...</span> | |
| 2080 2067 <span class="c">#</span> | |
| 2081 <a name="_GetFusedAndNonFusedRingsContainingAromaticAtoms-"></a>2068 <span class="k">sub </span><span class="m">_GetFusedAndNonFusedRingsContainingAromaticAtoms</span> <span class="s">{</span> | |
| 2082 2069 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2083 2070 <span class="k">my</span><span class="s">(</span><span class="i">$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">$PartiallyAromaticRingComponentsRef</span><span class="cm">,</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> <span class="i">@PotentialFullyAromaticRings</span><span class="cm">,</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@PotentialPartiallyAromaticRings</span><span class="cm">,</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="s">)</span><span class="sc">;</span> | |
| 2084 2071 | |
| 2085 2072 <span class="i">@FullyAromaticFusedRingSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2086 2073 | |
| 2087 2074 <span class="i">@PotentialFullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2088 2075 <span class="i">@FullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2089 2076 | |
| 2090 2077 <span class="i">@PotentialPartiallyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2091 2078 <span class="i">@PartiallyAromaticRingComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2092 2079 | |
| 2093 2080 <span class="s">(</span><span class="i">$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> | |
| 2094 2081 | |
| 2095 2082 <span class="c"># Go over fused ring sets...</span> | |
| 2096 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">$FusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2097 2084 <span class="i">$FusedRingSetRef</span> = <span class="i">$FusedRingSetsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 2098 2085 | |
| 2099 2086 <span class="i">$SetAtomsCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2100 2087 <span class="i">$SetAromaticAtomsCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2101 2088 | |
| 2102 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> | |
| 2103 2090 <span class="i">$SetAtomsCount</span> += <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span> | |
| 2104 2091 | |
| 2105 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> | |
| 2106 2093 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2107 2094 <span class="i">$SetAromaticAtomsCount</span> += <span class="n">1</span><span class="sc">;</span> | |
| 2108 2095 <span class="s">}</span> | |
| 2109 2096 <span class="s">}</span> | |
| 2110 2097 <span class="s">}</span> | |
| 2111 2098 | |
| 2112 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> | |
| 2113 2100 <span class="k">next</span> <span class="j">RINGSET</span><span class="sc">;</span> | |
| 2114 2101 <span class="s">}</span> | |
| 2115 2102 | |
| 2116 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> | |
| 2117 2104 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> <span class="i">$FusedRingSetRef</span><span class="sc">;</span> | |
| 2118 2105 <span class="s">}</span> | |
| 2119 2106 <span class="k">else</span> <span class="s">{</span> | |
| 2120 2107 <span class="c"># Identify any individual rings in partial aromatic fused ring sets which might be</span> | |
| 2121 2108 <span class="c"># fully or partially aromatic...</span> | |
| 2122 2109 <span class="c">#</span> | |
| 2123 2110 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2124 2111 <span class="i">$RingAtomsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span> | |
| 2125 2112 <span class="i">$AromaticAtomsCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2126 2113 | |
| 2127 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> | |
| 2128 2115 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2129 2116 <span class="k">next</span> <span class="j">RINGATOM</span><span class="sc">;</span> | |
| 2130 2117 <span class="s">}</span> | |
| 2131 2118 <span class="i">$AromaticAtomsCount</span> += <span class="n">1</span><span class="sc">;</span> | |
| 2132 2119 <span class="s">}</span> | |
| 2133 2120 | |
| 2134 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> | |
| 2135 2122 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span> | |
| 2136 2123 <span class="s">}</span> | |
| 2137 2124 | |
| 2138 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> | |
| 2139 2126 <span class="k">push</span> <span class="i">@PotentialFullyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span> | |
| 2140 2127 <span class="s">}</span> | |
| 2141 2128 <span class="k">else</span> <span class="s">{</span> | |
| 2142 2129 <span class="c"># Track partially aromatic rings in an different list before removing them for</span> | |
| 2143 2130 <span class="c"># any overlap with other rings and then add to fully aromatic rings...</span> | |
| 2144 2131 <span class="k">push</span> <span class="i">@PotentialPartiallyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span> | |
| 2145 2132 <span class="s">}</span> | |
| 2146 2133 <span class="s">}</span> | |
| 2147 2134 <span class="s">}</span> | |
| 2148 2135 <span class="s">}</span> | |
| 2149 2136 | |
| 2150 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> | |
| 2151 2138 <span class="c"># Get any fully aromatic fused ring subsets from potentially fully aromatic rings...</span> | |
| 2152 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> | |
| 2153 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">$This</span><span class="i">->_GetFullyAromaticFusedAndNonFusedRingsInFusedSubset</span><span class="s">(</span>\<span class="i">@PotentialFullyAromaticRings</span><span class="s">)</span><span class="sc">;</span> | |
| 2154 2141 | |
| 2155 2142 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FullyAromaticFusedRingSetsRefs</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2156 2143 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FullyAromaticFusedRingSetsRefs</span>}<span class="sc">;</span> | |
| 2157 2144 <span class="s">}</span> | |
| 2158 2145 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FullyAromaticNonFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2159 2146 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FullyAromaticNonFusedRingsRef</span>}<span class="sc">;</span> | |
| 2160 2147 <span class="s">}</span> | |
| 2161 2148 <span class="s">}</span> | |
| 2162 2149 <span class="k">else</span> <span class="s">{</span> | |
| 2163 2150 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@PotentialFullyAromaticRings</span><span class="sc">;</span> | |
| 2164 2151 <span class="s">}</span> | |
| 2165 2152 | |
| 2166 2153 <span class="c"># Go over partial aromatic ring components...</span> | |
| 2167 2154 <span class="k">if</span> <span class="s">(</span><span class="i">@PotentialPartiallyAromaticRings</span><span class="s">)</span> <span class="s">{</span> | |
| 2168 2155 <span class="i">$PartiallyAromaticRingComponentsRef</span> = <span class="i">$This</span><span class="i">->_GetPartiallyAromaticRingComponents</span><span class="s">(</span>\<span class="i">@PotentialPartiallyAromaticRings</span><span class="cm">,</span> \<span class="i">@PotentialFullyAromaticRings</span><span class="s">)</span><span class="sc">;</span> | |
| 2169 2156 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2170 2157 <span class="k">push</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span> | |
| 2171 2158 <span class="s">}</span> | |
| 2172 2159 <span class="s">}</span> | |
| 2173 2160 | |
| 2174 2161 <span class="c"># Go over non-fused rings...</span> | |
| 2175 2162 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2176 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> | |
| 2177 2164 | |
| 2178 2165 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedFullyAromaticRingsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2179 2166 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$NonFusedFullyAromaticRingsRef</span>}<span class="sc">;</span> | |
| 2180 2167 <span class="s">}</span> | |
| 2181 2168 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedPartiallyAromaticRingComponentsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2182 2169 <span class="k">push</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$NonFusedPartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span> | |
| 2183 2170 <span class="s">}</span> | |
| 2184 2171 <span class="s">}</span> | |
| 2185 2172 | |
| 2186 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> | |
| 2187 2174 <span class="s">}</span> | |
| 2188 2175 | |
| 2189 2176 <span class="c"># Identify fully aromatic fused sets and non-fused rings in potentially fully aromatic</span> | |
| 2190 2177 <span class="c"># rings in fused ring sets...</span> | |
| 2191 2178 <span class="c">#</span> | |
| 2192 2179 <span class="c"># Fully aromatic rings in fused ring sets might contain fully aromatic fused subsets. These</span> | |
| 2193 2180 <span class="c"># fused subets need to be tracked and treated as fused sets.</span> | |
| 2194 2181 <span class="c">#</span> | |
| 2195 2182 <span class="c"># Note:</span> | |
| 2196 2183 <span class="c"># . Fused ring sets share at least one common bond, which could be used to identify</span> | |
| 2197 2184 <span class="c"># any multiple fully aromatic fused rings sets; absence of a shared ring bond implies</span> | |
| 2198 2185 <span class="c"># there are no fused ring sets.</span> | |
| 2199 2186 <span class="c">#</span> | |
| 2200 2187 <span class="c">#</span> | |
| 2201 <a name="_GetFullyAromaticFusedAndNonFusedRingsInFusedSubset-"></a>2188 <span class="k">sub </span><span class="m">_GetFullyAromaticFusedAndNonFusedRingsInFusedSubset</span> <span class="s">{</span> | |
| 2202 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> | |
| 2203 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> | |
| 2204 2191 | |
| 2205 2192 <span class="i">@FullyAromaticFusedRingSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2206 2193 <span class="i">@FullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2207 2194 | |
| 2208 2195 <span class="c"># Setup a ring index map for ring atoms...</span> | |
| 2209 2196 <span class="c">#</span> | |
| 2210 2197 <span class="i">%RingIndexToAtomIDMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2211 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">$PotentialFullyAromaticFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2212 2199 <span class="i">%</span>{<span class="i">$RingIndexToAtomIDMap</span>{<span class="i">$RingIndex</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2213 2200 <span class="k">for</span> <span class="i">$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> | |
| 2214 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> | |
| 2215 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> | |
| 2216 2203 <span class="s">}</span> | |
| 2217 2204 <span class="s">}</span> | |
| 2218 2205 | |
| 2219 2206 <span class="c"># Identify fused ring pairs...</span> | |
| 2220 2207 <span class="c">#</span> | |
| 2221 2208 <span class="i">@RingIndices</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2222 2209 <span class="i">@FusedRingPairIndices</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2223 2210 | |
| 2224 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">$PotentialFullyAromaticFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2225 2212 <span class="k">push</span> <span class="i">@RingIndices</span><span class="cm">,</span> <span class="i">$RingIndex1</span><span class="sc">;</span> | |
| 2226 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> | |
| 2227 2214 <span class="i">$RingIsFuesd</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2228 2215 <span class="j">RINGATOM:</span> <span class="k">for</span> <span class="i">$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> | |
| 2229 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> | |
| 2230 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">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2231 2218 <span class="i">$RingIsFuesd</span> = <span class="n">1</span><span class="sc">;</span> | |
| 2232 2219 <span class="k">last</span> <span class="j">RINGATOM</span><span class="sc">;</span> | |
| 2233 2220 <span class="s">}</span> | |
| 2234 2221 <span class="s">}</span> | |
| 2235 2222 <span class="k">if</span> <span class="s">(</span><span class="i">$RingIsFuesd</span><span class="s">)</span> <span class="s">{</span> | |
| 2236 2223 <span class="k">push</span> <span class="i">@FusedRingPairIndices</span><span class="cm">,</span> <span class="s">(</span><span class="i">$RingIndex1</span><span class="cm">,</span> <span class="i">$RingIndex2</span><span class="s">)</span><span class="sc">;</span> | |
| 2237 2224 <span class="s">}</span> | |
| 2238 2225 <span class="s">}</span> | |
| 2239 2226 <span class="s">}</span> | |
| 2240 2227 | |
| 2241 2228 <span class="k">if</span> <span class="s">(</span>!<span class="i">@FusedRingPairIndices</span><span class="s">)</span> <span class="s">{</span> | |
| 2242 2229 <span class="c"># No fused ring subset out there...</span> | |
| 2243 2230 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>}<span class="sc">;</span> | |
| 2244 2231 | |
| 2245 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> | |
| 2246 2233 <span class="s">}</span> | |
| 2247 2234 | |
| 2248 2235 <span class="c"># Identify fused ring sets...</span> | |
| 2249 2236 <span class="c">#</span> | |
| 2250 2237 <span class="i">$RingIndicesGraph</span> = <span class="i">new</span> <span class="i">Graph</span><span class="s">(</span><span class="i">@RingIndices</span><span class="s">)</span><span class="sc">;</span> | |
| 2251 2238 <span class="i">$RingIndicesGraph</span><span class="i">->AddEdges</span><span class="s">(</span><span class="i">@FusedRingPairIndices</span><span class="s">)</span><span class="sc">;</span> | |
| 2252 2239 <span class="i">@FusedRingSetIndicesRefs</span> = <span class="i">$RingIndicesGraph</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2253 2240 | |
| 2254 2241 <span class="c"># Collect fully aromatic fused ring sets...</span> | |
| 2255 2242 <span class="c">#</span> | |
| 2256 2243 <span class="i">%FullyAromaticFusedRingIndexMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2257 2244 <span class="k">for</span> <span class="i">$FusedRingSetIndicesRef</span> <span class="s">(</span><span class="i">@FusedRingSetIndicesRefs</span><span class="s">)</span> <span class="s">{</span> | |
| 2258 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> | |
| 2259 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> | |
| 2260 2247 <span class="i">$FullyAromaticFusedRingIndexMap</span>{<span class="i">$RingIndex</span>} = <span class="i">$RingIndex</span><span class="sc">;</span> | |
| 2261 2248 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSet</span><span class="cm">,</span> <span class="i">$PotentialFullyAromaticFusedRingsRef</span>->[<span class="i">$RingIndex</span>]<span class="sc">;</span> | |
| 2262 2249 <span class="s">}</span> | |
| 2263 2250 <span class="k">if</span> <span class="s">(</span><span class="i">@FullyAromaticFusedRingSet</span><span class="s">)</span> <span class="s">{</span> | |
| 2264 2251 <span class="c"># Sort rings by size with in the fused ring set...</span> | |
| 2265 2252 <span class="i">@FullyAromaticFusedRingSet</span> = <span class="k">sort</span> <span class="s">{</span> <span class="k">scalar</span> <span class="i">@$a</span> <=> <span class="k">scalar</span> <span class="i">@$b</span> <span class="s">}</span> <span class="i">@FullyAromaticFusedRingSet</span><span class="sc">;</span> | |
| 2266 2253 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> \<span class="i">@FullyAromaticFusedRingSet</span><span class="sc">;</span> | |
| 2267 2254 <span class="s">}</span> | |
| 2268 2255 <span class="s">}</span> | |
| 2269 2256 | |
| 2270 2257 <span class="c"># Collect fully aromatic non-fused rings...</span> | |
| 2271 2258 <span class="c">#</span> | |
| 2272 2259 <span class="j">RINGINDEX:</span> <span class="k">for</span> <span class="i">$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> | |
| 2273 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> | |
| 2274 2261 <span class="k">next</span> <span class="j">RINGINDEX</span><span class="sc">;</span> | |
| 2275 2262 <span class="s">}</span> | |
| 2276 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> | |
| 2277 2264 <span class="s">}</span> | |
| 2278 2265 | |
| 2279 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> | |
| 2280 2267 <span class="s">}</span> | |
| 2281 2268 | |
| 2282 2269 <span class="c"># Identify individual non-fused rings containing aromatic atoms...</span> | |
| 2283 2270 <span class="c">#</span> | |
| 2284 <a name="_GetIndividualRingsContainingAromaticAtoms-"></a>2271 <span class="k">sub </span><span class="m">_GetIndividualRingsContainingAromaticAtoms</span> <span class="s">{</span> | |
| 2285 2272 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2286 2273 | |
| 2287 2274 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRingsContainingAromaticAtoms</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 2288 2275 <span class="s">}</span> | |
| 2289 2276 | |
| 2290 2277 <span class="c"># Identify individual non-fused rings containing aromatic atoms...</span> | |
| 2291 2278 <span class="c">#</span> | |
| 2292 <a name="_GetRingsContainingAromaticAtoms-"></a>2279 <span class="k">sub </span><span class="m">_GetRingsContainingAromaticAtoms</span> <span class="s">{</span> | |
| 2293 2280 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2294 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">$PartiallyAromaticRingComponentsRef</span><span class="cm">,</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@PartiallyAromaticRings</span><span class="s">)</span><span class="sc">;</span> | |
| 2295 2282 | |
| 2296 2283 <span class="i">@FullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2297 2284 <span class="i">@PartiallyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2298 2285 | |
| 2299 2286 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span> | |
| 2300 2287 <span class="i">$RingAtomsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span> | |
| 2301 2288 <span class="i">$AromaticAtomsCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2302 2289 | |
| 2303 2290 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2304 2291 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2305 2292 <span class="i">$AromaticAtomsCount</span> += <span class="n">1</span><span class="sc">;</span> | |
| 2306 2293 <span class="s">}</span> | |
| 2307 2294 <span class="s">}</span> | |
| 2308 2295 | |
| 2309 2296 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$AromaticAtomsCount</span> && <span class="i">$RingAtomsCount</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2310 2297 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span> | |
| 2311 2298 <span class="s">}</span> | |
| 2312 2299 | |
| 2313 2300 <span class="k">if</span> <span class="s">(</span><span class="i">$AromaticAtomsCount</span> == <span class="i">$RingAtomsCount</span><span class="s">)</span> <span class="s">{</span> | |
| 2314 2301 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span> | |
| 2315 2302 <span class="s">}</span> | |
| 2316 2303 <span class="k">else</span> <span class="s">{</span> | |
| 2317 2304 <span class="k">push</span> <span class="i">@PartiallyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span> | |
| 2318 2305 <span class="s">}</span> | |
| 2319 2306 <span class="s">}</span> | |
| 2320 2307 | |
| 2321 2308 <span class="i">$PartiallyAromaticRingComponentsRef</span> = <span class="i">$This</span><span class="i">->_GetPartiallyAromaticRingComponents</span><span class="s">(</span>\<span class="i">@PartiallyAromaticRings</span><span class="s">)</span><span class="sc">;</span> | |
| 2322 2309 | |
| 2323 2310 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 2324 2311 <span class="s">}</span> | |
| 2325 2312 | |
| 2326 2313 <span class="c"># Get connected aromatic components with in partially aromatic rings...</span> | |
| 2327 2314 <span class="c">#</span> | |
| 2328 <a name="_GetPartiallyAromaticRingComponents-"></a>2315 <span class="k">sub </span><span class="m">_GetPartiallyAromaticRingComponents</span> <span class="s">{</span> | |
| 2329 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">$FullyAromaticRingsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2330 2317 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Index</span><span class="cm">,</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="cm">,</span> <span class="i">%FullyAromaticRingAtomsMap</span><span class="s">)</span><span class="sc">;</span> | |
| 2331 2318 | |
| 2332 2319 <span class="i">@PartiallyAromaticRingComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2333 2320 | |
| 2334 2321 <span class="c"># Setup a map for atoms involve in fully aromatic rings to remove remove partial rings</span> | |
| 2335 2322 <span class="c"># containing only those atoms which are already part of some other fully aromatic ring</span> | |
| 2336 2323 <span class="c"># in fused ring scenarios or some other partially aromatic ring...</span> | |
| 2337 2324 <span class="c">#</span> | |
| 2338 2325 <span class="i">%FullyAromaticRingAtomsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2339 2326 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$FullyAromaticRingsRef</span><span class="s">)</span> <span class="s">{</span> | |
| 2340 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> | |
| 2341 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> | |
| 2342 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> | |
| 2343 2330 <span class="i">$FullyAromaticRingAtomsMap</span>{<span class="i">$RingAtomID</span>} = <span class="i">$RingAtomID</span><span class="sc">;</span> | |
| 2344 2331 <span class="s">}</span> | |
| 2345 2332 <span class="s">}</span> | |
| 2346 2333 <span class="s">}</span> | |
| 2347 2334 | |
| 2348 2335 <span class="c"># . Identify any connected components with in each partially aromatic ring.</span> | |
| 2349 2336 <span class="c"># . Use ring atom indices to figure out connnected components in rings: All ring atoms</span> | |
| 2350 2337 <span class="c"># in a connected component have sequential indices and a difference by more than</span> | |
| 2351 2338 <span class="c"># 1 indicates a new component in the list.</span> | |
| 2352 2339 <span class="c">#</span> | |
| 2353 2340 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PotentialPartiallyAromaticRingsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2354 2341 <span class="k">my</span><span class="s">(</span><span class="i">@AromaticRingAtoms</span><span class="cm">,</span> <span class="i">@AromaticRingAtomsIndices</span><span class="s">)</span><span class="sc">;</span> | |
| 2355 2342 | |
| 2356 2343 <span class="i">@AromaticRingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2357 2344 <span class="i">@AromaticRingAtomsIndices</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2358 2345 | |
| 2359 2346 <span class="j">RINGATOM:</span> <span class="k">for</span> <span class="i">$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> | |
| 2360 2347 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 2361 2348 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2362 2349 | |
| 2363 2350 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$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> | |
| 2364 2351 <span class="k">next</span> <span class="j">RINGATOM</span><span class="sc">;</span> | |
| 2365 2352 <span class="s">}</span> | |
| 2366 2353 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2367 2354 <span class="k">next</span> <span class="j">RINGATOM</span><span class="sc">;</span> | |
| 2368 2355 <span class="s">}</span> | |
| 2369 2356 <span class="k">push</span> <span class="i">@AromaticRingAtoms</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="sc">;</span> | |
| 2370 2357 <span class="k">push</span> <span class="i">@AromaticRingAtomsIndices</span><span class="cm">,</span> <span class="i">$Index</span><span class="sc">;</span> | |
| 2371 2358 | |
| 2372 2359 <span class="s">}</span> | |
| 2373 2360 <span class="k">if</span> <span class="s">(</span>!<span class="i">@AromaticRingAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 2374 2361 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span> | |
| 2375 2362 <span class="s">}</span> | |
| 2376 2363 | |
| 2377 2364 <span class="c"># Start off with a new connected component...</span> | |
| 2378 2365 <span class="c">#</span> | |
| 2379 2366 <span class="k">my</span><span class="s">(</span><span class="i">$ComponentNum</span><span class="s">)</span><span class="sc">;</span> | |
| 2380 2367 <span class="i">$ComponentNum</span> = <span class="k">scalar</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="sc">;</span> | |
| 2381 2368 <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponents</span>[<span class="i">$ComponentNum</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2382 2369 | |
| 2383 2370 <span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2384 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> | |
| 2385 2372 | |
| 2386 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> | |
| 2387 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> | |
| 2388 2375 <span class="c"># New connected component...</span> | |
| 2389 2376 <span class="i">$ComponentNum</span> += <span class="n">1</span><span class="sc">;</span> | |
| 2390 2377 <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponents</span>[<span class="i">$ComponentNum</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2391 2378 <span class="s">}</span> | |
| 2392 2379 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponents</span>[<span class="i">$ComponentNum</span>]}<span class="cm">,</span> <span class="i">$AromaticRingAtoms</span>[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 2393 2380 <span class="s">}</span> | |
