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3 <title>MayaChemTools:Code:Atom.pm</title>
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14 <a name="package-Atom-"></a> 1 <span class="k">package </span><span class="i">Atom</span><span class="sc">;</span>
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: Atom.pm,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:47:02 $</span>
18 5 <span class="c"># $Revision: 1.62 $</span>
19 6 <span class="c">#</span>
20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</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 &lt;http://www.gnu.org/licenses/&gt; 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">PeriodicTable</span><span class="sc">;</span>
49 36 <span class="k">use</span> <span class="w">Vector</span><span class="sc">;</span>
50 37 <span class="k">use</span> <span class="w">MathUtil</span><span class="sc">;</span>
51 38 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
52 39 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
53 40 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
54 41
55 42 <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>
56 43
57 44 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span>
58 45 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
59 46 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
60 47
61 48 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=&gt;</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>
62 49
63 50 <span class="c"># Setup class variables...</span>
64 51 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">$ObjectID</span><span class="cm">,</span> <span class="i">%MDLValenceModelDataMap</span><span class="cm">,</span> <span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span>
65 52 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
66 53
67 54 <span class="c"># Overload Perl functions...</span>
68 55 <span class="k">use</span> <span class="w">overload</span> <span class="q">&#39;&quot;&quot;&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;StringifyAtom&#39;</span><span class="sc">;</span>
69 56
70 57 <span class="c"># Class constructor...</span>
71 <a name="new-"></a> 58 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
72 59 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73 60
74 61 <span class="c"># Initialize object...</span>
75 62 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span>
76 63 <span class="k">bless</span> <span class="i">$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>
77 64 <span class="i">$This</span><span class="i">-&gt;_InitializeAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
78 65
79 66 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
80 67
81 68 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
82 69 <span class="s">}</span>
83 70
84 71 <span class="c"># Initialize object data...</span>
85 <a name="_InitializeAtom-"></a> 72 <span class="k">sub </span><span class="m">_InitializeAtom</span> <span class="s">{</span>
86 73 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
87 74 <span class="k">my</span><span class="s">(</span><span class="i">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
88 75
89 76 <span class="c"># All other property names and values along with all Set/Get&lt;PropertyName&gt; methods</span>
90 77 <span class="c"># are implemented on-demand using ObjectProperty class.</span>
91 78 <span class="i">$This