| 2394 2381 <span class="s">}</span> | |
| 2395 2382 | |
| 2396 2383 <span class="k">return</span> <span class="s">(</span>\<span class="i">@PartiallyAromaticRingComponents</span><span class="s">)</span><span class="sc">;</span> | |
| 2397 2384 <span class="s">}</span> | |
| 2398 2385 | |
| 2399 2386 <span class="c"># Kekulize fully aromatic fused and individual rings along with any partially aromatic ring</span> | |
| 2400 2387 <span class="c"># components...</span> | |
| 2401 2388 <span class="c">#</span> | |
| 2402 <a name="_KekulizeCompleteAndPartialAromaticRings-"></a>2389 <span class="k">sub </span><span class="m">_KekulizeCompleteAndPartialAromaticRings</span> <span class="s">{</span> | |
| 2403 2390 <span class="k">my</span><span class="s">(</span><span class="i">$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">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2404 2391 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 2405 2392 | |
| 2406 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">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 2407 2394 | |
| 2408 2395 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$ConnectedPathsAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2409 2396 <span class="c"># Nothing to do...</span> | |
| 2410 2397 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2411 2398 <span class="s">}</span> | |
| 2412 2399 | |
| 2413 2400 <span class="c"># Delete any aromaticity property set for non-ring bonds connected any two ring</span> | |
| 2414 2401 <span class="c"># aromatic atoms...</span> | |
| 2415 2402 <span class="c">#</span> | |
| 2416 2403 <span class="i">$This</span><span class="i">->_ProcessNonRingAromaticBondsBetweenAromaticRingAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2417 2404 | |
| 2418 2405 <span class="i">%PathAtomsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2419 2406 <span class="i">%PathBondsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2420 2407 | |
| 2421 2408 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> | |
| 2422 2409 | |
| 2423 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">$ConnectedPathsAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2424 2411 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 2425 2412 | |
| 2426 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">$PathSetProcessingStatusRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> | |
| 2427 2414 | |
| 2428 2415 <span class="k">if</span> <span class="s">(</span><span class="i">$ConnectdPathsSetsTypesRef</span>->[<span class="i">$PathSetIndex</span>] =~ <span class="q">/^FusedAromatic$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2429 2416 <span class="c"># Fused set of connected paths...</span> | |
| 2430 2417 <span class="c">#</span> | |
| 2431 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> | |
| 2432 2419 | |
| 2433 2420 <span class="i">$FusedConnectedPathAtomsSetRef</span> = <span class="i">$ConnectedPathsAtomsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="sc">;</span> | |
| 2434 2421 <span class="i">$FusedConnectedPathBondsSetRef</span> = <span class="i">$ConnectedPathsBondsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="sc">;</span> | |
| 2435 2422 | |
| 2436 2423 <span class="c"># Prepare for kekulization...</span> | |
| 2437 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> | |
| 2438 2425 | |
| 2439 2426 <span class="c"># Perform kekulization starting with the first path set...</span> | |
| 2440 2427 <span class="i">$PathSetProcessingStatusRef</span>->[<span class="n">0</span>] = <span class="q">'Processed'</span><span class="sc">;</span> | |
| 2441 2428 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">$PathSetProcessingStatusRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2442 2429 <span class="c"># Kekulization failed for the current fused paths set...</span> | |
| 2443 2430 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2444 2431 <span class="s">}</span> | |
| 2445 2432 <span class="s">}</span> | |
| 2446 2433 <span class="k">else</span> <span class="s">{</span> | |
| 2447 2434 <span class="c"># An individual connected path...</span> | |
| 2448 2435 <span class="c">#</span> | |
| 2449 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> | |
| 2450 2437 | |
| 2451 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> | |
| 2452 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> | |
| 2453 2440 | |
| 2454 2441 <span class="c"># Prepare for kekulization...</span> | |
| 2455 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">$This</span><span class="i">->_SetupConnectedPathSetsForKekulization</span><span class="s">(</span>\<span class="i">@ConnectedPathAtomsSet</span><span class="cm">,</span> \<span class="i">@ConnectedPathBondsSet</span><span class="s">)</span><span class="sc">;</span> | |
| 2456 2443 | |
| 2457 2444 <span class="c"># Perform kekulization...</span> | |
| 2458 2445 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 2459 2446 <span class="c"># Kekulization failed for the current path...</span> | |
| 2460 2447 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2461 2448 <span class="s">}</span> | |
| 2462 2449 <span class="s">}</span> | |
| 2463 2450 | |
| 2464 2451 <span class="c"># Did kekulization succeed for the current path or path set?</span> | |
| 2465 2452 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span> | |
| 2466 2453 <span class="k">last</span> <span class="j">PATHSET</span><span class="sc">;</span> | |
| 2467 2454 <span class="s">}</span> | |
| 2468 2455 | |
| 2469 2456 <span class="c"># Track atom and bond processing state for final assignment after kekulization</span> | |
| 2470 2457 <span class="c"># is successfully completed for all the paths and fused path sets...</span> | |
| 2471 2458 <span class="c">#</span> | |
| 2472 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> | |
| 2473 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> | |
| 2474 2461 <span class="s">}</span> | |
| 2475 2462 | |
| 2476 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> | |
| 2477 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> | |
| 2478 2465 <span class="s">}</span> | |
| 2479 2466 <span class="s">}</span> | |
| 2480 2467 | |
| 2481 2468 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span> | |
| 2482 2469 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_KekulizeCompleteAndPartialAromaticRings: Couldn't perform kekulization for marked ring aromatic atoms..."</span><span class="sc">;</span> | |
| 2483 2470 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2484 2471 <span class="s">}</span> | |
| 2485 2472 | |
| 2486 2473 <span class="c"># Use PathAtomsProcessingStatusMap and PathBondsProcessingStatusMap to set</span> | |
| 2487 2474 <span class="c"># single/double bonds in the molecule after successful kekulization along with modification of</span> | |
| 2488 2475 <span class="c"># any aromatic flags...</span> | |
| 2489 2476 | |
| 2490 2477 <span class="k">for</span> <span class="i">$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> | |
| 2491 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> | |
| 2492 2479 | |
| 2493 2480 <span class="k">if</span> <span class="s">(</span><span class="i">$ConnectdPathsSetsTypesRef</span>->[<span class="i">$PathSetIndex</span>] =~ <span class="q">/^FusedAromatic$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2494 2481 <span class="k">for</span> <span class="i">$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> | |
| 2495 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">$DeleteBondsAromaticity</span><span class="s">)</span><span class="sc">;</span> | |
| 2496 2483 <span class="s">}</span> | |
| 2497 2484 <span class="s">}</span> | |
| 2498 2485 <span class="k">else</span> <span class="s">{</span> | |
| 2499 2486 <span class="k">if</span> <span class="s">(</span><span class="i">$ConnectdPathsSetsTypesRef</span>->[<span class="i">$PathSetIndex</span>] =~ <span class="q">/^PartiallyAromatic$/i</span> <span class="s">)</span> <span class="s">{</span> | |
| 2500 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> | |
| 2501 2488 <span class="s">}</span> | |
| 2502 2489 | |
| 2503 2490 <span class="k">if</span> <span class="s">(</span><span class="i">$DeleteAtomsAromaticity</span><span class="s">)</span> <span class="s">{</span> | |
| 2504 2491 <span class="k">for</span> <span class="i">$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> | |
| 2505 2492 <span class="i">$PathAtom</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2506 2493 <span class="s">}</span> | |
| 2507 2494 <span class="s">}</span> | |
| 2508 2495 | |
| 2509 2496 <span class="i">$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">$DeleteBondsAromaticity</span><span class="s">)</span><span class="sc">;</span> | |
| 2510 2497 <span class="s">}</span> | |
| 2511 2498 <span class="s">}</span> | |
| 2512 2499 | |
| 2513 2500 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2514 2501 <span class="s">}</span> | |
| 2515 2502 | |
| 2516 2503 <span class="c"># Look for any aromatic bonds outside the rings between two ring aromatic atoms</span> | |
| 2517 2504 <span class="c"># and turn them into single non-aromatic bonds before kekulization; otherwise, kekulization</span> | |
| 2518 2505 <span class="c"># fails.</span> | |
| 2519 2506 <span class="c">#</span> | |
| 2520 2507 <span class="c"># Note:</span> | |
| 2521 2508 <span class="c"># . Two atoms marked as aromatic atoms in two different rings, such as two rings</span> | |
| 2522 2509 <span class="c"># connected through a single bond, are still aromatic, but the bond is outside</span> | |
| 2523 2510 <span class="c"># the ring and shouldn't be marked as aromatic. It should be set to single bond without</span> | |
| 2524 2511 <span class="c"># any aromatic property for kekulization to succeed.</span> | |
| 2525 2512 <span class="c">#</span> | |
| 2526 2513 <span class="c"># For example, the molecule generated by SMILES parser for biphenyl SMILES string</span> | |
| 2527 2514 <span class="c"># "c1ccccc1c2ccccc2" sets up an aromatic bond between the two phenyl rings, as</span> | |
| 2528 2515 <span class="c"># it's connected to two aromatic atoms.</span> | |
| 2529 2516 <span class="c">#</span> | |
| 2530 <a name="_ProcessNonRingAromaticBondsBetweenAromaticRingAtoms-"></a>2517 <span class="k">sub </span><span class="m">_ProcessNonRingAromaticBondsBetweenAromaticRingAtoms</span> <span class="s">{</span> | |
| 2531 2518 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2532 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">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 2533 2520 | |
| 2534 2521 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2535 2522 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Bond</span><span class="i">->IsNotInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2536 2523 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 2537 2524 <span class="s">}</span> | |
| 2538 2525 | |
| 2539 2526 <span class="s">(</span><span class="i">$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> | |
| 2540 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> | |
| 2541 2528 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 2542 2529 <span class="s">}</span> | |
| 2543 2530 | |
| 2544 2531 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 2545 2532 <span class="i">$Bond</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2546 2533 <span class="s">}</span> | |
| 2547 2534 | |
| 2548 2535 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 2549 2536 <span class="s">}</span> | |
| 2550 2537 | |
| 2551 2538 <span class="c"># Setup completelty aromatic fused and individual rings along with partially aromatic ring</span> | |
| 2552 2539 <span class="c"># components as sets of connected paths...</span> | |
| 2553 2540 <span class="c">#</span> | |
| 2554 <a name="_SetupCompleteAndPartialAromaticRingsForKekulizaiton-"></a>2541 <span class="k">sub </span><span class="m">_SetupCompleteAndPartialAromaticRingsForKekulizaiton</span> <span class="s">{</span> | |
| 2555 2542 <span class="k">my</span><span class="s">(</span><span class="i">$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">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2556 2543 <span class="k">my</span><span class="s">(</span><span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> <span class="i">@ConnectdPathsSetsTypes</span><span class="s">)</span><span class="sc">;</span> | |
| 2557 2544 | |
| 2558 2545 <span class="i">@ConnectedPathsSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2559 2546 <span class="i">@ConnectedPathsBondsSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2560 2547 <span class="i">@ConnectdPathsSetsTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2561 2548 | |
| 2562 2549 <span class="c"># Setup atoms and bonds for connected paths in fused aromatic ring sets...</span> | |
| 2563 2550 <span class="c">#</span> | |
| 2564 2551 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticFusedRingSetsRef</span> && <span class="i">@</span>{<span class="i">$AromaticFusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2565 2552 <span class="k">my</span><span class="s">(</span><span class="i">$RingSetIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 2566 2553 | |
| 2567 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">$AromaticFusedRingSetsRef</span>}<span class="sc">;</span> | |
| 2568 2555 <span class="k">push</span> <span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AromaticFusedRingSetsRef</span>}<span class="sc">;</span> | |
| 2569 2556 | |
| 2570 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">$AromaticFusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2571 2558 <span class="k">my</span><span class="s">(</span><span class="i">@AromaticFusedRingBondsSet</span><span class="s">)</span><span class="sc">;</span> | |
| 2572 2559 | |
| 2573 2560 <span class="c"># Get ring bonds for each ring set...</span> | |
| 2574 2561 <span class="c">#</span> | |
| 2575 2562 <span class="i">@AromaticFusedRingBondsSet</span> = <span class="i">$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> | |
| 2576 2563 <span class="k">push</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> \<span class="i">@AromaticFusedRingBondsSet</span><span class="sc">;</span> | |
| 2577 2564 <span class="s">}</span> | |
| 2578 2565 <span class="s">}</span> | |
| 2579 2566 | |
| 2580 2567 <span class="c"># Set up atoms and bonds for connected paths in aromatic rings...</span> | |
| 2581 2568 <span class="c">#</span> | |
| 2582 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> | |
| 2583 2570 <span class="k">my</span><span class="s">(</span><span class="i">@AromaticRingBondsSets</span><span class="s">)</span><span class="sc">;</span> | |
| 2584 2571 | |
| 2585 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">$AromaticRingsRef</span>}<span class="sc">;</span> | |
| 2586 2573 <span class="k">push</span> <span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AromaticRingsRef</span>}<span class="sc">;</span> | |
| 2587 2574 | |
| 2588 2575 <span class="c"># Get ring bonds for each ring...</span> | |
| 2589 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> | |
| 2590 2577 <span class="k">push</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> <span class="i">@AromaticRingBondsSets</span><span class="sc">;</span> | |
| 2591 2578 <span class="s">}</span> | |
| 2592 2579 | |
| 2593 2580 <span class="c"># Set up atoms and bonds for connected paths in partially aromatic rings...</span> | |
| 2594 2581 <span class="c">#</span> | |
| 2595 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> | |
| 2596 2583 <span class="k">my</span><span class="s">(</span><span class="i">$ComponentIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 2597 2584 | |
| 2598 2585 <span class="k">push</span> <span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span> | |
| 2599 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">$PartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span> | |
| 2600 2587 | |
| 2601 2588 <span class="k">for</span> <span class="i">$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> | |
| 2602 2589 <span class="k">my</span><span class="s">(</span><span class="i">@ComponentBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 2603 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> | |
| 2604 2591 <span class="k">push</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> \<span class="i">@ComponentBonds</span><span class="sc">;</span> | |
| 2605 2592 <span class="s">}</span> | |
| 2606 2593 <span class="s">}</span> | |
| 2607 2594 | |
| 2608 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> | |
| 2609 2596 <span class="s">}</span> | |
| 2610 2597 | |
| 2611 2598 <span class="c"># Process non-ring connected atoms which are marked aromatic and set connected</span> | |
| 2612 2599 <span class="c"># bonds as alternate single/double bonds...</span> | |
| 2613 2600 <span class="c">#</span> | |
| 2614 2601 <span class="c"># Notes:</span> | |
| 2615 2602 <span class="c"># . Atom and bond aromaticity is deleted during kekulization of non-ring atoms.</span> | |
| 2616 2603 <span class="c">#</span> | |
| 2617 <a name="_KekulizeAromaticAtomsNotInRings-"></a>2604 <span class="k">sub </span><span class="m">_KekulizeAromaticAtomsNotInRings</span> <span class="s">{</span> | |
| 2618 2605 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2619 2606 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 2620 2607 | |
| 2621 2608 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasAromaticAtomsNotInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2622 2609 <span class="c"># Nothing to do...</span> | |
| 2623 2610 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2624 2611 <span class="s">}</span> | |
| 2625 2612 | |
| 2626 2613 <span class="c"># Identify paths for connected components containing non-ring aromatic atoms...</span> | |
| 2627 2614 <span class="s">(</span><span class="i">$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> | |
| 2628 2615 | |
| 2629 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> | |
| 2630 2617 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_KekulizeAromaticAtomsNotInRings: Couldn't perform kekulization for marked non-ring aromatic atoms..."</span><span class="sc">;</span> | |
| 2631 2618 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2632 2619 <span class="s">}</span> | |
| 2633 2620 | |
| 2634 2621 <span class="i">%PathAtomsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2635 2622 <span class="i">%PathBondsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2636 2623 | |
| 2637 2624 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> | |
| 2638 2625 | |
| 2639 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">$ConnectedPathsAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2640 2627 <span class="k">my</span><span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">@ConnectedPathAtomsSet</span><span class="cm">,</span> <span class="i">@ConnectedPathBondsSet</span><span class="s">)</span><span class="sc">;</span> | |
| 2641 2628 | |
| 2642 2629 <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">2</span><span class="sc">;</span> | |
| 2643 2630 | |
| 2644 2631 <span class="i">@ConnectedPathAtomsSet</span> = <span class="s">(</span><span class="i">$ConnectedPathsAtomsRef</span>->[<span class="i">$PathIndex</span>]<span class="s">)</span><span class="sc">;</span> | |
| 2645 2632 <span class="i">@ConnectedPathBondsSet</span> = <span class="s">(</span><span class="i">$ConnectedPathsBondsRef</span>->[<span class="i">$PathIndex</span>]<span class="s">)</span><span class="sc">;</span> | |
| 2646 2633 | |
| 2647 2634 <span class="c"># Prepare for kekulization...</span> | |
| 2648 2635 <span class="s">(</span><span class="i">$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> | |
| 2649 2636 | |
| 2650 2637 <span class="c"># Perform kekulization...</span> | |
| 2651 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">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2652 2639 <span class="c"># Kekulization failed for the current path...</span> | |
| 2653 2640 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2654 2641 <span class="k">last</span> <span class="j">PATH</span><span class="sc">;</span> | |
| 2655 2642 <span class="s">}</span> | |
| 2656 2643 | |
| 2657 2644 <span class="c"># Track atom and bond processing state for final assignment after kekulization</span> | |
| 2658 2645 <span class="c"># is successfully completed for all the paths and fused path sets...</span> | |
| 2659 2646 <span class="c">#</span> | |
| 2660 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> | |
| 2661 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> | |
| 2662 2649 <span class="s">}</span> | |
| 2663 2650 | |
| 2664 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> | |
| 2665 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> | |
| 2666 2653 <span class="s">}</span> | |
| 2667 2654 <span class="s">}</span> | |
| 2668 2655 | |
| 2669 2656 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span> | |
| 2670 2657 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_KekulizeAromaticAtomsNotInRings: Couldn't perform kekulization for marked non-ring aromatic atoms..."</span><span class="sc">;</span> | |
| 2671 2658 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2672 2659 <span class="s">}</span> | |
| 2673 2660 | |
| 2674 2661 <span class="i">$DeleteAtomsAromaticity</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$DeleteBondsAromaticity</span> = <span class="n">1</span><span class="sc">;</span> | |
| 2675 2662 <span class="k">for</span> <span class="i">$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> | |
| 2676 2663 <span class="k">if</span> <span class="s">(</span><span class="i">$DeleteAtomsAromaticity</span><span class="s">)</span> <span class="s">{</span> | |
| 2677 2664 <span class="k">for</span> <span class="i">$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> | |
| 2678 2665 <span class="i">$PathAtom</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2679 2666 <span class="s">}</span> | |
| 2680 2667 <span class="s">}</span> | |
| 2681 2668 <span class="i">$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">$DeleteBondsAromaticity</span><span class="s">)</span><span class="sc">;</span> | |
| 2682 2669 <span class="s">}</span> | |
| 2683 2670 | |
| 2684 2671 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2685 2672 <span class="s">}</span> | |
| 2686 2673 | |
| 2687 2674 <span class="c"># Collect path atoms for connected components paths containing non-ring aromatic atoms...</span> | |
| 2688 2675 <span class="c">#</span> | |
| 2689 <a name="_GetConnectedComponentsPathsForNonRingAromaticAtoms-"></a>2676 <span class="k">sub </span><span class="m">_GetConnectedComponentsPathsForNonRingAromaticAtoms</span> <span class="s">{</span> | |
| 2690 2677 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2691 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> | |
| 2692 2679 | |
| 2693 2680 <span class="c"># Retrieve information for marked aromatic atoms not in the rings...</span> | |
| 2694 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">$This</span><span class="i">->_GetNonRingAromaticAtomIDs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2695 2682 | |
| 2696 2683 <span class="c"># Identify connected components containing marked aromatic atoms not in the rings...</span> | |
| 2697 2684 <span class="s">(</span><span class="i">$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">$AtomIDsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 2698 2685 | |
| 2699 2686 <span class="c"># Identify paths for connected components containing non-ring aromatic atoms...</span> | |
| 2700 2687 <span class="s">(</span><span class="i">$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">$ConnectedComponentsAtomIDsMapRef</span><span class="s">)</span><span class="sc">;</span> | |
| 2701 2688 | |
| 2702 2689 <span class="k">return</span> <span class="s">(</span><span class="i">$ConnectedComponentsPathsAtomsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsPathsBondsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 2703 2690 <span class="s">}</span> | |
| 2704 2691 | |
| 2705 2692 <span class="c"># Collect information for marked aromatic atoms not in the rings...</span> | |
| 2706 2693 <span class="c">#</span> | |
| 2707 <a name="_GetNonRingAromaticAtomIDs-"></a>2694 <span class="k">sub </span><span class="m">_GetNonRingAromaticAtomIDs</span> <span class="s">{</span> | |
| 2708 2695 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2709 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> | |
| 2710 2697 | |
| 2711 2698 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2712 2699 <span class="i">%AtomIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2713 2700 | |
| 2714 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> | |
| 2715 2702 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2716 2703 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 2717 2704 <span class="s">}</span> | |
| 2718 2705 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2719 2706 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 2720 2707 <span class="s">}</span> | |
| 2721 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> | |
| 2722 2709 | |
| 2723 2710 <span class="k">push</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="sc">;</span> | |
| 2724 2711 <span class="i">$AtomIDsMap</span>{<span class="i">$AtomID</span>} = <span class="i">$Atom</span><span class="sc">;</span> | |
| 2725 2712 <span class="s">}</span> | |
| 2726 2713 | |
| 2727 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> | |
| 2728 2715 <span class="s">}</span> | |
| 2729 2716 | |
| 2730 2717 <span class="c"># Retrieve connected non-ring atom components as a reference to an array of references</span> | |
| 2731 2718 <span class="c"># containing atom IDs of connecnted components...</span> | |
| 2732 2719 <span class="c">#</span> | |
| 2733 <a name="_GetConnectedComponentsForNonRingAromaticAtoms-"></a>2720 <span class="k">sub </span><span class="m">_GetConnectedComponentsForNonRingAromaticAtoms</span> <span class="s">{</span> | |
| 2734 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> | |
| 2735 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">$AtomIDsGraph</span><span class="cm">,</span> <span class="i">@BondedAtomPairIDs</span><span class="cm">,</span> <span class="i">@ComponentsAtomIDsRefs</span><span class="cm">,</span> <span class="i">@ComponentsAtomIDsMapRefs</span><span class="s">)</span><span class="sc">;</span> | |
| 2736 2723 | |
| 2737 2724 <span class="i">@ComponentsAtomIDsRefs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2738 2725 <span class="i">@ComponentsAtomIDsMapRefs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2739 2726 | |
| 2740 2727 <span class="c"># Get bonded atom pair IDs...</span> | |
| 2741 2728 <span class="i">@BondedAtomPairIDs</span> = <span class="i">$This</span><span class="i">->_GetBondedAtomPairAtomIDsFromAtomIDs</span><span class="s">(</span><span class="i">@</span>{<span class="i">$AtomIDsRef</span>}<span class="s">)</span><span class="sc">;</span> | |
| 2742 2729 | |
| 2743 2730 <span class="k">if</span> <span class="s">(</span>!<span class="i">@BondedAtomPairIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 2744 2731 <span class="k">return</span> <span class="s">(</span>\<span class="i">@ComponentsAtomIDsRefs</span><span class="cm">,</span> \<span class="i">@ComponentsAtomIDsMapRefs</span><span class="s">)</span><span class="sc">;</span> | |
| 2745 2732 <span class="s">}</span> | |
| 2746 2733 | |
| 2747 2734 <span class="i">$AtomIDsGraph</span> = <span class="i">new</span> <span class="i">Graph</span><span class="s">(</span><span class="i">@</span>{<span class="i">$AtomIDsRef</span>}<span class="s">)</span><span class="sc">;</span> | |
| 2748 2735 <span class="i">$AtomIDsGraph</span><span class="i">->AddEdges</span><span class="s">(</span><span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 2749 2736 | |
| 2750 2737 <span class="i">@ComponentsAtomIDsRefs</span> = <span class="i">$AtomIDsGraph</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2751 2738 | |
| 2752 2739 <span class="c"># Setup atom IDs map for each component...</span> | |
| 2753 2740 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ComponentsAtomIDsRefs</span><span class="s">)</span> <span class="s">{</span> | |
| 2754 2741 <span class="i">%</span>{<span class="i">$ComponentsAtomIDsMapRefs</span>[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2755 2742 | |
| 2756 2743 <span class="k">for</span> <span class="i">$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> | |
| 2757 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> | |
| 2758 2745 <span class="s">}</span> | |
| 2759 2746 <span class="s">}</span> | |
| 2760 2747 | |
| 2761 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> | |
| 2762 2749 <span class="s">}</span> | |
| 2763 2750 | |
| 2764 2751 <span class="c"># Get linear paths for connected components starting and ending at terminal aromatic atoms,</span> | |
| 2765 2752 <span class="c"># which are connected to only one other aromatic atom in the connected component..</span> | |
| 2766 2753 <span class="c">#</span> | |
| 2767 <a name="_GetConnectedComponentsPathsAtomsAndBondsForNonRingAromaticAtoms-"></a>2754 <span class="k">sub </span><span class="m">_GetConnectedComponentsPathsAtomsAndBondsForNonRingAromaticAtoms</span> <span class="s">{</span> | |
| 2768 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> | |
| 2769 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">$EndTerminalAtomID</span><span class="cm">,</span> <span class="i">@Paths</span><span class="cm">,</span> <span class="i">@PathAtomIDs</span><span class="cm">,</span> <span class="i">@PathsAtoms</span><span class="cm">,</span> <span class="i">@PathsBonds</span><span class="cm">,</span> <span class="i">@TerminalAtomIDs</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 2770 2757 | |
| 2771 2758 <span class="i">@PathsAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2772 2759 <span class="i">@PathsBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2773 2760 | |
| 2774 2761 <span class="i">@TerminalAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2775 2762 | |
| 2776 2763 <span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2777 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">$ComponentsAtomIDsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2778 2765 <span class="i">@</span>{<span class="i">$TerminalAtomIDs</span>[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2779 2766 | |
| 2780 2767 <span class="c"># Identify terminal atoms for connected components...</span> | |
| 2781 2768 <span class="c">#</span> | |
| 2782 2769 <span class="c"># Notes:</span> | |
| 2783 2770 <span class="c"># . Terminal atoms are defined as atoms connected to only one marked</span> | |
| 2784 2771 <span class="c"># aromatic atom.</span> | |
| 2785 2772 <span class="c"># . Linear connected compoents contain only two terminal atoms.</span> | |
| 2786 2773 <span class="c">#</span> | |
| 2787 2774 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$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> | |
| 2788 2775 <span class="i">$Atom</span> = <span class="i">$AtomIDsMapRef</span>->{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
| 2789 2776 <span class="i">$NumOfNonRingAromaticNbrs</span> = <span class="n">0</span><span class="sc">;</span> | |
| 2790 2777 | |
| 2791 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> | |
| 2792 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> | |
| 2793 2780 | |
| 2794 2781 <span class="c"># Is neighbor in the same connected components containing aromatic atoms?</span> | |
| 2795 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">$AtomNbrID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2796 2783 <span class="k">next</span> <span class="j">ATOMNBRID</span><span class="sc">;</span> | |
| 2797 2784 <span class="s">}</span> | |
| 2798 2785 <span class="i">$NumOfNonRingAromaticNbrs</span>++<span class="sc">;</span> | |
| 2799 2786 <span class="s">}</span> | |
| 2800 2787 | |
| 2801 2788 <span class="c"># Is it a terminal atom?</span> | |
| 2802 2789 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNonRingAromaticNbrs</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 2803 2790 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 2804 2791 <span class="s">}</span> | |
| 2805 2792 <span class="k">push</span> <span class="i">@</span>{<span class="i">$TerminalAtomIDs</span>[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">$AtomID</span><span class="sc">;</span> | |
| 2806 2793 <span class="s">}</span> | |
| 2807 2794 | |
| 2808 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> | |
| 2809 2796 <span class="k">next</span> <span class="j">COMPONENT</span><span class="sc">;</span> | |
| 2810 2797 <span class="s">}</span> | |
| 2811 2798 | |
| 2812 2799 <span class="c"># Setup bonded atom pair IDs for connected component...</span> | |
| 2813 2800 <span class="c">#</span> | |
| 2814 2801 <span class="i">@AtomIDs</span> = <span class="i">@</span>{<span class="i">$ComponentsAtomIDsRef</span>->[<span class="i">$Index</span>]}<span class="sc">;</span> | |
| 2815 2802 <span class="i">@BondedAtomPairIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2816 2803 | |
| 2817 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> | |
| 2818 2805 <span class="i">$AtomID1</span> = <span class="i">$AtomIDs</span>[<span class="i">$AtomIndex1</span>]<span class="sc">;</span> | |
| 2819 2806 <span class="i">$Atom1</span> = <span class="i">$AtomIDsMapRef</span>->{<span class="i">$AtomID1</span>}<span class="sc">;</span> | |
| 2820 2807 | |
| 2821 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">$#AtomIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 2822 2809 <span class="i">$AtomID2</span> = <span class="i">$AtomIDs</span>[<span class="i">$AtomIndex2</span>]<span class="sc">;</span> | |
| 2823 2810 <span class="i">$Atom2</span> = <span class="i">$AtomIDsMapRef</span>->{<span class="i">$AtomID2</span>}<span class="sc">;</span> | |
| 2824 2811 | |
| 2825 2812 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsBondedToAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2826 2813 <span class="k">push</span> <span class="i">@BondedAtomPairIDs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 2827 2814 <span class="s">}</span> | |
| 2828 2815 <span class="s">}</span> | |
| 2829 2816 <span class="s">}</span> | |
| 2830 2817 | |
| 2831 2818 <span class="k">if</span> <span class="s">(</span>!<span class="i">@BondedAtomPairIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 2832 2819 <span class="k">next</span> <span class="j">COMPONENT</span><span class="sc">;</span> | |
| 2833 2820 <span class="s">}</span> | |
| 2834 2821 | |
| 2835 2822 <span class="c"># Get path for connected component...</span> | |
| 2836 2823 <span class="i">$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> | |
| 2837 2824 <span class="i">$AtomIDsGraph</span><span class="i">->AddEdges</span><span class="s">(</span><span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 2838 2825 | |
| 2839 2826 <span class="s">(</span><span class="i">$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">$Index</span>]}<span class="sc">;</span> | |
| 2840 2827 <span class="i">@Paths</span> = <span class="i">$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> | |
| 2841 2828 | |
| 2842 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> | |
| 2843 2830 <span class="k">next</span> <span class="j">COMPONENT</span><span class="sc">;</span> | |
| 2844 2831 <span class="s">}</span> | |
| 2845 2832 | |
| 2846 2833 <span class="i">@PathAtomIDs</span> = <span class="i">$Paths</span>[<span class="n">0</span>]<span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2847 2834 | |
| 2848 2835 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 2849 2836 <span class="i">@PathAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 2850 2837 <span class="k">push</span> <span class="i">@PathsAtoms</span><span class="cm">,</span> \<span class="i">@PathAtoms</span><span class="sc">;</span> | |
| 2851 2838 | |
| 2852 2839 <span class="k">my</span><span class="s">(</span><span class="i">@PathBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 2853 2840 <span class="i">@PathBonds</span> = <span class="i">$This</span><span class="i">->_GetPathBonds</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 2854 2841 <span class="k">push</span> <span class="i">@PathsBonds</span><span class="cm">,</span> \<span class="i">@PathBonds</span><span class="sc">;</span> | |
| 2855 2842 | |
| 2856 2843 <span class="s">}</span> | |
| 2857 2844 | |
| 2858 2845 <span class="k">return</span> <span class="s">(</span>\<span class="i">@PathsAtoms</span><span class="cm">,</span> \<span class="i">@PathsBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 2859 2846 <span class="s">}</span> | |
| 2860 2847 | |
| 2861 2848 <span class="c"># Setup initial processing status of atoms and bonds involved in connected paths</span> | |
| 2862 2849 <span class="c"># before starting kekulization...</span> | |
| 2863 2850 <span class="c">#</span> | |
| 2864 2851 <span class="c"># Possible atom processing status: DoubleBondPossible, DoubleBondAssigned, DoubleBondNotPossible</span> | |
| 2865 2852 <span class="c"># Initial status: DoubleBondPossible or DoubleBondNotPossible</span> | |
| 2866 2853 <span class="c">#</span> | |
| 2867 2854 <span class="c"># Possible bond processing status: DoubleBondAssigned, SingleBondAssigned, NotProcessed</span> | |
| 2868 2855 <span class="c">#</span> | |
| 2869 2856 <span class="c"># Possible paths processing status: Processed, NotProcessed</span> | |
| 2870 2857 <span class="c"># Initial status: NotProcessed</span> | |
| 2871 2858 <span class="c">#</span> | |
| 2872 <a name="_SetupConnectedPathSetsForKekulization-"></a>2859 <span class="k">sub </span><span class="m">_SetupConnectedPathSetsForKekulization</span> <span class="s">{</span> | |
| 2873 2860 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 2874 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">$BondID</span><span class="cm">,</span> <span class="i">%AtomProcessingStatusMap</span><span class="cm">,</span> <span class="i">%BondProcessingStatusMap</span><span class="cm">,</span> <span class="i">@PathsProcessingStatus</span><span class="cm">,</span> <span class="i">%InitialPathBondOrderMap</span><span class="s">)</span><span class="sc">;</span> | |
| 2875 2862 | |
| 2876 2863 <span class="c"># Possible path set status values: Processed, NotProcessed</span> | |
| 2877 2864 <span class="c"># Initial value: NotProcessed</span> | |
| 2878 2865 <span class="c">#</span> | |
| 2879 2866 <span class="i">@PathsProcessingStatus</span> = <span class="s">(</span><span class="q">'NotProcessed'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsSetsRef</span>}<span class="sc">;</span> | |
| 2880 2867 | |
| 2881 2868 <span class="c"># Collect initial bond order of path bonds before setting bond orders to 1</span> | |
| 2882 2869 <span class="c"># and use it to set the bond order back to intial value after it has been processed for</span> | |
| 2883 2870 <span class="c"># availability of double bonds...</span> | |
| 2884 2871 <span class="c">#</span> | |
| 2885 2872 <span class="i">%InitialPathBondOrderMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2886 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> | |
| 2887 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> | |
| 2888 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> | |
| 2889 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> | |
| 2890 2877 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 2891 2878 <span class="s">}</span> | |
| 2892 2879 <span class="i">$InitialPathBondOrderMap</span>{<span class="i">$BondID</span>} = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2893 2880 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 2894 2881 <span class="s">}</span> | |
| 2895 2882 <span class="s">}</span> | |
| 2896 2883 | |
| 2897 2884 <span class="i">%AtomProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2898 2885 <span class="i">%BondProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 2899 2886 | |
| 2900 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">$PathAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2901 2888 | |
| 2902 2889 <span class="i">$PathAtomsRef</span> = <span class="i">$PathAtomsSetsRef</span>->[<span class="i">$PathIndex</span>]<span class="sc">;</span> | |
| 2903 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> | |
| 2904 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> | |
| 2905 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> | |
| 2906 2893 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 2907 2894 <span class="s">}</span> | |
| 2908 2895 <span class="i">$AtomProcessingStatusMap</span>{<span class="i">$AtomID</span>} = <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetNumOfBondsAvailableForNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> >= <span class="n">1</span><span class="s">)</span> ? <span class="q">'DoubleBondPossible'</span> <span class="co">:</span> <span class="q">'DoubleBondNotPossible'</span><span class="sc">;</span> | |
| 2909 2896 <span class="s">}</span> | |
| 2910 2897 | |
| 2911 2898 <span class="i">$PathBondsRef</span> = <span class="i">$PathBondsSetsRef</span>->[<span class="i">$PathIndex</span>]<span class="sc">;</span> | |
| 2912 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> | |
| 2913 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> | |
| 2914 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> | |
| 2915 2902 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 2916 2903 <span class="s">}</span> | |
| 2917 2904 <span class="i">$BondProcessingStatusMap</span>{<span class="i">$BondID</span>} = <span class="q">'NotProcessed'</span><span class="sc">;</span> | |
| 2918 2905 <span class="s">}</span> | |
| 2919 2906 <span class="s">}</span> | |
| 2920 2907 | |
| 2921 2908 <span class="c"># Set bond orders back to initial bond orders...</span> | |
| 2922 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">$PathAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 2923 2910 <span class="i">$PathBondsRef</span> = <span class="i">$PathBondsSetsRef</span>->[<span class="i">$PathIndex</span>]<span class="sc">;</span> | |
| 2924 2911 | |
| 2925 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> | |
| 2926 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> | |
| 2927 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> | |
| 2928 2915 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="i">$InitialPathBondOrderMap</span>{<span class="i">$BondID</span>}<span class="s">)</span><span class="sc">;</span> | |
| 2929 2916 <span class="s">}</span> | |
| 2930 2917 <span class="s">}</span> | |
| 2931 2918 <span class="s">}</span> | |
| 2932 2919 | |
| 2933 2920 <span class="k">return</span> <span class="s">(</span>\<span class="i">%AtomProcessingStatusMap</span><span class="cm">,</span> \<span class="i">%BondProcessingStatusMap</span><span class="cm">,</span> \<span class="i">@PathsProcessingStatus</span><span class="s">)</span><span class="sc">;</span> | |
| 2934 2921 <span class="s">}</span> | |
| 2935 2922 | |
| 2936 2923 <span class="c"># Kekulize connected path sets corresponding to fused rings, individual rings, or any other</span> | |
| 2937 2924 <span class="c"># connected path...</span> | |
| 2938 2925 <span class="c">#</span> | |
| 2939 2926 <span class="c"># Note:</span> | |
| 2940 2927 <span class="c"># . PathAtomsRef and PathBondsRef contain paths and bonds corresponding to path</span> | |
| 2941 2928 <span class="c"># under consideration for kekulization</span> | |
| 2942 2929 <span class="c"># . PathAtomsSetsRef and PathBondsSetsRef contain any other available paths fused</span> | |
| 2943 2930 <span class="c"># to the path being kekulized</span> | |
| 2944 2931 <span class="c"># . _KekulizeConnectedPathSets is invoked recursively to kekulize all available paths</span> | |
| 2945 2932 <span class="c">#</span> | |
| 2946 <a name="_KekulizeConnectedPathSets-"></a>2933 <span class="k">sub </span><span class="m">_KekulizeConnectedPathSets</span> <span class="s">{</span> | |
| 2947 2934 <span class="k">my</span><span class="s">(</span><span class="i">$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">$PathsProcessingStatusRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 2948 2935 <span class="k">my</span><span class="s">(</span><span class="i">$PathBond</span><span class="s">)</span><span class="sc">;</span> | |
| 2949 2936 | |
| 2950 2937 <span class="c"># Get next available path bond...</span> | |
| 2951 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> | |
| 2952 2939 | |
| 2953 2940 <span class="k">if</span> <span class="s">(</span><span class="i">$PathBond</span><span class="s">)</span> <span class="s">{</span> | |
| 2954 2941 <span class="k">return</span> <span class="i">$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> | |
| 2955 2942 <span class="s">}</span> | |
| 2956 2943 | |
| 2957 2944 <span class="c"># Did kekulization succeed for the current path bonds?</span> | |
| 2958 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">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 2959 2946 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 2960 2947 <span class="s">}</span> | |
| 2961 2948 | |
| 2962 2949 <span class="c"># Is there any other path available for kekulization?</span> | |
| 2963 2950 <span class="s">(</span><span class="i">$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">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="sc">;</span> | |
| 2964 2951 | |
| 2965 2952 <span class="k">if</span> <span class="s">(</span><span class="i">$PathAtomsRef</span> && <span class="i">$PathBondsRef</span><span class="s">)</span> <span class="s">{</span> | |
| 2966 2953 <span class="c"># Recursively call itself to kekulize next path, which could either be a new path or part</span> | |
| 2967 2954 <span class="c"># of a fused paths corresponding to fused ring sets...</span> | |
| 2968 2955 <span class="c">#</span> | |
| 2969 2956 <span class="k">return</span> <span class="i">$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">$PathsProcessingStatusRef</span><span class="s">)</span><span class="sc">;</span> | |
| 2970 2957 <span class="s">}</span> | |
| 2971 2958 | |
| 2972 2959 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 2973 2960 <span class="s">}</span> | |
| 2974 2961 | |
| 2975 2962 <span class="c"># Get next available path bond in a list of path bonds...</span> | |
| 2976 2963 <span class="c">#</span> | |
| 2977 <a name="_GetNextAvailablePathBondForKekulization-"></a>2964 <span class="k">sub </span><span class="m">_GetNextAvailablePathBondForKekulization</span> <span class="s">{</span> | |
| 2978 2965 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 2979 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">$PathBondID</span><span class="s">)</span><span class="sc">;</span> | |
| 2980 2967 | |
| 2981 2968 <span class="i">$AvailablePathBond</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 2982 2969 | |
| 2983 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> | |
| 2984 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> | |
| 2985 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> | |
| 2986 2973 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 2987 2974 <span class="s">}</span> | |
| 2988 2975 <span class="k">if</span> <span class="s">(</span><span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} =~ <span class="q">/^NotProcessed$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 2989 2976 <span class="i">$AvailablePathBond</span> = <span class="i">$PathBond</span><span class="sc">;</span> | |
| 2990 2977 <span class="k">last</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 2991 2978 <span class="s">}</span> | |
| 2992 2979 <span class="s">}</span> | |
| 2993 2980 | |
| 2994 2981 <span class="k">return</span> <span class="s">(</span><span class="i">$AvailablePathBond</span><span class="s">)</span><span class="sc">;</span> | |
| 2995 2982 <span class="s">}</span> | |
| 2996 2983 | |
| 2997 2984 <span class="c"># Process next available path bond for kekulizaiton...</span> | |
| 2998 2985 <span class="c">#</span> | |
| 2999 <a name="_ProcessNextAvailablePathBondForKekulization-"></a>2986 <span class="k">sub </span><span class="m">_ProcessNextAvailablePathBondForKekulization</span> <span class="s">{</span> | |
| 3000 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">$PathsProcessingStatusRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3001 2988 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3002 2989 | |
| 3003 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> | |
| 3004 2991 | |
| 3005 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">$PathBond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3006 2993 <span class="s">(</span><span class="i">$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">$PathAtom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3007 2994 | |
| 3008 2995 <span class="i">%CurrentAtomProcessingStatusMap</span> = <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>}<span class="sc">;</span> | |
| 3009 2996 <span class="i">%CurrentBondProcessingStatusMap</span> = <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>}<span class="sc">;</span> | |
| 3010 2997 | |
| 3011 2998 <span class="c"># Is it possible to assign a double bond to the current path bond?</span> | |
| 3012 2999 <span class="k">if</span> <span class="s">(</span><span class="i">$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$/i</span> <span class="s">)</span> <span class="s">{</span> | |
| 3013 3000 <span class="c"># Set current bond to double bond by appropriately marking atom and bond process status...</span> | |
| 3014 3001 <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID1</span>} = <span class="q">'DoubleBondAssigned'</span><span class="sc">;</span> | |
| 3015 3002 <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID2</span>} = <span class="q">'DoubleBondAssigned'</span><span class="sc">;</span> | |
| 3016 3003 | |
| 3017 3004 <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} = <span class="q">'DoubleBondAssigned'</span><span class="sc">;</span> | |
| 3018 3005 | |
| 3019 3006 <span class="c"># Recursively call _KekulizeConnectedPathSets to kekulize next available bond...</span> | |
| 3020 3007 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$PathsProcessingStatusRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3021 3008 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3022 3009 <span class="s">}</span> | |
| 3023 3010 | |
| 3024 3011 <span class="c"># Double bond at the current ring bond position didn't lead to successful kekulization...</span> | |
| 3025 3012 <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>} = <span class="i">%CurrentAtomProcessingStatusMap</span><span class="sc">;</span> | |
| 3026 3013 <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>} = <span class="i">%CurrentBondProcessingStatusMap</span><span class="sc">;</span> | |
| 3027 3014 <span class="s">}</span> | |
| 3028 3015 | |
| 3029 3016 <span class="c"># Try single bond at the current ring bond position and recursively call _KekulizeConnectedPathSets to kekulize</span> | |
| 3030 3017 <span class="c"># rest of the ring bonds...</span> | |
| 3031 3018 <span class="c">#</span> | |
| 3032 3019 <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} = <span class="q">'SingleBondAssigned'</span><span class="sc">;</span> | |
| 3033 3020 | |
| 3034 3021 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$PathsProcessingStatusRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3035 3022 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3036 3023 <span class="s">}</span> | |
| 3037 3024 | |
| 3038 3025 <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>} = <span class="i">%CurrentAtomProcessingStatusMap</span><span class="sc">;</span> | |
| 3039 3026 <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>} = <span class="i">%CurrentBondProcessingStatusMap</span><span class="sc">;</span> | |
| 3040 3027 | |
| 3041 3028 <span class="c"># Kekulization didn't work out for path bonds...</span> | |
| 3042 3029 | |
| 3043 3030 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3044 3031 | |
| 3045 3032 <span class="s">}</span> | |
| 3046 3033 | |
| 3047 3034 <span class="c"># Get next available path for kekulization from a set of fused ring paths...</span> | |
| 3048 3035 <span class="c">#</span> | |
| 3049 <a name="_GetNextAvailablePathForKekulization-"></a>3036 <span class="k">sub </span><span class="m">_GetNextAvailablePathForKekulization</span> <span class="s">{</span> | |
| 3050 3037 <span class="k">my</span><span class="s">(</span><span class="i">$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">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3051 3038 <span class="k">my</span><span class="s">(</span><span class="i">$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">$NumOfPathBondsProcessed</span><span class="s">)</span><span class="sc">;</span> | |
| 3052 3039 | |
| 3053 3040 <span class="s">(</span><span class="i">$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> | |
| 3054 3041 | |
| 3055 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">$PathsProcessingStatusRef</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3056 3043 <span class="k">return</span> <span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 3057 3044 <span class="s">}</span> | |
| 3058 3045 | |
| 3059 3046 <span class="i">$MaxNumOfPathBondsProcessed</span> = <span class="n">-999</span><span class="sc">;</span> | |
| 3060 3047 <span class="i">$AvailablePathIndex</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 3061 3048 | |
| 3062 3049 <span class="j">PATHINDEX:</span> <span class="k">for</span> <span class="i">$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> | |
| 3063 3050 <span class="k">if</span> <span class="s">(</span><span class="i">$PathsProcessingStatusRef</span>->[<span class="i">$PathIndex</span>] =~ <span class="q">/^Processed$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3064 3051 <span class="k">next</span> <span class="j">PATHINDEX</span><span class="sc">;</span> | |
| 3065 3052 <span class="s">}</span> | |
| 3066 3053 | |
| 3067 3054 <span class="c"># Count of already processed bonds in an unprocessed path bonds through</span> | |
| 3068 3055 <span class="c"># their participation in any fused bonds sets...</span> | |
| 3069 3056 <span class="c">#</span> | |
| 3070 3057 <span class="i">$NumOfPathBondsProcessed</span> = <span class="n">0</span><span class="sc">;</span> | |
| 3071 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">$PathIndex</span>]}<span class="s">)</span> <span class="s">{</span> | |
| 3072 3059 <span class="i">$PathBondID</span> = <span class="i">$PathBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3073 3060 <span class="k">if</span> <span class="s">(</span><span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} =~ <span class="q">/^NotProcessed$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 3074 3061 <span class="k">next</span> <span class="j">PATHBOND</span><span class="sc">;</span> | |
| 3075 3062 <span class="s">}</span> | |
| 3076 3063 <span class="i">$NumOfPathBondsProcessed</span>++<span class="sc">;</span> | |
| 3077 3064 <span class="s">}</span> | |
| 3078 3065 | |
| 3079 3066 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfPathBondsProcessed</span> > <span class="i">$MaxNumOfPathBondsProcessed</span><span class="s">)</span> <span class="s">{</span> | |
| 3080 3067 <span class="i">$AvailablePathIndex</span> = <span class="i">$PathIndex</span><span class="sc">;</span> | |
| 3081 3068 <span class="i">$MaxNumOfPathBondsProcessed</span> = <span class="i">$NumOfPathBondsProcessed</span><span class="sc">;</span> | |
| 3082 3069 <span class="s">}</span> | |
| 3083 3070 | |
| 3084 3071 <span class="s">}</span> | |
| 3085 3072 | |
| 3086 3073 <span class="c"># Is any path available?</span> | |
| 3087 3074 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AvailablePathIndex</span><span class="s">)</span> <span class="s">{</span> | |
| 3088 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> | |
| 3089 3076 <span class="s">}</span> | |
| 3090 3077 | |
| 3091 3078 <span class="i">$PathsProcessingStatusRef</span>->[<span class="i">$AvailablePathIndex</span>] = <span class="q">'Processed'</span><span class="sc">;</span> | |
| 3092 3079 | |
| 3093 3080 <span class="i">$PathAtomsRef</span> = <span class="i">$PathAtomsSetsRef</span>->[<span class="i">$AvailablePathIndex</span>]<span class="sc">;</span> | |
| 3094 3081 <span class="i">$PathBondsRef</span> = <span class="i">$PathBondsSetsRef</span>->[<span class="i">$AvailablePathIndex</span>]<span class="sc">;</span> | |
| 3095 3082 | |
| 3096 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> | |
| 3097 3084 <span class="s">}</span> | |
| 3098 3085 | |
| 3099 3086 <span class="c"># Check for kekulization in a specific set of path bonds. For successful kekulization, all</span> | |
| 3100 3087 <span class="c"># all path atoms marked with DoubleBondPossible must be involved in a path double bond...</span> | |
| 3101 3088 <span class="c">#</span> | |
| 3102 <a name="_DidKekulizationSucceedForPathBonds-"></a>3089 <span class="k">sub </span><span class="m">_DidKekulizationSucceedForPathBonds</span> <span class="s">{</span> | |
| 3103 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">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3104 3091 <span class="k">my</span><span class="s">(</span><span class="i">$PathAtom</span><span class="cm">,</span> <span class="i">$PathAtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 3105 3092 | |
| 3106 3093 <span class="k">for</span> <span class="i">$PathAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 3107 3094 <span class="i">$PathAtomID</span> = <span class="i">$PathAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3108 3095 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$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> | |
| 3109 3096 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3110 3097 <span class="s">}</span> | |
| 3111 3098 <span class="s">}</span> | |
| 3112 3099 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3113 3100 <span class="s">}</span> | |
| 3114 3101 | |
| 3115 3102 <span class="c"># Assign bond orders to the bonds in a molecule which have been successfully</span> | |
| 3116 3103 <span class="c"># kekulized along with optional clearing of aromaticty property...</span> | |
| 3117 3104 <span class="c">#</span> | |
| 3118 <a name="_ProcessBondOrdersAssignedDuringSuccessfulKekulization-"></a>3105 <span class="k">sub </span><span class="m">_ProcessBondOrdersAssignedDuringSuccessfulKekulization</span> <span class="s">{</span> | |
| 3119 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> | |
| 3120 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">$BondOrder</span><span class="s">)</span><span class="sc">;</span> | |
| 3121 3108 | |
| 3122 3109 <span class="i">$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> | |
| 3123 3110 | |
| 3124 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> | |
| 3125 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> | |
| 3126 3113 | |
| 3127 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> | |
| 3128 3115 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessBondOrdersAssignedDuringSuccessfulKekulization: Couldn't process bond with bond ID, $BondID: It's not available in the list of bonds processed for kekulization..."</span><span class="sc">;</span> | |
| 3129 3116 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
| 3130 3117 <span class="s">}</span> | |
| 3131 3118 | |
| 3132 3119 <span class="i">$BondOrder</span> = <span class="s">(</span><span class="i">$BondsProcessingStatusMapRef</span>->{<span class="i">$BondID</span>} =~ <span class="q">/^DoubleBondAssigned$/i</span><span class="s">)</span> ? <span class="n">2</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> | |
| 3133 3120 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="i">$BondOrder</span><span class="s">)</span><span class="sc">;</span> | |
| 3134 3121 | |
| 3135 3122 <span class="k">if</span> <span class="s">(</span><span class="i">$DeleteBondsAromaticity</span><span class="s">)</span> <span class="s">{</span> | |
| 3136 3123 <span class="i">$Bond</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3137 3124 <span class="s">}</span> | |
| 3138 3125 <span class="s">}</span> | |
| 3139 3126 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 3140 3127 <span class="s">}</span> | |
| 3141 3128 | |
| 3142 3129 <span class="c"># Does molecule contains aromatic rings?</span> | |
| 3143 3130 <span class="c">#</span> | |
| 3144 <a name="HasAromaticRings-"></a>3131 <span class="k">sub </span><span class="m">HasAromaticRings</span> <span class="s">{</span> | |
| 3145 3132 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3146 3133 | |
| 3147 3134 <span class="k">return</span> <span class="i">$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> | |
| 3148 3135 <span class="s">}</span> | |
| 3149 3136 | |
| 3150 3137 <span class="c"># Does molecule contains any aromatic atom in a ring?</span> | |
| 3151 3138 <span class="c">#</span> | |
| 3152 <a name="HasAromaticAtomsInRings-"></a>3139 <span class="k">sub </span><span class="m">HasAromaticAtomsInRings</span> <span class="s">{</span> | |
| 3153 3140 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3154 3141 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 3155 3142 | |
| 3156 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> | |
| 3157 3144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3158 3145 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 3159 3146 <span class="s">}</span> | |
| 3160 3147 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3161 3148 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3162 3149 <span class="s">}</span> | |
| 3163 3150 <span class="s">}</span> | |
| 3164 3151 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3165 3152 <span class="s">}</span> | |
| 3166 3153 | |
| 3167 3154 <span class="c"># Does molecule contains any aromatic atom not in a ring?</span> | |
| 3168 3155 <span class="c">#</span> | |
| 3169 <a name="HasAromaticAtomsNotInRings-"></a>3156 <span class="k">sub </span><span class="m">HasAromaticAtomsNotInRings</span> <span class="s">{</span> | |
| 3170 3157 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3171 3158 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 3172 3159 | |
| 3173 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> | |
| 3174 3161 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3175 3162 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 3176 3163 <span class="s">}</span> | |
| 3177 3164 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsNotInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3178 3165 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 3179 3166 <span class="s">}</span> | |
| 3180 3167 <span class="s">}</span> | |
| 3181 3168 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 3182 3169 <span class="s">}</span> | |
| 3183 3170 | |
| 3184 3171 <span class="c"># Does molecule contains rings?</span> | |
| 3185 3172 <span class="c">#</span> | |
| 3186 <a name="HasRings-"></a>3173 <span class="k">sub </span><span class="m">HasRings</span> <span class="s">{</span> | |
| 3187 3174 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3188 3175 | |
| 3189 3176 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsCyclic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3190 3177 <span class="s">}</span> | |
| 3191 3178 | |
| 3192 3179 <span class="c"># Does molecule contains only one ring?</span> | |
| 3193 3180 <span class="c">#</span> | |
| 3194 <a name="HasOnlyOneRing-"></a>3181 <span class="k">sub </span><span class="m">HasOnlyOneRing</span> <span class="s">{</span> | |
| 3195 3182 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3196 3183 | |
| 3197 3184 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUnicyclic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3198 3185 <span class="s">}</span> | |
| 3199 3186 | |
| 3200 3187 <span class="c"># Does molecule contains any rings?</span> | |
| 3201 3188 <span class="c">#</span> | |
| 3202 <a name="HasNoRings-"></a>3189 <span class="k">sub </span><span class="m">HasNoRings</span> <span class="s">{</span> | |
| 3203 3190 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3204 3191 | |
| 3205 3192 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsAcyclic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3206 3193 <span class="s">}</span> | |
| 3207 3194 | |
| 3208 3195 <span class="c"># Get size of smallest ring...</span> | |
| 3209 3196 <span class="c">#</span> | |
| 3210 <a name="GetSizeOfSmallestRing-"></a>3197 <span class="k">sub </span><span class="m">GetSizeOfSmallestRing</span> <span class="s">{</span> | |
| 3211 3198 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3212 3199 | |
| 3213 3200 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfSmallestCycle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3214 3201 <span class="s">}</span> | |
| 3215 3202 | |
| 3216 3203 <span class="c"># Get size of largest ring...</span> | |
| 3217 3204 <span class="c">#</span> | |
| 3218 <a name="GetSizeOfLargestRing-"></a>3205 <span class="k">sub </span><span class="m">GetSizeOfLargestRing</span> <span class="s">{</span> | |
| 3219 3206 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3220 3207 | |
| 3221 3208 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfLargestCycle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3222 3209 <span class="s">}</span> | |
| 3223 3210 | |
| 3224 3211 <span class="c"># Get number of rings...</span> | |
| 3225 3212 <span class="c">#</span> | |
| 3226 <a name="GetNumOfRings-"></a>3213 <span class="k">sub </span><span class="m">GetNumOfRings</span> <span class="s">{</span> | |
| 3227 3214 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3228 3215 | |
| 3229 3216 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3230 3217 <span class="s">}</span> | |
| 3231 3218 | |
| 3232 3219 <span class="c"># Get number of aromatic rings...</span> | |
| 3233 3220 <span class="c">#</span> | |
| 3234 <a name="GetNumOfAromaticRings-"></a>3221 <span class="k">sub </span><span class="m">GetNumOfAromaticRings</span> <span class="s">{</span> | |
| 3235 3222 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3236 3223 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfRings</span><span class="s">)</span><span class="sc">;</span> | |
| 3237 3224 | |
| 3238 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> | |
| 3239 3226 | |
| 3240 3227 <span class="k">return</span> <span class="i">$NumOfRings</span><span class="sc">;</span> | |
| 3241 3228 <span class="s">}</span> | |
| 3242 3229 | |
| 3243 3230 <span class="c"># Get num of rings with odd size...</span> | |
| 3244 3231 <span class="c">#</span> | |
| 3245 <a name="GetNumOfRingsWithOddSize-"></a>3232 <span class="k">sub </span><span class="m">GetNumOfRingsWithOddSize</span> <span class="s">{</span> | |
| 3246 3233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3247 3234 | |
| 3248 3235 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithOddSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3249 3236 <span class="s">}</span> | |
| 3250 3237 | |
| 3251 3238 <span class="c"># Get num of rings with even size...</span> | |
| 3252 3239 <span class="c">#</span> | |
| 3253 <a name="GetNumOfRingsWithEvenSize-"></a>3240 <span class="k">sub </span><span class="m">GetNumOfRingsWithEvenSize</span> <span class="s">{</span> | |
| 3254 3241 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3255 3242 | |
| 3256 3243 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithEvenSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3257 3244 <span class="s">}</span> | |
| 3258 3245 | |
| 3259 3246 <span class="c"># Get num of rings with specified size...</span> | |
| 3260 3247 <span class="c">#</span> | |
| 3261 <a name="GetNumOfRingsWithSize-"></a>3248 <span class="k">sub </span><span class="m">GetNumOfRingsWithSize</span> <span class="s">{</span> | |
| 3262 3249 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3263 3250 | |
| 3264 3251 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithSize</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3265 3252 <span class="s">}</span> | |
| 3266 3253 | |
| 3267 3254 <span class="c"># Get num of rings with size less than a specified size...</span> | |
| 3268 3255 <span class="c">#</span> | |
| 3269 <a name="GetNumOfRingsWithSizeLessThan-"></a>3256 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeLessThan</span> <span class="s">{</span> | |
| 3270 3257 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3271 3258 | |
| 3272 3259 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3273 3260 <span class="s">}</span> | |
| 3274 3261 | |
| 3275 3262 <span class="c"># Get num of rings with size greater than a specified size...</span> | |
| 3276 3263 <span class="c">#</span> | |
| 3277 <a name="GetNumOfRingsWithSizeGreaterThan-"></a>3264 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
| 3278 3265 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3279 3266 | |
| 3280 3267 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3281 3268 <span class="s">}</span> | |
| 3282 3269 | |
| 3283 3270 <span class="c"># Get largest ring as an array containing ring atoms...</span> | |
| 3284 3271 <span class="c">#</span> | |
| 3285 <a name="GetLargestRing-"></a>3272 <span class="k">sub </span><span class="m">GetLargestRing</span> <span class="s">{</span> | |
| 3286 3273 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3287 3274 | |
| 3288 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> | |
| 3289 3276 <span class="s">}</span> | |
| 3290 3277 | |
| 3291 3278 <span class="c"># Get smallest ring as an array containing ring atoms...</span> | |
| 3292 3279 <span class="c">#</span> | |
| 3293 <a name="GetSmallestRing-"></a>3280 <span class="k">sub </span><span class="m">GetSmallestRing</span> <span class="s">{</span> | |
| 3294 3281 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3295 3282 | |
| 3296 3283 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetSmallestCycle</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3297 3284 <span class="s">}</span> | |
| 3298 3285 | |
| 3299 3286 <span class="c"># Get rings as an array containing references to arrays with ring atoms...</span> | |
| 3300 3287 <span class="c">#</span> | |
| 3301 <a name="GetRings-"></a>3288 <span class="k">sub </span><span class="m">GetRings</span> <span class="s">{</span> | |
| 3302 3289 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3303 3290 | |
| 3304 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> | |
| 3305 3292 <span class="s">}</span> | |
| 3306 3293 | |
| 3307 3294 <span class="c"># Get aromatic rings as an array containing references to arrays with ring atoms...</span> | |
| 3308 3295 <span class="c">#</span> | |
| 3309 <a name="GetAromaticRings-"></a>3296 <span class="k">sub </span><span class="m">GetAromaticRings</span> <span class="s">{</span> | |
| 3310 3297 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3311 3298 | |
| 3312 3299 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAromaticRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCycles</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3313 3300 <span class="s">}</span> | |
| 3314 3301 | |
| 3315 3302 <span class="c"># Get odd size rings as an array containing references to arrays with ring atoms...</span> | |
| 3316 3303 <span class="c">#</span> | |
| 3317 <a name="GetRingsWithOddSize-"></a>3304 <span class="k">sub </span><span class="m">GetRingsWithOddSize</span> <span class="s">{</span> | |
| 3318 3305 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3319 3306 | |
| 3320 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> | |
| 3321 3308 <span class="s">}</span> | |
| 3322 3309 | |
| 3323 3310 <span class="c"># Get even size rings as an array containing references to arrays with ring atoms...</span> | |
| 3324 3311 <span class="c">#</span> | |
| 3325 <a name="GetRingsWithEvenSize-"></a>3312 <span class="k">sub </span><span class="m">GetRingsWithEvenSize</span> <span class="s">{</span> | |
| 3326 3313 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3327 3314 | |
| 3328 3315 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCyclesWithEvenSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3329 3316 <span class="s">}</span> | |
| 3330 3317 | |
| 3331 3318 <span class="c"># Get rings with a specific size as an array containing references to arrays with ring atoms...</span> | |
| 3332 3319 <span class="c">#</span> | |
| 3333 <a name="GetRingsWithSize-"></a>3320 <span class="k">sub </span><span class="m">GetRingsWithSize</span> <span class="s">{</span> | |
| 3334 3321 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3335 3322 | |
| 3336 3323 <span class="k">return</span> <span class="i">$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> | |
| 3337 3324 <span class="s">}</span> | |
| 3338 3325 | |
| 3339 3326 <span class="c"># Get rings with size less than a specific size as an array containing references to arrays with ring atoms...</span> | |
| 3340 3327 <span class="c">#</span> | |
| 3341 <a name="GetRingsWithSizeLessThan-"></a>3328 <span class="k">sub </span><span class="m">GetRingsWithSizeLessThan</span> <span class="s">{</span> | |
| 3342 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> | |
| 3343 3330 | |
| 3344 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">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3345 3332 <span class="s">}</span> | |
| 3346 3333 | |
| 3347 3334 <span class="c"># Get rings with size greater than a specific size as an array containing references to arrays with ring atoms...</span> | |
| 3348 3335 <span class="c">#</span> | |
| 3349 <a name="GetRingsWithSizeGreaterThan-"></a>3336 <span class="k">sub </span><span class="m">GetRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
| 3350 3337 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3351 3338 | |
| 3352 3339 <span class="k">return</span> <span class="i">$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> | |
| 3353 3340 <span class="s">}</span> | |
| 3354 3341 | |
| 3355 3342 <span class="c"># Generate an array of bond objects for an array of ring atoms and return an array</span> | |
| 3356 3343 <span class="c"># of bond objects...</span> | |
| 3357 3344 <span class="c">#</span> | |
| 3358 <a name="GetRingBonds-"></a>3345 <span class="k">sub </span><span class="m">GetRingBonds</span> <span class="s">{</span> | |
| 3359 3346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3360 3347 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> | |
| 3361 3348 | |
| 3362 3349 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3363 3350 <span class="k">if</span> <span class="s">(</span>!<span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 3364 3351 <span class="c"># Return an empty ring bonds list...</span> | |
| 3365 3352 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span> | |
| 3366 3353 <span class="s">}</span> | |
| 3367 3354 | |
| 3368 3355 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 3369 3356 | |
| 3370 3357 <span class="i">@RingAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3371 3358 <span class="i">@RingAtomIDs</span> = <span class="i">$This</span><span class="i">->_GetAtomsIDsFromAtoms</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 3372 3359 <span class="k">if</span> <span class="s">(</span>!<span class="i">@RingAtomIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 3373 3360 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetRingBonds: No ring bonds retrieved: Atom IDs couldn't be retrieved for specified atoms..."</span><span class="sc">;</span> | |
| 3374 3361 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span> | |
| 3375 3362 <span class="s">}</span> | |
| 3376 3363 | |
| 3377 3364 <span class="c"># Add start atom to the end to make it a cyclic path for ring: It's taken out during conversion</span> | |
| 3378 3365 <span class="c"># of cyclic path to a ring...</span> | |
| 3379 3366 <span class="k">push</span> <span class="i">@RingAtomIDs</span><span class="cm">,</span> <span class="i">$RingAtomIDs</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 3380 3367 | |
| 3381 3368 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPathBonds</span><span class="s">(</span><span class="i">@RingAtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 3382 3369 <span class="s">}</span> | |
| 3383 3370 | |
| 3384 3371 <span class="c"># Generate an array containing references to arrays of ring bond objects for rings specified</span> | |
| 3385 3372 <span class="c"># in an array of references to ring atoms...</span> | |
| 3386 3373 <span class="c">#</span> | |
| 3387 <a name="GetRingBondsFromRings-"></a>3374 <span class="k">sub </span><span class="m">GetRingBondsFromRings</span> <span class="s">{</span> | |
| 3388 3375 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtomsSets</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3389 3376 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">@RingBondsSets</span><span class="s">)</span><span class="sc">;</span> | |
| 3390 3377 | |
| 3391 3378 <span class="i">@RingBondsSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3392 3379 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@RingAtomsSets</span><span class="s">)</span> <span class="s">{</span> | |
| 3393 3380 <span class="k">my</span><span class="s">(</span><span class="i">@RingBonds</span><span class="s">)</span><span class="sc">;</span> | |
| 3394 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> | |
| 3395 3382 | |
| 3396 3383 <span class="k">push</span> <span class="i">@RingBondsSets</span><span class="cm">,</span> \<span class="i">@RingBonds</span><span class="sc">;</span> | |
| 3397 3384 <span class="s">}</span> | |
| 3398 3385 | |
| 3399 3386 <span class="k">return</span> <span class="i">@RingBondsSets</span><span class="sc">;</span> | |
| 3400 3387 <span class="s">}</span> | |
| 3401 3388 | |
| 3402 3389 <span class="c"># Does molecule has any fused rings?</span> | |
| 3403 3390 <span class="c">#</span> | |
| 3404 <a name="HasFusedRings-"></a>3391 <span class="k">sub </span><span class="m">HasFusedRings</span> <span class="s">{</span> | |
| 3405 3392 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3406 3393 | |
| 3407 3394 <span class="k">return</span> <span class="i">$This</span><span class="i">->HasFusedCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3408 3395 <span class="s">}</span> | |
| 3409 3396 | |
| 3410 3397 <span class="c"># Get references to array of fused ring sets and non-fused rings. Fused ring sets array reference</span> | |
| 3411 3398 <span class="c"># contains refernces to arrays of rings; Non-fused rings array reference contains references to</span> | |
| 3412 3399 <span class="c"># arrays of ring atoms...</span> | |
| 3413 3400 <span class="c"># rings.</span> | |
| 3414 3401 <span class="c">#</span> | |
| 3415 <a name="GetFusedAndNonFusedRings-"></a>3402 <span class="k">sub </span><span class="m">GetFusedAndNonFusedRings</span> <span class="s">{</span> | |
| 3416 3403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3417 3404 <span class="k">my</span><span class="s">(</span><span class="i">$FusedCyclesSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedCyclesRef</span><span class="cm">,</span> <span class="i">@FusedRingSets</span><span class="cm">,</span> <span class="i">@NonFusedRings</span><span class="s">)</span><span class="sc">;</span> | |
| 3418 3405 | |
| 3419 3406 <span class="i">@FusedRingSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@NonFusedRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3420 3407 <span class="s">(</span><span class="i">$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> | |
| 3421 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> | |
| 3422 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> | |
| 3423 3410 <span class="s">}</span> | |
| 3424 3411 <span class="k">my</span><span class="s">(</span><span class="i">$FusedCyclesSetRef</span><span class="s">)</span><span class="sc">;</span> | |
| 3425 3412 | |
| 3426 3413 <span class="k">for</span> <span class="i">$FusedCyclesSetRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedCyclesSetsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 3427 3414 <span class="k">my</span><span class="s">(</span><span class="i">@FusedRingSet</span><span class="s">)</span><span class="sc">;</span> | |
| 3428 3415 <span class="i">@FusedRingSet</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3429 3416 <span class="i">@FusedRingSet</span> = <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">@</span>{<span class="i">$FusedCyclesSetRef</span>}<span class="s">)</span><span class="sc">;</span> | |
| 3430 3417 <span class="k">push</span> <span class="i">@FusedRingSets</span><span class="cm">,</span> \<span class="i">@FusedRingSet</span><span class="sc">;</span> | |
| 3431 3418 <span class="s">}</span> | |
| 3432 3419 | |
| 3433 3420 <span class="i">@NonFusedRings</span> = <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedCyclesRef</span>}<span class="s">)</span><span class="sc">;</span> | |
| 3434 3421 | |
| 3435 3422 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FusedRingSets</span><span class="cm">,</span> \<span class="i">@NonFusedRings</span><span class="s">)</span><span class="sc">;</span> | |
| 3436 3423 <span class="s">}</span> | |
| 3437 3424 | |
| 3438 3425 <span class="c"># Get rings as an array containing references to arrays with ring atoms...</span> | |
| 3439 3426 <span class="c">#</span> | |
| 3440 <a name="_GetRings-"></a>3427 <span class="k">sub </span><span class="m">_GetRings</span> <span class="s">{</span> | |
| 3441 3428 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@CyclicPaths</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3442 3429 <span class="k">my</span><span class="s">(</span><span class="i">$CyclicPath</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span><span class="sc">;</span> | |
| 3443 3430 | |
| 3444 3431 <span class="i">@Rings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3445 3432 <span class="k">if</span> <span class="s">(</span>!<span class="i">@CyclicPaths</span><span class="s">)</span> <span class="s">{</span> | |
| 3446 3433 <span class="k">return</span> <span class="i">@Rings</span><span class="sc">;</span> | |
| 3447 3434 <span class="s">}</span> | |
| 3448 3435 <span class="k">if</span> <span class="s">(</span>!<span class="i">@CyclicPaths</span><span class="s">)</span> <span class="s">{</span> | |
| 3449 3436 <span class="c"># Return an empty ring list...</span> | |
| 3450 3437 <span class="k">return</span> <span class="i">@Rings</span><span class="sc">;</span> | |
| 3451 3438 <span class="s">}</span> | |
| 3452 3439 | |
| 3453 3440 <span class="k">for</span> <span class="i">$CyclicPath</span> <span class="s">(</span><span class="i">@CyclicPaths</span><span class="s">)</span> <span class="s">{</span> | |
| 3454 3441 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 3455 3442 <span class="i">@RingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3456 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> | |
| 3457 3444 | |
| 3458 3445 <span class="k">push</span> <span class="i">@Rings</span><span class="cm">,</span> \<span class="i">@RingAtoms</span><span class="sc">;</span> | |
| 3459 3446 <span class="s">}</span> | |
| 3460 3447 <span class="k">return</span> <span class="i">@Rings</span><span class="sc">;</span> | |
| 3461 3448 <span class="s">}</span> | |
| 3462 3449 | |
| 3463 3450 <span class="c"># Get aromatic rings as an array containing references to arrays with ring atoms...</span> | |
| 3464 3451 <span class="c">#</span> | |
| 3465 <a name="_GetAromaticRings-"></a>3452 <span class="k">sub </span><span class="m">_GetAromaticRings</span> <span class="s">{</span> | |
| 3466 3453 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@CyclicPaths</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3467 3454 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3468 3455 | |
| 3469 3456 <span class="i">@AromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3470 3457 <span class="i">@Rings</span> = <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">@CyclicPaths</span><span class="s">)</span><span class="sc">;</span> | |
| 3471 3458 | |
| 3472 3459 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span> | |
| 3473 3460 <span class="k">return</span> <span class="i">@AromaticRings</span><span class="sc">;</span> | |
| 3474 3461 <span class="s">}</span> | |
| 3475 3462 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span> | |
| 3476 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> | |
| 3477 3464 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span> | |
| 3478 3465 <span class="s">}</span> | |
| 3479 3466 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 3480 3467 <span class="i">@RingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3481 3468 <span class="k">push</span> <span class="i">@RingAtoms</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span> | |
| 3482 3469 | |
| 3483 3470 <span class="k">push</span> <span class="i">@AromaticRings</span><span class="cm">,</span> \<span class="i">@RingAtoms</span><span class="sc">;</span> | |
| 3484 3471 <span class="s">}</span> | |
| 3485 3472 <span class="k">return</span> <span class="i">@AromaticRings</span><span class="sc">;</span> | |
| 3486 3473 <span class="s">}</span> | |
| 3487 3474 | |
| 3488 3475 <span class="c"># Map atom IDs in cyclic path to atoms and return a reference to an array containing ring atoms...</span> | |
| 3489 3476 <span class="c">#</span> | |
| 3490 3477 <span class="c"># Note:</span> | |
| 3491 3478 <span class="c"># . Start and end vertex is same for cyclic paths. So end atom is removed before</span> | |
| 3492 3479 <span class="c"># returning atoms array as ring atoms...</span> | |
| 3493 3480 <span class="c">#</span> | |
| 3494 <a name="_GetRing-"></a>3481 <span class="k">sub </span><span class="m">_GetRing</span> <span class="s">{</span> | |
| 3495 3482 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$CyclicPath</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3496 3483 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 3497 3484 | |
| 3498 3485 <span class="i">@RingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3499 3486 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$CyclicPath</span><span class="s">)</span> <span class="s">{</span> | |
| 3500 3487 <span class="c"># Return an empty atoms list...</span> | |
| 3501 3488 <span class="k">return</span> <span class="i">@RingAtoms</span><span class="sc">;</span> | |
| 3502 3489 <span class="s">}</span> | |
| 3503 3490 | |
| 3504 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> | |
| 3505 3492 <span class="k">if</span> <span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 3506 3493 <span class="k">pop</span> <span class="i">@RingAtoms</span><span class="sc">;</span> | |
| 3507 3494 <span class="s">}</span> | |
| 3508 3495 <span class="k">return</span> <span class="i">@RingAtoms</span><span class="sc">;</span> | |
| 3509 3496 <span class="s">}</span> | |
| 3510 3497 | |
| 3511 3498 <span class="c"># Map atom IDs to atoms and return a reference to an array containing these atoms...</span> | |
| 3512 3499 <span class="c">#</span> | |
| 3513 <a name="_GetPathAtoms-"></a>3500 <span class="k">sub </span><span class="m">_GetPathAtoms</span> <span class="s">{</span> | |
| 3514 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> | |
| 3515 3502 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 3516 3503 | |
| 3517 3504 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3518 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> | |
| 3519 3506 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetPathAtoms: No path atoms retrieved: Path must be defined..."</span><span class="sc">;</span> | |
| 3520 3507 <span class="k">return</span> <span class="i">@PathAtoms</span><span class="sc">;</span> | |
| 3521 3508 <span class="s">}</span> | |
| 3522 3509 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 3523 3510 | |
| 3524 3511 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3525 3512 <span class="i">@AtomIDs</span> = <span class="i">$Path</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3526 3513 | |
| 3527 3514 <span class="i">@PathAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 3528 3515 | |
| 3529 3516 <span class="k">return</span> <span class="i">@PathAtoms</span><span class="sc">;</span> | |
| 3530 3517 <span class="s">}</span> | |
| 3531 3518 | |
| 3532 3519 <span class="c"># Get bonds for a path specified by atom IDs...</span> | |
| 3533 3520 <span class="c">#</span> | |
| 3534 <a name="_GetPathBonds-"></a>3521 <span class="k">sub </span><span class="m">_GetPathBonds</span> <span class="s">{</span> | |
| 3535 3522 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3536 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">$AtomID2</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="cm">,</span> <span class="i">@EdgesAtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 3537 3524 | |
| 3538 3525 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@EdgesAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3539 3526 | |
| 3540 3527 <span class="k">if</span> <span class="s">(</span>!<span class="i">@AtomIDs</span> || <span class="i">@AtomIDs</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 3541 3528 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span> | |
| 3542 3529 <span class="s">}</span> | |
| 3543 3530 | |
| 3544 3531 <span class="c"># Setup edges...</span> | |
| 3545 3532 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$#AtomIDs</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 3546 3533 <span class="i">$AtomID1</span> = <span class="i">$AtomIDs</span>[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 3547 3534 <span class="i">$AtomID2</span> = <span class="i">$AtomIDs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> | |
| 3548 3535 <span class="k">push</span> <span class="i">@EdgesAtomIDs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 3549 3536 <span class="s">}</span> | |
| 3550 3537 <span class="i">@Bonds</span> = <span class="i">$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> | |
| 3551 3538 | |
| 3552 3539 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span> | |
| 3553 3540 <span class="s">}</span> | |
| 3554 3541 | |
| 3555 3542 <span class="c"># Map atom ID to an atom...</span> | |
| 3556 3543 <span class="c">#</span> | |
| 3557 <a name="_GetAtomFromAtomID-"></a>3544 <span class="k">sub </span><span class="m">_GetAtomFromAtomID</span> <span class="s">{</span> | |
| 3558 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> | |
| 3559 3546 | |
| 3560 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> | |
| 3561 3548 <span class="s">}</span> | |
| 3562 3549 | |
| 3563 3550 <span class="c"># Map atom IDs to atoms and return an array containing these atoms...</span> | |
| 3564 3551 <span class="c">#</span> | |
| 3565 <a name="_GetAtomsFromAtomIDs-"></a>3552 <span class="k">sub </span><span class="m">_GetAtomsFromAtomIDs</span> <span class="s">{</span> | |
| 3566 3553 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3567 3554 | |
| 3568 3555 <span class="k">return</span> <span class="i">$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> | |
| 3569 3556 <span class="s">}</span> | |
| 3570 3557 | |
| 3571 3558 <span class="c"># Map atoms to atom IDs and return an array containing these atoms...</span> | |
| 3572 3559 <span class="c">#</span> | |
| 3573 <a name="_GetAtomsIDsFromAtoms-"></a>3560 <span class="k">sub </span><span class="m">_GetAtomsIDsFromAtoms</span> <span class="s">{</span> | |
| 3574 3561 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3575 3562 | |
| 3576 3563 <span class="k">return</span> <span class="k">map</span> <span class="s">{</span> <span class="i">$_</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> | |
| 3577 3564 <span class="s">}</span> | |
| 3578 3565 | |
| 3579 3566 <span class="c"># Get bonded atom pair atom IDs for specified list of atom IDs...</span> | |
| 3580 3567 <span class="c">#</span> | |
| 3581 <a name="_GetBondedAtomPairAtomIDsFromAtomIDs-"></a>3568 <span class="k">sub </span><span class="m">_GetBondedAtomPairAtomIDsFromAtomIDs</span> <span class="s">{</span> | |
| 3582 3569 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3583 3570 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Atom2</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 3584 3571 | |
| 3585 3572 <span class="i">@BondedAtomPairIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3586 3573 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 3587 3574 | |
| 3588 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> | |
| 3589 3576 <span class="i">$Atom1</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex1</span>]<span class="sc">;</span> | |
| 3590 3577 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3591 3578 | |
| 3592 3579 <span class="j">ATOMINDEX2:</span> <span class="k">for</span> <span class="i">$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> | |
| 3593 3580 <span class="i">$Atom2</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex2</span>]<span class="sc">;</span> | |
| 3594 3581 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom1</span><span class="i">->IsBondedToAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3595 3582 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span> | |
| 3596 3583 <span class="s">}</span> | |
| 3597 3584 <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3598 3585 | |
| 3599 3586 <span class="k">push</span> <span class="i">@BondedAtomPairIDs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
| 3600 3587 <span class="s">}</span> | |
| 3601 3588 <span class="s">}</span> | |
| 3602 3589 | |
| 3603 3590 <span class="k">return</span> <span class="i">@BondedAtomPairIDs</span><span class="sc">;</span> | |
| 3604 3591 <span class="s">}</span> | |
| 3605 3592 | |
| 3606 3593 <span class="c"># Get bonded atom pair atoms for specified list of atoms...</span> | |
| 3607 3594 <span class="c">#</span> | |
| 3608 <a name="_GetBondedAtomPairAtomsFromAtoms-"></a>3595 <span class="k">sub </span><span class="m">_GetBondedAtomPairAtomsFromAtoms</span> <span class="s">{</span> | |
| 3609 3596 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3610 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> | |
| 3611 3598 | |
| 3612 3599 <span class="i">@BondedAtomPairAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3613 3600 | |
| 3614 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> | |
| 3615 3602 <span class="i">$Atom1</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex1</span>]<span class="sc">;</span> | |
| 3616 3603 | |
| 3617 3604 <span class="j">ATOMINDEX2:</span> <span class="k">for</span> <span class="i">$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> | |
| 3618 3605 <span class="i">$Atom2</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex2</span>]<span class="sc">;</span> | |
| 3619 3606 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsBondedToAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 3620 3607 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span> | |
| 3621 3608 <span class="s">}</span> | |
| 3622 3609 | |
| 3623 3610 <span class="k">push</span> <span class="i">@BondedAtomPairAtoms</span><span class="cm">,</span> <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3624 3611 <span class="s">}</span> | |
| 3625 3612 <span class="s">}</span> | |
| 3626 3613 | |
| 3627 3614 <span class="k">return</span> <span class="i">@BondedAtomPairAtoms</span><span class="sc">;</span> | |
| 3628 3615 <span class="s">}</span> | |
| 3629 3616 | |
| 3630 3617 <span class="c"># Is atom in a ring?</span> | |
| 3631 3618 <span class="c">#</span> | |
| 3632 <a name="_IsAtomInRing-"></a>3619 <span class="k">sub </span><span class="m">_IsAtomInRing</span> <span class="s">{</span> | |
| 3633 3620 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3634 3621 | |
| 3635 3622 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsCyclicVertex</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3636 3623 <span class="s">}</span> | |
| 3637 3624 | |
| 3638 3625 <span class="c"># Is atom not in a ring?</span> | |
| 3639 3626 <span class="c">#</span> | |
| 3640 <a name="_IsAtomNotInRing-"></a>3627 <span class="k">sub </span><span class="m">_IsAtomNotInRing</span> <span class="s">{</span> | |
| 3641 3628 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3642 3629 | |
| 3643 3630 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsAcyclicVertex</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3644 3631 <span class="s">}</span> | |
| 3645 3632 | |
| 3646 3633 <span class="c"># Is atom only in one ring?</span> | |
| 3647 3634 <span class="c">#</span> | |
| 3648 <a name="_IsAtomInOnlyOneRing-"></a>3635 <span class="k">sub </span><span class="m">_IsAtomInOnlyOneRing</span> <span class="s">{</span> | |
| 3649 3636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3650 3637 | |
| 3651 3638 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUnicyclicVertex</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3652 3639 <span class="s">}</span> | |
| 3653 3640 | |
| 3654 3641 <span class="c"># Is atom in a ring of specified size?</span> | |
| 3655 3642 <span class="c">#</span> | |
| 3656 <a name="_IsAtomInRingOfSize-"></a>3643 <span class="k">sub </span><span class="m">_IsAtomInRingOfSize</span> <span class="s">{</span> | |
| 3657 3644 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3658 3645 | |
| 3659 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">$RingSize</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3660 3647 <span class="s">}</span> | |
| 3661 3648 | |
| 3662 3649 <span class="c"># Get size of smallest ring containing specified atom...</span> | |
| 3663 3650 <span class="c">#</span> | |
| 3664 <a name="_GetSizeOfSmallestAtomRing-"></a>3651 <span class="k">sub </span><span class="m">_GetSizeOfSmallestAtomRing</span> <span class="s">{</span> | |
| 3665 3652 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3666 3653 | |
| 3667 3654 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfSmallestVertexCycle</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3668 3655 <span class="s">}</span> | |
| 3669 3656 | |
| 3670 3657 <span class="c"># Get size of largest ring containing specified atom...</span> | |
| 3671 3658 <span class="c">#</span> | |
| 3672 <a name="_GetSizeOfLargestAtomRing-"></a>3659 <span class="k">sub </span><span class="m">_GetSizeOfLargestAtomRing</span> <span class="s">{</span> | |
| 3673 3660 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3674 3661 | |
| 3675 3662 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfLargestVertexCycle</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3676 3663 <span class="s">}</span> | |
| 3677 3664 | |
| 3678 3665 <span class="c"># Get number of rings containing specified atom...</span> | |
| 3679 3666 <span class="c">#</span> | |
| 3680 <a name="_GetNumOfAtomRings-"></a>3667 <span class="k">sub </span><span class="m">_GetNumOfAtomRings</span> <span class="s">{</span> | |
| 3681 3668 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3682 3669 | |
| 3683 3670 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCycles</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3684 3671 <span class="s">}</span> | |
| 3685 3672 | |
| 3686 3673 <span class="c"># Get number of rings with odd size containing specified atom...</span> | |
| 3687 3674 <span class="c">#</span> | |
| 3688 <a name="_GetNumOfAtomRingsWithOddSize-"></a>3675 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithOddSize</span> <span class="s">{</span> | |
| 3689 3676 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3690 3677 | |
| 3691 3678 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithOddSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3692 3679 <span class="s">}</span> | |
| 3693 3680 | |
| 3694 3681 <span class="c"># Get number of rings with even size containing specified atom...</span> | |
| 3695 3682 <span class="c">#</span> | |
| 3696 <a name="_GetNumOfAtomRingsWithEvenSize-"></a>3683 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithEvenSize</span> <span class="s">{</span> | |
| 3697 3684 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3698 3685 | |
| 3699 3686 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithEvenSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3700 3687 <span class="s">}</span> | |
| 3701 3688 | |
| 3702 3689 <span class="c"># Get number of rings with specified size containing specified atom...</span> | |
| 3703 3690 <span class="c">#</span> | |
| 3704 <a name="_GetNumOfAtomRingsWithSize-"></a>3691 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithSize</span> <span class="s">{</span> | |
| 3705 3692 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3706 3693 | |
| 3707 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">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3708 3695 <span class="s">}</span> | |
| 3709 3696 | |
| 3710 3697 <span class="c"># Get number of rings with size less than specified containing specified atom...</span> | |
| 3711 3698 <span class="c">#</span> | |
| 3712 <a name="_GetNumOfAtomRingsWithSizeLessThan-"></a>3699 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithSizeLessThan</span> <span class="s">{</span> | |
| 3713 3700 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3714 3701 | |
| 3715 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">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3716 3703 <span class="s">}</span> | |
| 3717 3704 | |
| 3718 3705 <span class="c"># Get number of rings with size greater than specified containing specified atom...</span> | |
| 3719 3706 <span class="c">#</span> | |
| 3720 <a name="_GetNumOfAtomRingsWithSizeGreaterThan-"></a>3707 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
| 3721 3708 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3722 3709 | |
| 3723 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">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3724 3711 <span class="s">}</span> | |
| 3725 3712 | |
| 3726 3713 <span class="c"># Get smallest ring as an array containing ring atoms...</span> | |
| 3727 3714 <span class="c">#</span> | |
| 3728 <a name="_GetSmallestAtomRing-"></a>3715 <span class="k">sub </span><span class="m">_GetSmallestAtomRing</span> <span class="s">{</span> | |
| 3729 3716 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3730 3717 | |
| 3731 3718 <span class="k">return</span> <span class="i">$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> | |
| 3732 3719 <span class="s">}</span> | |
| 3733 3720 | |
| 3734 3721 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> | |
| 3735 3722 <span class="c">#</span> | |
| 3736 <a name="_GetLargestAtomRing-"></a>3723 <span class="k">sub </span><span class="m">_GetLargestAtomRing</span> <span class="s">{</span> | |
| 3737 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> | |
| 3738 3725 | |
| 3739 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">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3740 3727 <span class="s">}</span> | |
| 3741 3728 | |
| 3742 3729 <span class="c"># Get all rings an array of references to arrays containing ring atoms...</span> | |
| 3743 3730 <span class="c">#</span> | |
| 3744 <a name="_GetAtomRings-"></a>3731 <span class="k">sub </span><span class="m">_GetAtomRings</span> <span class="s">{</span> | |
| 3745 3732 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3746 3733 | |
| 3747 3734 <span class="k">return</span> <span class="i">$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> | |
| 3748 3735 <span class="s">}</span> | |
| 3749 3736 | |
| 3750 3737 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> | |
| 3751 3738 <span class="c">#</span> | |
| 3752 <a name="_GetAtomRingsWithOddSize-"></a>3739 <span class="k">sub </span><span class="m">_GetAtomRingsWithOddSize</span> <span class="s">{</span> | |
| 3753 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> | |
| 3754 3741 | |
| 3755 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">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3756 3743 <span class="s">}</span> | |
| 3757 3744 | |
| 3758 3745 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span> | |
| 3759 3746 <span class="c">#</span> | |
| 3760 <a name="_GetAtomRingsWithEvenSize-"></a>3747 <span class="k">sub </span><span class="m">_GetAtomRingsWithEvenSize</span> <span class="s">{</span> | |
| 3761 3748 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3762 3749 | |
| 3763 3750 <span class="k">return</span> <span class="i">$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> | |
| 3764 3751 <span class="s">}</span> | |
| 3765 3752 | |
| 3766 3753 <span class="c"># Get rings with specified size an array of references to arrays containing ring atoms...</span> | |
| 3767 3754 <span class="c">#</span> | |
| 3768 <a name="_GetAtomRingsWithSize-"></a>3755 <span class="k">sub </span><span class="m">_GetAtomRingsWithSize</span> <span class="s">{</span> | |
| 3769 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">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3770 3757 | |
| 3771 3758 <span class="k">return</span> <span class="i">$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">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3772 3759 <span class="s">}</span> | |
| 3773 3760 | |
| 3774 3761 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> | |
| 3775 3762 <span class="c">#</span> | |
| 3776 <a name="_GetAtomRingsWithSizeLessThan-"></a>3763 <span class="k">sub </span><span class="m">_GetAtomRingsWithSizeLessThan</span> <span class="s">{</span> | |
| 3777 3764 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3778 3765 | |
| 3779 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> | |
| 3780 3767 <span class="s">}</span> | |
| 3781 3768 | |
| 3782 3769 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> | |
| 3783 3770 <span class="c">#</span> | |
| 3784 <a name="_GetAtomRingsWithSizeGreaterThan-"></a>3771 <span class="k">sub </span><span class="m">_GetAtomRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
| 3785 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">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3786 3773 | |
| 3787 3774 <span class="k">return</span> <span class="i">$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">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3788 3775 <span class="s">}</span> | |
| 3789 3776 | |
| 3790 3777 <span class="c"># Is bond in a ring?</span> | |
| 3791 3778 <span class="c">#</span> | |
| 3792 <a name="_IsBondInRing-"></a>3779 <span class="k">sub </span><span class="m">_IsBondInRing</span> <span class="s">{</span> | |
| 3793 3780 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3794 3781 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3795 3782 | |
| 3796 3783 <span class="s">(</span><span class="i">$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> | |
| 3797 3784 | |
| 3798 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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3799 3786 <span class="s">}</span> | |
| 3800 3787 | |
| 3801 3788 <span class="c"># Is bond not in a ring?</span> | |
| 3802 3789 <span class="c">#</span> | |
| 3803 <a name="_IsBondNotInRing-"></a>3790 <span class="k">sub </span><span class="m">_IsBondNotInRing</span> <span class="s">{</span> | |
| 3804 3791 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3805 3792 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3806 3793 | |
| 3807 3794 <span class="s">(</span><span class="i">$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> | |
| 3808 3795 | |
| 3809 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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3810 3797 <span class="s">}</span> | |
| 3811 3798 | |
| 3812 3799 <span class="c"># Is bond only in one ring?</span> | |
| 3813 3800 <span class="c">#</span> | |
| 3814 <a name="_IsBondInOnlyOneRing-"></a>3801 <span class="k">sub </span><span class="m">_IsBondInOnlyOneRing</span> <span class="s">{</span> | |
| 3815 3802 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3816 3803 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3817 3804 | |
| 3818 3805 <span class="s">(</span><span class="i">$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> | |
| 3819 3806 | |
| 3820 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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3821 3808 <span class="s">}</span> | |
| 3822 3809 | |
| 3823 3810 <span class="c"># Is bond in a ring of specified size?</span> | |
| 3824 3811 <span class="c">#</span> | |
| 3825 <a name="_IsBondInRingOfSize-"></a>3812 <span class="k">sub </span><span class="m">_IsBondInRingOfSize</span> <span class="s">{</span> | |
| 3826 3813 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3827 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> | |
| 3828 3815 | |
| 3829 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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3830 3817 | |
| 3831 3818 <span class="k">return</span> <span class="i">$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">$RingSize</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 3832 3819 <span class="s">}</span> | |
| 3833 3820 | |
| 3834 3821 <span class="c"># Get size of smallest ring containing specified bond...</span> | |
| 3835 3822 <span class="c">#</span> | |
| 3836 <a name="_GetSizeOfSmallestBondRing-"></a>3823 <span class="k">sub </span><span class="m">_GetSizeOfSmallestBondRing</span> <span class="s">{</span> | |
| 3837 3824 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3838 3825 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3839 3826 | |
| 3840 3827 <span class="s">(</span><span class="i">$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> | |
| 3841 3828 | |
| 3842 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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3843 3830 <span class="s">}</span> | |
| 3844 3831 | |
| 3845 3832 <span class="c"># Get size of largest ring containing specified bond...</span> | |
| 3846 3833 <span class="c">#</span> | |
| 3847 <a name="_GetSizeOfLargestBondRing-"></a>3834 <span class="k">sub </span><span class="m">_GetSizeOfLargestBondRing</span> <span class="s">{</span> | |
| 3848 3835 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3849 3836 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3850 3837 | |
| 3851 3838 <span class="s">(</span><span class="i">$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> | |
| 3852 3839 | |
| 3853 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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3854 3841 <span class="s">}</span> | |
| 3855 3842 | |
| 3856 3843 <span class="c"># Get number of rings containing specified bond...</span> | |
| 3857 3844 <span class="c">#</span> | |
| 3858 <a name="_GetNumOfBondRings-"></a>3845 <span class="k">sub </span><span class="m">_GetNumOfBondRings</span> <span class="s">{</span> | |
| 3859 3846 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3860 3847 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3861 3848 | |
| 3862 3849 <span class="s">(</span><span class="i">$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> | |
| 3863 3850 | |
| 3864 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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3865 3852 <span class="s">}</span> | |
| 3866 3853 | |
| 3867 3854 <span class="c"># Get number of rings with odd size containing specified bond...</span> | |
| 3868 3855 <span class="c">#</span> | |
| 3869 <a name="_GetNumOfBondRingsWithOddSize-"></a>3856 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithOddSize</span> <span class="s">{</span> | |
| 3870 3857 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3871 3858 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3872 3859 | |
| 3873 3860 <span class="s">(</span><span class="i">$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> | |
| 3874 3861 | |
| 3875 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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3876 3863 <span class="s">}</span> | |
| 3877 3864 | |
| 3878 3865 <span class="c"># Get number of rings with even size containing specified bond...</span> | |
| 3879 3866 <span class="c">#</span> | |
| 3880 <a name="_GetNumOfBondRingsWithEvenSize-"></a>3867 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithEvenSize</span> <span class="s">{</span> | |
| 3881 3868 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3882 3869 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3883 3870 | |
| 3884 3871 <span class="s">(</span><span class="i">$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> | |
| 3885 3872 | |
| 3886 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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3887 3874 <span class="s">}</span> | |
| 3888 3875 | |
| 3889 3876 <span class="c"># Get number of rings with specified size containing specified bond...</span> | |
| 3890 3877 <span class="c">#</span> | |
| 3891 <a name="_GetNumOfBondRingsWithSize-"></a>3878 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithSize</span> <span class="s">{</span> | |
| 3892 3879 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3893 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> | |
| 3894 3881 | |
| 3895 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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3896 3883 | |
| 3897 3884 <span class="k">return</span> <span class="i">$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">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3898 3885 <span class="s">}</span> | |
| 3899 3886 | |
| 3900 3887 <span class="c"># Get number of rings with size less than specified containing specified bond...</span> | |
| 3901 3888 <span class="c">#</span> | |
| 3902 <a name="_GetNumOfBondRingsWithSizeLessThan-"></a>3889 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithSizeLessThan</span> <span class="s">{</span> | |
| 3903 3890 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3904 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> | |
| 3905 3892 | |
| 3906 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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3907 3894 | |
| 3908 3895 <span class="k">return</span> <span class="i">$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">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3909 3896 <span class="s">}</span> | |
| 3910 3897 | |
| 3911 3898 <span class="c"># Get number of rings with size greater than specified containing specified bond...</span> | |
| 3912 3899 <span class="c">#</span> | |
| 3913 <a name="_GetNumOfBondRingsWithSizeGreaterThan-"></a>3900 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
| 3914 3901 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3915 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> | |
| 3916 3903 | |
| 3917 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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3918 3905 | |
| 3919 3906 <span class="k">return</span> <span class="i">$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">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
| 3920 3907 <span class="s">}</span> | |
| 3921 3908 | |
| 3922 3909 <span class="c"># Get smallest ring as an array containing ring atoms...</span> | |
| 3923 3910 <span class="c">#</span> | |
| 3924 <a name="_GetSmallestBondRing-"></a>3911 <span class="k">sub </span><span class="m">_GetSmallestBondRing</span> <span class="s">{</span> | |
| 3925 3912 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3926 3913 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3927 3914 | |
| 3928 3915 <span class="s">(</span><span class="i">$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> | |
| 3929 3916 | |
| 3930 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> | |
| 3931 3918 <span class="s">}</span> | |
| 3932 3919 | |
| 3933 3920 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> | |
| 3934 3921 <span class="c">#</span> | |
| 3935 <a name="_GetLargestBondRing-"></a>3922 <span class="k">sub </span><span class="m">_GetLargestBondRing</span> <span class="s">{</span> | |
| 3936 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> | |
| 3937 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> | |
| 3938 3925 | |
| 3939 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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3940 3927 | |
| 3941 3928 <span class="k">return</span> <span class="i">$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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3942 3929 <span class="s">}</span> | |
| 3943 3930 | |
| 3944 3931 <span class="c"># Get all rings an array of references to arrays containing ring atoms...</span> | |
| 3945 3932 <span class="c">#</span> | |
| 3946 <a name="_GetBondRings-"></a>3933 <span class="k">sub </span><span class="m">_GetBondRings</span> <span class="s">{</span> | |
| 3947 3934 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3948 3935 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3949 3936 | |
| 3950 3937 <span class="s">(</span><span class="i">$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> | |
| 3951 3938 | |
| 3952 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> | |
| 3953 3940 <span class="s">}</span> | |
| 3954 3941 | |
| 3955 3942 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> | |
| 3956 3943 <span class="c">#</span> | |
| 3957 <a name="_GetBondRingsWithOddSize-"></a>3944 <span class="k">sub </span><span class="m">_GetBondRingsWithOddSize</span> <span class="s">{</span> | |
| 3958 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> | |
| 3959 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> | |
| 3960 3947 | |
| 3961 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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3962 3949 | |
| 3963 3950 <span class="k">return</span> <span class="i">$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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3964 3951 <span class="s">}</span> | |
| 3965 3952 | |
| 3966 3953 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span> | |
| 3967 3954 <span class="c">#</span> | |
| 3968 <a name="_GetBondRingsWithEvenSize-"></a>3955 <span class="k">sub </span><span class="m">_GetBondRingsWithEvenSize</span> <span class="s">{</span> | |
| 3969 3956 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3970 3957 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3971 3958 | |
| 3972 3959 <span class="s">(</span><span class="i">$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> | |
| 3973 3960 | |
| 3974 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> | |
| 3975 3962 <span class="s">}</span> | |
| 3976 3963 | |
| 3977 3964 <span class="c"># Get rings with specified size an array of references to arrays containing ring atoms...</span> | |
| 3978 3965 <span class="c">#</span> | |
| 3979 <a name="_GetBondRingsWithSize-"></a>3966 <span class="k">sub </span><span class="m">_GetBondRingsWithSize</span> <span class="s">{</span> | |
| 3980 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">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 3981 3968 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 3982 3969 | |
| 3983 3970 <span class="s">(</span><span class="i">$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> | |
| 3984 3971 | |
| 3985 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">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 3986 3973 <span class="s">}</span> | |
| 3987 3974 | |
| 3988 3975 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> | |
| 3989 3976 <span class="c">#</span> | |
| 3990 <a name="_GetBondRingsWithSizeLessThan-"></a>3977 <span class="k">sub </span><span class="m">_GetBondRingsWithSizeLessThan</span> <span class="s">{</span> | |
| 3991 3978 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 3992 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> | |
| 3993 3980 | |
| 3994 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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 3995 3982 | |
| 3996 3983 <span class="k">return</span> <span class="i">$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> | |
| 3997 3984 <span class="s">}</span> | |
| 3998 3985 | |
| 3999 3986 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> | |
| 4000 3987 <span class="c">#</span> | |
| 4001 <a name="_GetBondRingsWithSizeGreaterThan-"></a>3988 <span class="k">sub </span><span class="m">_GetBondRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
| 4002 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">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4003 3990 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
| 4004 3991 | |
| 4005 3992 <span class="s">(</span><span class="i">$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> | |
| 4006 3993 | |
| 4007 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">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 4008 3995 <span class="s">}</span> | |
| 4009 3996 | |
| 4010 3997 | |
| 4011 3998 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> | |
| 4012 3999 <span class="c"># to arrays with path atoms.</span> | |
| 4013 4000 <span class="c">#</span> | |
| 4014 4001 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with length</span> | |
| 4015 4002 <span class="c"># upto a specified length and sharing of bonds in paths traversed. By default, rings are</span> | |
| 4016 4003 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4017 4004 <span class="c">#</span> | |
| 4018 4005 <span class="c"># Note:</span> | |
| 4019 4006 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> | |
| 4020 4007 <span class="c"># as GetAtomPathsStartingAtWithLengthUpto method.</span> | |
| 4021 4008 <span class="c">#</span> | |
| 4022 <a name="GetAllAtomPathsStartingAtWithLengthUpto-"></a>4009 <span class="k">sub </span><span class="m">GetAllAtomPathsStartingAtWithLengthUpto</span> <span class="s">{</span> | |
| 4023 4010 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4024 4011 | |
| 4025 4012 <span class="k">return</span> <span class="i">$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">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> | |
| 4026 4013 <span class="s">}</span> | |
| 4027 4014 | |
| 4028 4015 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> | |
| 4029 4016 <span class="c"># to arrays with path atoms.</span> | |
| 4030 4017 <span class="c">#</span> | |
| 4031 4018 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with</span> | |
| 4032 4019 <span class="c"># specified length and sharing of bonds in paths traversed. By default, rings are</span> | |
| 4033 4020 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4034 4021 <span class="c">#</span> | |
| 4035 4022 <span class="c"># Note:</span> | |
| 4036 4023 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> | |
| 4037 4024 <span class="c"># as GetAtomPathsStartingAtWithLengthUpto method.</span> | |
| 4038 4025 <span class="c">#</span> | |
| 4039 <a name="GetAllAtomPathsStartingAtWithLength-"></a>4026 <span class="k">sub </span><span class="m">GetAllAtomPathsStartingAtWithLength</span> <span class="s">{</span> | |
| 4040 4027 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4041 4028 | |
| 4042 4029 <span class="k">return</span> <span class="i">$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">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> | |
| 4043 4030 <span class="s">}</span> | |
| 4044 4031 | |
| 4045 4032 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> | |
| 4046 4033 <span class="c"># to arrays with path atoms.</span> | |
| 4047 4034 <span class="c">#</span> | |
| 4048 4035 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with all</span> | |
| 4049 4036 <span class="c"># possible lengths and sharing of bonds in paths traversed. By default, rings are</span> | |
| 4050 4037 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4051 4038 <span class="c">#</span> | |
| 4052 4039 <span class="c"># Note:</span> | |
| 4053 4040 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> | |
| 4054 4041 <span class="c"># as GetAtomPathsStartingAt method.</span> | |
| 4055 4042 <span class="c">#</span> | |
| 4056 <a name="GetAllAtomPathsStartingAt-"></a>4043 <span class="k">sub </span><span class="m">GetAllAtomPathsStartingAt</span> <span class="s">{</span> | |
| 4057 4044 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 4058 4045 | |
| 4059 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">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> | |
| 4060 4047 <span class="s">}</span> | |
| 4061 4048 | |
| 4062 4049 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> | |
| 4063 4050 <span class="c"># to arrays with path atoms.</span> | |
| 4064 4051 <span class="c">#</span> | |
| 4065 4052 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with length</span> | |
| 4066 4053 <span class="c"># upto a specified length and no sharing of bonds in paths traversed. By default, rings are</span> | |
| 4067 4054 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4068 4055 <span class="c">#</span> | |
| 4069 <a name="GetAtomPathsStartingAtWithLengthUpto-"></a>4056 <span class="k">sub </span><span class="m">GetAtomPathsStartingAtWithLengthUpto</span> <span class="s">{</span> | |
| 4070 4057 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4071 4058 | |
| 4072 4059 <span class="k">return</span> <span class="i">$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">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> | |
| 4073 4060 <span class="s">}</span> | |
| 4074 4061 | |
| 4075 4062 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> | |
| 4076 4063 <span class="c"># to arrays with path atoms.</span> | |
| 4077 4064 <span class="c">#</span> | |
| 4078 4065 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with</span> | |
| 4079 4066 <span class="c"># specified length and no sharing of bonds in paths traversed. By default, rings are</span> | |
| 4080 4067 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4081 4068 <span class="c">#</span> | |
| 4082 <a name="GetAtomPathsStartingAtWithLength-"></a>4069 <span class="k">sub </span><span class="m">GetAtomPathsStartingAtWithLength</span> <span class="s">{</span> | |
| 4083 4070 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4084 4071 | |
| 4085 4072 <span class="k">return</span> <span class="i">$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">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> | |
| 4086 4073 <span class="s">}</span> | |
| 4087 4074 | |
| 4088 4075 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span> | |
| 4089 4076 <span class="c"># to arrays with path atoms.</span> | |
| 4090 4077 <span class="c">#</span> | |
| 4091 4078 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with all</span> | |
| 4092 4079 <span class="c"># possible lengths and no sharing of bonds in paths traversed. By default, rings are</span> | |
| 4093 4080 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4094 4081 <span class="c">#</span> | |
| 4095 4082 <span class="c">#</span> | |
| 4096 <a name="GetAtomPathsStartingAt-"></a>4083 <span class="k">sub </span><span class="m">GetAtomPathsStartingAt</span> <span class="s">{</span> | |
| 4097 4084 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 4098 4085 | |
| 4099 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">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> | |
| 4100 4087 <span class="s">}</span> | |
| 4101 4088 | |
| 4102 4089 <span class="c"># Get atom paths as an array containing references to arrays with path atoms...</span> | |
| 4103 4090 <span class="c">#</span> | |
| 4104 <a name="_GetAtomPathsStartingAt-"></a>4091 <span class="k">sub </span><span class="m">_GetAtomPathsStartingAt</span> <span class="s">{</span> | |
| 4105 4092 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 4106 4093 <span class="k">my</span><span class="s">(</span><span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span> | |
| 4107 4094 | |
| 4108 4095 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4109 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> | |
| 4110 4097 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Start atom is not defined..."</span><span class="sc">;</span> | |
| 4111 4098 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span> | |
| 4112 4099 <span class="s">}</span> | |
| 4113 4100 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
| 4114 4101 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Start atom doesn't exist..."</span><span class="sc">;</span> | |
| 4115 4102 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span> | |
| 4116 4103 <span class="s">}</span> | |
| 4117 4104 <span class="k">my</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span> | |
| 4118 4105 | |
| 4119 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> | |
| 4120 4107 <span class="i">@Paths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4121 4108 | |
| 4122 4109 <span class="c"># Collect appropriate atom paths...</span> | |
| 4123 4110 <span class="j">MODE:</span> <span class="s">{</span> | |
| 4124 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> | |
| 4125 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> | |
| 4126 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">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> | |
| 4127 4114 | |
| 4128 4115 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> | |
| 4129 4116 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> | |
| 4130 4117 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 4131 4118 | |
| 4132 4119 <span class="k">print</span> <span class="q">"Warn: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Mode, $Mode, is not supported..."</span><span class="sc">;</span> | |
| 4133 4120 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span> | |
| 4134 4121 <span class="s">}</span> | |
| 4135 4122 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsFromPaths</span><span class="s">(</span>\<span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span> | |
| 4136 4123 <span class="s">}</span> | |
| 4137 4124 | |
| 4138 4125 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> | |
| 4139 4126 <span class="c"># path atoms.</span> | |
| 4140 4127 <span class="c">#</span> | |
| 4141 4128 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with length</span> | |
| 4142 4129 <span class="c"># upto a specified length and sharing of bonds in paths traversed. By default, rings are</span> | |
| 4143 4130 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4144 4131 <span class="c">#</span> | |
| 4145 4132 <span class="c"># Notes:</span> | |
| 4146 4133 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> | |
| 4147 4134 <span class="c"># as GetAtomPathsWithLengthUpto method.</span> | |
| 4148 4135 <span class="c">#</span> | |
| 4149 <a name="GetAllAtomPathsWithLengthUpto-"></a>4136 <span class="k">sub </span><span class="m">GetAllAtomPathsWithLengthUpto</span> <span class="s">{</span> | |
| 4150 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">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4151 4138 | |
| 4152 4139 <span class="k">return</span> <span class="i">$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> | |
| 4153 4140 <span class="s">}</span> | |
| 4154 4141 | |
| 4155 4142 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> | |
| 4156 4143 <span class="c"># path atoms.</span> | |
| 4157 4144 <span class="c">#</span> | |
| 4158 4145 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with</span> | |
| 4159 4146 <span class="c"># a specified length and sharing of bonds in paths traversed. By default, rings are</span> | |
| 4160 4147 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4161 4148 <span class="c">#</span> | |
| 4162 4149 <span class="c"># Notes:</span> | |
| 4163 4150 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> | |
| 4164 4151 <span class="c"># as GetAtomPathsWithLengthUpto method.</span> | |
| 4165 4152 <span class="c">#</span> | |
| 4166 <a name="GetAllAtomPathsWithLength-"></a>4153 <span class="k">sub </span><span class="m">GetAllAtomPathsWithLength</span> <span class="s">{</span> | |
| 4167 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">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4168 4155 | |
| 4169 4156 <span class="k">return</span> <span class="i">$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> | |
| 4170 4157 <span class="s">}</span> | |
| 4171 4158 | |
| 4172 4159 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> | |
| 4173 4160 <span class="c"># path atoms.</span> | |
| 4174 4161 <span class="c">#</span> | |
| 4175 4162 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with all</span> | |
| 4176 4163 <span class="c"># possible lengths and sharing of bonds in paths traversed. By default, rings are</span> | |
| 4177 4164 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4178 4165 <span class="c">#</span> | |
| 4179 4166 <span class="c"># Notes:</span> | |
| 4180 4167 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span> | |
| 4181 4168 <span class="c"># as GetAtomPaths method.</span> | |
| 4182 4169 <span class="c">#</span> | |
| 4183 <a name="GetAllAtomPaths-"></a>4170 <span class="k">sub </span><span class="m">GetAllAtomPaths</span> <span class="s">{</span> | |
| 4184 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> | |
| 4185 4172 | |
| 4186 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> | |
| 4187 4174 <span class="s">}</span> | |
| 4188 4175 | |
| 4189 4176 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> | |
| 4190 4177 <span class="c"># path atoms.</span> | |
| 4191 4178 <span class="c">#</span> | |
| 4192 4179 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with length</span> | |
| 4193 4180 <span class="c"># upto a specified length and no sharing of bonds in paths traversed. By default, rings are</span> | |
| 4194 4181 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4195 4182 <span class="c">#</span> | |
| 4196 <a name="GetAtomPathsWithLengthUpto-"></a>4183 <span class="k">sub </span><span class="m">GetAtomPathsWithLengthUpto</span> <span class="s">{</span> | |
| 4197 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">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4198 4185 | |
| 4199 4186 <span class="k">return</span> <span class="i">$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> | |
| 4200 4187 <span class="s">}</span> | |
| 4201 4188 | |
| 4202 4189 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> | |
| 4203 4190 <span class="c"># path atoms.</span> | |
| 4204 4191 <span class="c">#</span> | |
| 4205 4192 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with</span> | |
| 4206 4193 <span class="c"># a specified length and no sharing of bonds in paths traversed. By default, rings are</span> | |
| 4207 4194 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4208 4195 <span class="c">#</span> | |
| 4209 <a name="GetAtomPathsWithLength-"></a>4196 <span class="k">sub </span><span class="m">GetAtomPathsWithLength</span> <span class="s">{</span> | |
| 4210 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">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4211 4198 | |
| 4212 4199 <span class="k">return</span> <span class="i">$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> | |
| 4213 4200 <span class="s">}</span> | |
| 4214 4201 | |
| 4215 4202 | |
| 4216 4203 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> | |
| 4217 4204 <span class="c"># path atoms.</span> | |
| 4218 4205 <span class="c">#</span> | |
| 4219 4206 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with all</span> | |
| 4220 4207 <span class="c"># possible lengths and no sharing of bonds in paths traversed. By default, rings are</span> | |
| 4221 4208 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span> | |
| 4222 4209 <span class="c">#</span> | |
| 4223 <a name="GetAtomPaths-"></a>4210 <span class="k">sub </span><span class="m">GetAtomPaths</span> <span class="s">{</span> | |
| 4224 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> | |
| 4225 4212 | |
| 4226 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> | |
| 4227 4214 <span class="s">}</span> | |
| 4228 4215 | |
| 4229 4216 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span> | |
| 4230 4217 <span class="c"># path atoms.</span> | |
| 4231 4218 <span class="c">#</span> | |
| 4232 <a name="_GetAtomPaths-"></a>4219 <span class="k">sub </span><span class="m">_GetAtomPaths</span> <span class="s">{</span> | |
| 4233 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> | |
| 4234 4221 <span class="k">my</span><span class="s">(</span><span class="i">$PathsRef</span><span class="cm">,</span> <span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span> | |
| 4235 4222 | |
| 4236 4223 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4237 4224 <span class="c"># Collect appropriate atom paths...</span> | |
| 4238 4225 <span class="j">MODE:</span> <span class="s">{</span> | |
| 4239 4226 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> | |
| 4240 4227 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> | |
| 4241 4228 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 4242 4229 | |
| 4243 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> | |
| 4244 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> | |
| 4245 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> | |
| 4246 4233 | |
| 4247 4234 <span class="k">print</span> <span class="q">"Warn: ${ClassName}->_GetAtomPaths: No atom paths retrieved: Mode, $Mode, is not supported..."</span><span class="sc">;</span> | |
| 4248 4235 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span> | |
| 4249 4236 <span class="s">}</span> | |
| 4250 4237 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsFromPaths</span><span class="s">(</span><span class="i">$PathsRef</span><span class="s">)</span><span class="sc">;</span> | |
| 4251 4238 <span class="s">}</span> | |
| 4252 4239 | |
| 4253 4240 <span class="c"># Get atom paths as an array reference containing references to arrays with path atoms...</span> | |
| 4254 4241 <span class="c">#</span> | |
| 4255 <a name="_GetAtomPathsFromPaths-"></a>4242 <span class="k">sub </span><span class="m">_GetAtomPathsFromPaths</span> <span class="s">{</span> | |
| 4256 4243 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4257 4244 <span class="k">my</span><span class="s">(</span><span class="i">$Path</span><span class="cm">,</span> <span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span> | |
| 4258 4245 | |
| 4259 4246 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4260 4247 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$PathsRef</span><span class="s">)</span> <span class="s">{</span> | |
| 4261 4248 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span> | |
| 4262 4249 <span class="s">}</span> | |
| 4263 4250 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$PathsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 4264 4251 <span class="c"># Return an empty atom paths list...</span> | |
| 4265 4252 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span> | |
| 4266 4253 <span class="s">}</span> | |
| 4267 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> | |
| 4268 4255 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 4269 4256 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4270 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> | |
| 4271 4258 | |
| 4272 4259 <span class="k">push</span> <span class="i">@AtomPaths</span><span class="cm">,</span> \<span class="i">@PathAtoms</span><span class="sc">;</span> | |
| 4273 4260 <span class="s">}</span> | |
| 4274 4261 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span> | |
| 4275 4262 <span class="s">}</span> | |
| 4276 4263 | |
| 4277 4264 <span class="c"># Generate an array of bond objects for an array of path atoms and return an array</span> | |
| 4278 4265 <span class="c"># of bond objects...</span> | |
| 4279 4266 <span class="c">#</span> | |
| 4280 <a name="GetAtomPathBonds-"></a>4267 <span class="k">sub </span><span class="m">GetAtomPathBonds</span> <span class="s">{</span> | |
| 4281 4268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@PathAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4282 4269 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span> | |
| 4283 4270 | |
| 4284 4271 <span class="k">if</span> <span class="s">(</span>!<span class="i">@PathAtoms</span><span class="s">)</span> <span class="s">{</span> | |
| 4285 4272 <span class="c"># Return an empty ring bonds list...</span> | |
| 4286 4273 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span> | |
| 4287 4274 <span class="s">}</span> | |
| 4288 4275 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 4289 4276 | |
| 4290 4277 <span class="i">@PathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4291 4278 <span class="i">@PathAtomIDs</span> = <span class="i">$This</span><span class="i">->_GetAtomsIDsFromAtoms</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 4292 4279 | |
| 4293 4280 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPathBonds</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 4294 4281 <span class="s">}</span> | |
| 4295 4282 | |
| 4296 4283 <span class="c"># Map atom IDs in path to atoms and return a reference to an array containing ring atoms...</span> | |
| 4297 4284 <span class="c">#</span> | |
| 4298 <a name="_GetAtomPathFromPath-"></a>4285 <span class="k">sub </span><span class="m">_GetAtomPathFromPath</span> <span class="s">{</span> | |
| 4299 4286 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Path</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4300 4287 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 4301 4288 | |
| 4302 4289 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4303 4290 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Path</span><span class="s">)</span> <span class="s">{</span> | |
| 4304 4291 <span class="c"># Return an empty atoms list...</span> | |
| 4305 4292 <span class="k">return</span> <span class="i">@PathAtoms</span><span class="sc">;</span> | |
| 4306 4293 <span class="s">}</span> | |
| 4307 4294 | |
| 4308 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> | |
| 4309 4296 <span class="s">}</span> | |
| 4310 4297 | |
| 4311 4298 <span class="c"># Get atom paths between two specified atoms as a reference to an array containing references</span> | |
| 4312 4299 <span class="c"># to arrays with path atoms. For molecules with rings, atom paths array contains may contain</span> | |
| 4313 4300 <span class="c"># two paths.</span> | |
| 4314 4301 <span class="c">#</span> | |
| 4315 <a name="GetAtomPathsBetween-"></a>4302 <span class="k">sub </span><span class="m">GetAtomPathsBetween</span> <span class="s">{</span> | |
| 4316 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">$EndAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4317 4304 <span class="k">my</span><span class="s">(</span><span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span> | |
| 4318 4305 | |
| 4319 4306 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4320 4307 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$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> | |
| 4321 4308 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsBetween: No atom paths retrieved: Start atom is not defined or it doesn't exist..."</span><span class="sc">;</span> | |
| 4322 4309 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span> | |
| 4323 4310 <span class="s">}</span> | |
| 4324 4311 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$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> | |
| 4325 4312 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsBetween: No atom paths retrieved: End atom is not defined or it doesn't exist..."</span><span class="sc">;</span> | |
| 4326 4313 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span> | |
| 4327 4314 <span class="s">}</span> | |
| 4328 4315 <span class="k">return</span> <span class="i">$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> | |
| 4329 4316 <span class="s">}</span> | |
| 4330 4317 | |
| 4331 4318 <span class="c"># Get atom paths between two specified atoms as a reference to an array containing references</span> | |
| 4332 4319 <span class="c"># to arrays with path atoms.</span> | |
| 4333 4320 <span class="c">#</span> | |
| 4334 <a name="_GetAtomPathsBetween-"></a>4321 <span class="k">sub </span><span class="m">_GetAtomPathsBetween</span> <span class="s">{</span> | |
| 4335 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">$EndAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4336 4323 <span class="k">my</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$EndAtomID</span><span class="cm">,</span> <span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span> | |
| 4337 4324 | |
| 4338 4325 <span class="i">$StartAtomID</span> = <span class="i">$StartAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4339 4326 <span class="i">$EndAtomID</span> = <span class="i">$EndAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4340 4327 | |
| 4341 4328 <span class="i">@Paths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4342 4329 <span class="i">@Paths</span> = <span class="i">$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> | |
| 4343 4330 | |
| 4344 4331 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsFromPaths</span><span class="s">(</span>\<span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span> | |
| 4345 4332 <span class="s">}</span> | |
| 4346 4333 | |
| 4347 4334 <span class="c"># Get atom neighborhoods around a specified atom as an array containing references</span> | |
| 4348 4335 <span class="c"># to arrays with neighborhood atoms at different radii upto specified radius...</span> | |
| 4349 4336 <span class="c">#</span> | |
| 4350 <a name="GetAtomNeighborhoodsWithRadiusUpto-"></a>4337 <span class="k">sub </span><span class="m">GetAtomNeighborhoodsWithRadiusUpto</span> <span class="s">{</span> | |
| 4351 4338 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 4352 4339 | |
| 4353 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">$Radius</span><span class="s">)</span><span class="sc">;</span> | |
| 4354 4341 <span class="s">}</span> | |
| 4355 4342 | |
| 4356 4343 <span class="c"># Get atom neighborhoods around a specified atom as an array containing references</span> | |
| 4357 4344 <span class="c"># to arrays with neighborhood atoms at possible radii...</span> | |
| 4358 4345 <span class="c">#</span> | |
| 4359 <a name="GetAtomNeighborhoods-"></a>4346 <span class="k">sub </span><span class="m">GetAtomNeighborhoods</span> <span class="s">{</span> | |
| 4360 4347 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4361 4348 | |
| 4362 4349 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="q">'AllRadii'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 4363 4350 <span class="s">}</span> | |
| 4364 4351 | |
| 4365 4352 <span class="c"># Get atom neighborhood around a specified atom, along with their successor connected atoms, collected</span> | |
| 4366 4353 <span class="c"># with in a specified radius as a list containing references to lists with first value corresponding to neighborhood</span> | |
| 4367 4354 <span class="c"># atom at a specific radius and second value as reference to a list containing its successor connected atoms.</span> | |
| 4368 4355 <span class="c">#</span> | |
| 4369 4356 <span class="c"># For a neighborhood atom at each radius level, the successor connected atoms correspond to the</span> | |
| 4370 4357 <span class="c"># neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last</span> | |
| 4371 4358 <span class="c"># radius level don't contain any successor atoms which fall outside the range of specified radius.</span> | |
| 4372 4359 <span class="c">#</span> | |
| 4373 <a name="GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto-"></a>4360 <span class="k">sub </span><span class="m">GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto</span> <span class="s">{</span> | |
| 4374 4361 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 4375 4362 | |
| 4376 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">$Radius</span><span class="s">)</span><span class="sc">;</span> | |
| 4377 4364 <span class="s">}</span> | |
| 4378 4365 | |
| 4379 4366 <span class="c"># Get atom neighborhood around a specified atom, along with their successor connected atoms, collected</span> | |
| 4380 4367 <span class="c"># at all radii as a list containing references to lists with first value corresponding to neighborhood</span> | |
| 4381 4368 <span class="c"># atom at a specific radius and second value as reference to a list containing its successor connected atoms.</span> | |
| 4382 4369 <span class="c">#</span> | |
| 4383 4370 <span class="c"># For a neighborhood atom at each radius level, the successor connected atoms correspond to the</span> | |
| 4384 4371 <span class="c"># neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last</span> | |
| 4385 4372 <span class="c"># radius level don't contain any successor atoms which fall outside the range of specified radius.</span> | |
| 4386 4373 <span class="c">#</span> | |
| 4387 4374 <span class="c">#</span> | |
| 4388 <a name="GetAtomNeighborhoodsWithSuccessorAtoms-"></a>4375 <span class="k">sub </span><span class="m">GetAtomNeighborhoodsWithSuccessorAtoms</span> <span class="s">{</span> | |
| 4389 4376 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4390 4377 | |
| 4391 4378 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="q">'WithSuccessorsAndAllRadii'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 4392 4379 <span class="s">}</span> | |
| 4393 4380 | |
| 4394 4381 <span class="c"># Get atom neighborhoods...</span> | |
| 4395 4382 <span class="c">#</span> | |
| 4396 <a name="_GetAtomNeighborhoods-"></a>4383 <span class="k">sub </span><span class="m">_GetAtomNeighborhoods</span> <span class="s">{</span> | |
| 4397 4384 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Radius</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4398 4385 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighborhoods</span><span class="s">)</span><span class="sc">;</span> | |
| 4399 4386 | |
| 4400 4387 <span class="i">@AtomNeighborhoods</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4401 4388 | |
| 4402 4389 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$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> | |
| 4403 4390 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomNeighborhoods: No atom neighborhoods retrieved: Start atom is not defined or it doesn't exist..."</span><span class="sc">;</span> | |
| 4404 4391 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> | |
| 4405 4392 <span class="s">}</span> | |
| 4406 4393 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(RadiusUpto|WithSuccessorsAndRadiusUpto)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 4407 4394 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$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> | |
| 4408 4395 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomNeighborhoods: No atom neighborhoods retrieved: Radius is not defined or it's <= 0 ..."</span><span class="sc">;</span> | |
| 4409 4396 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> | |
| 4410 4397 <span class="s">}</span> | |
| 4411 4398 <span class="s">}</span> | |
| 4412 4399 | |
| 4413 4400 <span class="c"># Collect neighborhood atom IDs...</span> | |
| 4414 4401 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 4415 4402 | |
| 4416 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> | |
| 4417 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> | |
| 4418 4405 | |
| 4419 4406 <span class="j">MODE:</span> <span class="s">{</span> | |
| 4420 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">$Radius</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> | |
| 4421 4408 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$StartAtomID</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> | |
| 4422 4409 | |
| 4423 4410 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 4424 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> | |
| 4425 4412 | |
| 4426 4413 <span class="k">print</span> <span class="q">"Warn: ${ClassName}->_GetAtomNeighborhood: No atom neighborhoods retrieved: Mode, $Mode, is not supported..."</span><span class="sc">;</span> | |
| 4427 4414 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> | |
| 4428 4415 <span class="s">}</span> | |
| 4429 4416 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(RadiusUpto|AllRadii)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 4430 4417 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNeighborhoodAtomsFromAtomIDs</span><span class="s">(</span>\<span class="i">@NeighborhoodAtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 4431 4418 <span class="s">}</span> | |
| 4432 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> | |
| 4433 4420 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNeighborhoodAtomsWithSuccessorsFromAtomIDs</span><span class="s">(</span>\<span class="i">@NeighborhoodAtomIDsWithSuccessors</span><span class="s">)</span><span class="sc">;</span> | |
| 4434 4421 <span class="s">}</span> | |
| 4435 4422 | |
| 4436 4423 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> | |
| 4437 4424 <span class="s">}</span> | |
| 4438 4425 | |
| 4439 4426 <span class="c"># Map neighborhood atom IDs to atoms...</span> | |
| 4440 4427 <span class="c">#</span> | |
| 4441 <a name="_GetNeighborhoodAtomsFromAtomIDs-"></a>4428 <span class="k">sub </span><span class="m">_GetNeighborhoodAtomsFromAtomIDs</span> <span class="s">{</span> | |
| 4442 4429 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NeighborhoodsAtomIDsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4443 4430 <span class="k">my</span><span class="s">(</span><span class="i">$NeighborhoodAtomIDsRef</span><span class="cm">,</span> <span class="i">@AtomNeighborhoods</span><span class="s">)</span><span class="sc">;</span> | |
| 4444 4431 | |
| 4445 4432 <span class="i">@AtomNeighborhoods</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4446 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> | |
| 4447 4434 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighborhood</span><span class="s">)</span><span class="sc">;</span> | |
| 4448 4435 | |
| 4449 4436 <span class="i">@AtomNeighborhood</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4450 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> | |
| 4451 4438 <span class="k">push</span> <span class="i">@AtomNeighborhoods</span><span class="cm">,</span> \<span class="i">@AtomNeighborhood</span><span class="sc">;</span> | |
| 4452 4439 <span class="s">}</span> | |
| 4453 4440 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> | |
| 4454 4441 <span class="s">}</span> | |
| 4455 4442 | |
| 4456 4443 <span class="c"># Map neighborhood atom IDs with successors to atoms...</span> | |
| 4457 4444 <span class="c">#</span> | |
| 4458 <a name="_GetNeighborhoodAtomsWithSuccessorsFromAtomIDs-"></a>4445 <span class="k">sub </span><span class="m">_GetNeighborhoodAtomsWithSuccessorsFromAtomIDs</span> <span class="s">{</span> | |
| 4459 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> | |
| 4460 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">$NeighborhoodAtomSuccessorsIDsRef</span><span class="cm">,</span> <span class="i">@AtomNeighborhoods</span><span class="s">)</span><span class="sc">;</span> | |
| 4461 4448 | |
| 4462 4449 <span class="i">$Depth</span> = <span class="n">0</span><span class="sc">;</span> | |
| 4463 4450 <span class="i">@AtomNeighborhoods</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4464 4451 | |
| 4465 4452 <span class="c"># Go over neighborhoods at each level...</span> | |
| 4466 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> | |
| 4467 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> | |
| 4468 4455 | |
| 4469 4456 <span class="c"># Go over the neighborhood atoms and their successors at a specific level..</span> | |
| 4470 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> | |
| 4471 4458 <span class="k">my</span><span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">@NeighborhoodAtomWithSuccessors</span><span class="cm">,</span> <span class="i">@NeighborhoodAtomSuccessorAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 4472 4459 | |
| 4473 4460 <span class="i">@NeighborhoodAtomWithSuccessors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@NeighborhoodAtomSuccessorAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4474 4461 <span class="s">(</span><span class="i">$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> | |
| 4475 4462 | |
| 4476 4463 <span class="c"># Map atom IDs to atoms...</span> | |
| 4477 4464 <span class="i">$NeighborhoodAtom</span> = <span class="i">$This</span><span class="i">->_GetAtomFromAtomID</span><span class="s">(</span><span class="i">$NeighborhoodAtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 4478 4465 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorsIDsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 4479 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> | |
| 4480 4467 <span class="s">}</span> | |
| 4481 4468 | |
| 4482 4469 <span class="c"># Store an atom and its successors at each level in an array...</span> | |
| 4483 4470 <span class="k">push</span> <span class="i">@NeighborhoodAtomWithSuccessors</span><span class="cm">,</span> <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> \<span class="i">@NeighborhoodAtomSuccessorAtoms</span><span class="s">)</span><span class="sc">;</span> | |
| 4484 4471 | |
| 4485 4472 <span class="k">push</span> <span class="i">@</span>{<span class="i">$AtomNeighborhoods</span>[<span class="i">$Depth</span>]} <span class="cm">,</span> \<span class="i">@NeighborhoodAtomWithSuccessors</span><span class="sc">;</span> | |
| 4486 4473 <span class="s">}</span> | |
| 4487 4474 <span class="i">$Depth</span>++<span class="sc">;</span> | |
| 4488 4475 <span class="s">}</span> | |
| 4489 4476 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span> | |
| 4490 4477 <span class="s">}</span> | |
| 4491 4478 | |
| 4492 4479 <span class="c"># Get next object ID...</span> | |
| 4493 <a name="_GetNewObjectID-"></a>4480 <span class="k">sub </span><span class="m">_GetNewObjectID</span> <span class="s">{</span> | |
| 4494 4481 <span class="i">$ObjectID</span>++<span class="sc">;</span> | |
| 4495 4482 <span class="k">return</span> <span class="i">$ObjectID</span><span class="sc">;</span> | |
| 4496 4483 <span class="s">}</span> | |
| 4497 4484 | |
| 4498 4485 <span class="c"># Is aromatic property set for the molecule?</span> | |
| 4499 <a name="IsAromatic-"></a>4486 <span class="k">sub </span><span class="m">IsAromatic</span> <span class="s">{</span> | |
| 4500 4487 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4501 4488 <span class="k">my</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span><span class="sc">;</span> | |
| 4502 4489 | |
| 4503 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> | |
| 4504 4491 | |
| 4505 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> | |
| 4506 4493 <span class="s">}</span> | |
| 4507 4494 | |
| 4508 4495 <span class="c"># Does molecule contains any atoms with non-zero Z coordiantes?</span> | |
| 4509 <a name="IsThreeDimensional-"></a>4496 <span class="k">sub </span><span class="m">IsThreeDimensional</span> <span class="s">{</span> | |
| 4510 4497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4511 4498 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> | |
| 4512 4499 | |
| 4513 4500 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4514 4501 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 4515 4502 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetZ</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 4516 4503 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 4517 4504 <span class="s">}</span> | |
| 4518 4505 <span class="s">}</span> | |
| 4519 4506 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 4520 4507 <span class="s">}</span> | |
| 4521 4508 | |
| 4522 4509 <span class="c"># Does molecule contains any atoms with non-zero X or Y coordinates</span> | |
| 4523 4510 <span class="c"># and only zero Z-coordinates?</span> | |
| 4524 <a name="IsTwoDimensional-"></a>4511 <span class="k">sub </span><span class="m">IsTwoDimensional</span> <span class="s">{</span> | |
| 4525 4512 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4526 4513 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> | |
| 4527 4514 | |
| 4528 4515 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4529 4516 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 4530 4517 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 4531 4518 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 4532 4519 <span class="s">}</span> | |
| 4533 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> | |
| 4534 4521 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 4535 4522 <span class="s">}</span> | |
| 4536 4523 <span class="s">}</span> | |
| 4537 4524 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 4538 4525 <span class="s">}</span> | |
| 4539 4526 | |
| 4540 4527 <span class="c"># Get dimensionality of the molecule using one of the following two methods:</span> | |
| 4541 4528 <span class="c"># . Using explicitly set Dimensionality</span> | |
| 4542 4529 <span class="c"># . Going over atomic coordinates</span> | |
| 4543 4530 <span class="c">#</span> | |
| 4544 4531 <span class="c"># The valid dimensionality values are:</span> | |
| 4545 4532 <span class="c"># . 3D - Three dimensional: One of X, Y or Z coordinate is non-zero</span> | |
| 4546 4533 <span class="c"># . 2D - Two dimensional: One of X or Y coordinate is non-zero; All Z coordinates are zero</span> | |
| 4547 4534 <span class="c"># . 0D - Zero dimensional: All atomic coordinates are zero</span> | |
| 4548 4535 <span class="c">#</span> | |
| 4549 <a name="GetDimensionality-"></a>4536 <span class="k">sub </span><span class="m">GetDimensionality</span> <span class="s">{</span> | |
| 4550 4537 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4551 4538 | |
| 4552 4539 <span class="c"># Is Dimensionality property explicitly set?</span> | |
| 4553 4540 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 4554 4541 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Dimensionality'</span><span class="s">)</span><span class="sc">;</span> | |
| 4555 4542 <span class="s">}</span> | |
| 4556 4543 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> | |
| 4557 4544 | |
| 4558 4545 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4559 4546 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span> | |
| 4560 4547 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetZ</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 4561 4548 <span class="k">return</span> <span class="q">'3D'</span><span class="sc">;</span> | |
| 4562 4549 <span class="s">}</span> | |
| 4563 4550 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetX</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span> || <span class="i">$Atom</span><span class="i">->GetY</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
| 4564 4551 <span class="k">return</span> <span class="q">'2D'</span><span class="sc">;</span> | |
| 4565 4552 <span class="s">}</span> | |
| 4566 4553 <span class="s">}</span> | |
| 4567 4554 <span class="k">return</span> <span class="q">'0D'</span><span class="sc">;</span> | |
| 4568 4555 <span class="s">}</span> | |
| 4569 4556 | |
| 4570 4557 <span class="c"># Is it a molecule object?</span> | |
| 4571 <a name="IsMolecule-"></a>4558 <span class="k">sub </span><span class="m">IsMolecule ($)</span> <span class="s">{</span> | |
| 4572 4559 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4573 4560 | |
| 4574 4561 <span class="k">return</span> <span class="i">_IsMolecule</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span><span class="sc">;</span> | |
| 4575 4562 <span class="s">}</span> | |
| 4576 4563 | |
| 4577 4564 <span class="c"># Return a string containing vertices, edges and other properties...</span> | |
| 4578 <a name="StringifyMolecule-"></a>4565 <span class="k">sub </span><span class="m">StringifyMolecule</span> <span class="s">{</span> | |
| 4579 4566 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4580 4567 <span class="k">my</span><span class="s">(</span><span class="i">$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">$ElementalComposition</span><span class="s">)</span><span class="sc">;</span> | |
| 4581 4568 | |
| 4582 4569 <span class="i">$ID</span> = <span class="i">$This</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4583 4570 <span class="i">$Name</span> = <span class="i">$This</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4584 4571 <span class="i">$NumOfAtoms</span> = <span class="i">$This</span><span class="i">->GetNumOfAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4585 4572 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4586 4573 | |
| 4587 4574 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4588 4575 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NumOfRings</span><span class="s">)</span> <span class="s">{</span> | |
| 4589 4576 <span class="i">$NumOfRings</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
| 4590 4577 <span class="s">}</span> | |
| 4591 4578 | |
| 4592 4579 <span class="i">$MolecularFormula</span> = <span class="i">$This</span><span class="i">->GetMolecularFormula</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4593 4580 | |
| 4594 4581 <span class="i">$MolecularWeight</span> = <span class="i">$This</span><span class="i">->GetMolecularWeight</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4595 4582 <span class="i">$MolecularWeight</span> = <span class="i">round</span><span class="s">(</span><span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="n">4</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> | |
| 4596 4583 | |
| 4597 4584 <span class="i">$ExactMass</span> = <span class="i">$This</span><span class="i">->GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4598 4585 <span class="i">$ExactMass</span> = <span class="i">round</span><span class="s">(</span><span class="i">$ExactMass</span><span class="cm">,</span> <span class="n">4</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> | |
| 4599 4586 | |
| 4600 4587 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4601 4588 <span class="i">$Charge</span> = <span class="i">$This</span><span class="i">->GetCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4602 4589 | |
| 4603 4590 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4604 4591 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4605 4592 | |
| 4606 4593 <span class="s">(</span><span class="i">$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> | |
| 4607 4594 <span class="i">$ElementalComposition</span> = <span class="q">'None'</span><span class="sc">;</span> | |
| 4608 4595 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ElementsRef</span>}<span class="s">)</span> <span class="s">{</span> | |
| 4609 4596 <span class="i">$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> | |
| 4610 4597 <span class="s">}</span> | |
| 4611 4598 | |
| 4612 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: $ElementalComposition"</span><span class="sc">;</span> | |
| 4613 4600 | |
| 4614 4601 <span class="k">return</span> <span class="i">$MoleculeString</span><span class="sc">;</span> | |
| 4615 4602 <span class="s">}</span> | |
| 4616 4603 | |
| 4617 4604 <span class="c"># Load appropriate atom data files from <MayaChemTools>/lib directory used by various</span> | |
| 4618 4605 <span class="c"># object methods in the current class...</span> | |
| 4619 4606 <span class="c">#</span> | |
| 4620 <a name="_LoadMoleculeClassData-"></a>4607 <span class="k">sub </span><span class="m">_LoadMoleculeClassData</span> <span class="s">{</span> | |
| 4621 4608 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span> | |
| 4622 4609 | |
| 4623 4610 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4624 4611 | |
| 4625 4612 <span class="c"># Load and process data for aromaticity models...</span> | |
| 4626 4613 <span class="i">_LoadAromaticityModelsData</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span> | |
| 4627 4614 <span class="i">_ProcessAromaticityModelsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4628 4615 <span class="s">}</span> | |
| 4629 4616 | |
| 4630 4617 <span class="c">#</span> | |
| 4631 4618 <span class="c"># Load data for supported aromaticity models...</span> | |
| 4632 4619 <span class="c">#</span> | |
| 4633 <a name="_LoadAromaticityModelsData-"></a>4620 <span class="k">sub </span><span class="m">_LoadAromaticityModelsData</span> <span class="s">{</span> | |
| 4634 4621 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4635 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> | |
| 4636 4623 | |
| 4637 4624 <span class="i">%AromaticityModelsDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4638 4625 <span class="i">%CanonicalAromaticityModelNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4639 4626 | |
| 4640 4627 <span class="c"># File format:</span> | |
| 4641 4628 <span class="c">#</span> | |
| 4642 4629 <span class="c"># "ParameterName","MDLAromaticityModel","TriposAromaticityModel","MMFFAromaticityModel","ChemAxonBasicAromaticityModel","ChemAxonGeneralAromaticityModel","DaylightAromaticityModel","MayaChemToolsAromaticityModel"</span> | |
| 4643 4630 <span class="c"># "AllowHeteroRingAtoms","No","No","Yes","Yes","Yes","Yes","Yes"</span> | |
| 4644 4631 <span class="c">#</span> | |
| 4645 4632 <span class="i">$DataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">"/data/AromaticityModelsData.csv"</span><span class="sc">;</span> | |
| 4646 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> | |
| 4647 4634 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAromaticityModelsData: MayaChemTools package file, $DataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> | |
| 4648 4635 <span class="s">}</span> | |
| 4649 4636 | |
| 4650 4637 <span class="c"># Setup a list of currently supported aromaticity parameters...</span> | |
| 4651 4638 <span class="c">#</span> | |
| 4652 4639 <span class="k">my</span><span class="s">(</span><span class="i">@KnownNames</span><span class="s">)</span><span class="sc">;</span> | |
| 4653 4640 <span class="i">@KnownNames</span> = <span class="q">qw(AllowHeteroRingAtoms HeteroRingAtomsList AllowExocyclicDoubleBonds AllowHomoNuclearExocyclicDoubleBonds AllowElectronegativeRingAtomExocyclicDoubleBonds AllowRingAtomFormalCharge AllowHeteroRingAtomFormalCharge MinimumRingSize)</span><span class="sc">;</span> | |
| 4654 4641 | |
| 4655 4642 <span class="i">%SupportedParameterNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4656 4643 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="i">@KnownNames</span><span class="s">)</span> <span class="s">{</span> | |
| 4657 4644 <span class="i">$SupportedParameterNames</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterName</span><span class="sc">;</span> | |
| 4658 4645 <span class="s">}</span> | |
| 4659 4646 | |
| 4660 4647 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span> | |
| 4661 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: $! ..."</span><span class="sc">;</span> | |
| 4662 4649 | |
| 4663 4650 <span class="c"># Skip lines up to column labels...</span> | |
| 4664 4651 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$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> | |
| 4665 4652 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> | |
| 4666 4653 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 4667 4654 <span class="s">}</span> | |
| 4668 4655 <span class="s">}</span> | |
| 4669 4656 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 4670 4657 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span> | |
| 4671 4658 | |
| 4672 4659 <span class="i">%ColIndexToModelName</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4673 4660 | |
| 4674 4661 <span class="c"># Process names of aromaticity models...</span> | |
| 4675 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> | |
| 4676 4663 <span class="i">$ModelName</span> = <span class="i">$ColLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 4677 4664 <span class="i">$ModelName</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 4678 4665 | |
| 4679 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> | |
| 4680 4667 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAromaticityModelsData: The aromaticity model name, $ModelName, in $DataFile has already exists.\nLine: $Line..."</span><span class="sc">;</span> | |
| 4681 4668 <span class="s">}</span> | |
| 4682 4669 <span class="i">%</span>{<span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4683 4670 | |
| 4684 4671 <span class="c"># Cannonicalize aromatic model name by converting into all lowercase...</span> | |
| 4685 4672 <span class="i">$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> | |
| 4686 4673 | |
| 4687 4674 <span class="i">$ColIndexToModelName</span>{<span class="i">$Index</span>} = <span class="i">$ModelName</span><span class="sc">;</span> | |
| 4688 4675 <span class="s">}</span> | |
| 4689 4676 | |
| 4690 4677 <span class="c"># Process paramater name and their values for specified aromaticity models...</span> | |
| 4691 4678 <span class="c">#</span> | |
| 4692 4679 <span class="i">%ParameterNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4693 4680 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$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> | |
| 4694 4681 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> | |
| 4695 4682 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 4696 4683 <span class="s">}</span> | |
| 4697 4684 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4698 4685 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 4699 4686 <span class="k">if</span> <span class="s">(</span><span class="i">@LineWords</span> != <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span> | |
| 4700 4687 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAromaticityModelsData: The number of data fields, @LineWords, in $DataFile must be $NumOfCols.\nLine: $Line..."</span><span class="sc">;</span> | |
| 4701 4688 <span class="s">}</span> | |
| 4702 4689 | |
| 4703 4690 <span class="c"># Process parameter name and values for aromaticity models...</span> | |
| 4704 4691 <span class="c">#</span> | |
| 4705 4692 <span class="i">$ParameterName</span> = <span class="i">$LineWords</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 4706 4693 | |
| 4707 4694 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$SupportedParameterNames</span>{<span class="i">$ParameterName</span>}<span class="s">)</span> <span class="s">{</span> | |
| 4708 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: $Line..."</span><span class="sc">;</span> | |
| 4709 4696 <span class="s">}</span> | |
| 4710 4697 | |
| 4711 4698 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ParameterNames</span>{<span class="i">$ParameterName</span>}<span class="s">)</span> <span class="s">{</span> | |
| 4712 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: $Line..."</span><span class="sc">;</span> | |
| 4713 4700 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 4714 4701 <span class="s">}</span> | |
| 4715 4702 <span class="i">$ParameterNames</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterName</span><span class="sc">;</span> | |
| 4716 4703 | |
| 4717 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> | |
| 4718 4705 <span class="i">$ModelName</span> = <span class="i">$ColIndexToModelName</span>{<span class="i">$Index</span>}<span class="sc">;</span> | |
| 4719 4706 <span class="i">$ParameterValue</span> = <span class="i">$LineWords</span>[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 4720 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> | |
| 4721 4708 <span class="s">}</span> | |
| 4722 4709 <span class="s">}</span> | |
| 4723 4710 <span class="k">close</span> <span class="w">DATAFILE</span><span class="sc">;</span> | |
| 4724 4711 <span class="s">}</span> | |
| 4725 4712 | |
| 4726 4713 <span class="c"># Process already loaded aromaticity model data...</span> | |
| 4727 4714 <span class="c">#</span> | |
| 4728 <a name="_ProcessAromaticityModelsData-"></a>4715 <span class="k">sub </span><span class="m">_ProcessAromaticityModelsData</span> <span class="s">{</span> | |
| 4729 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> | |
| 4730 4717 | |
| 4731 4718 <span class="k">for</span> <span class="i">$ModelName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AromaticityModelsDataMap</span><span class="s">)</span> <span class="s">{</span> | |
| 4732 4719 <span class="k">for</span> <span class="i">$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> | |
| 4733 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> | |
| 4734 4721 <span class="i">$ParameterValue</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 4735 4722 | |
| 4736 4723 <span class="j">VALUE:</span> <span class="s">{</span> | |
| 4737 4724 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 4738 4725 <span class="i">$NewParameterValue</span> = <span class="n">1</span><span class="sc">;</span> | |
| 4739 4726 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> | |
| 4740 4727 <span class="s">}</span> | |
| 4741 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> | |
| 4742 4729 <span class="i">$NewParameterValue</span> = <span class="n">0</span><span class="sc">;</span> | |
| 4743 4730 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> | |
| 4744 4731 <span class="s">}</span> | |
| 4745 4732 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 4746 4733 <span class="i">$NewParameterValue</span> = <span class="q">''</span><span class="sc">;</span> | |
| 4747 4734 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> | |
| 4748 4735 <span class="s">}</span> | |
| 4749 4736 <span class="i">$NewParameterValue</span> = <span class="i">$ParameterValue</span><span class="sc">;</span> | |
| 4750 4737 <span class="s">}</span> | |
| 4751 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> | |
| 4752 4739 | |
| 4753 4740 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/List/i</span><span class="s">)</span> <span class="s">{</span> | |
| 4754 4741 <span class="c"># Setup a new parameter conatining a reference to a hash for the specified values...</span> | |
| 4755 4742 <span class="k">my</span><span class="s">(</span><span class="i">$DataMapRefName</span><span class="cm">,</span> <span class="i">$DataValue</span><span class="cm">,</span> <span class="i">%DataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 4756 4743 | |
| 4757 4744 <span class="i">$DataMapRefName</span> = <span class="q">"${ParameterName}MapRef"</span><span class="sc">;</span> | |
| 4758 4745 | |
| 4759 4746 <span class="i">%DataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 4760 4747 <span class="k">for</span> <span class="i">$DataValue</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NewParameterValue</span><span class="s">)</span> <span class="s">{</span> | |
| 4761 4748 <span class="i">$DataMap</span>{<span class="i">$DataValue</span>} = <span class="i">$DataValue</span><span class="sc">;</span> | |
| 4762 4749 <span class="s">}</span> | |
| 4763 4750 <span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}{<span class="i">$DataMapRefName</span>} = \<span class="i">%DataMap</span><span class="sc">;</span> | |
| 4764 4751 <span class="s">}</span> | |
| 4765 4752 <span class="s">}</span> | |
| 4766 4753 <span class="s">}</span> | |
| 4767 4754 <span class="s">}</span> | |
| 4768 4755 | |
| 4769 4756 <span class="c"># Is it a molecule object?</span> | |
| 4770 <a name="_IsMolecule-"></a>4757 <span class="k">sub </span><span class="m">_IsMolecule</span> <span class="s">{</span> | |
| 4771 4758 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 4772 4759 | |
| 4773 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> | |
| 4774 4761 <span class="s">}</span> | |
| 4775 4762 | |
| 4776 <a name="EOF-"></a></pre> | |
| 4777 <p> </p> | |
| 4778 <br /> | |
| 4779 <center> | |
| 4780 <img src="../../../images/h2o2.png"> | |
| 4781 </center> | |
| 4782 </body> | |
| 4783 </html> |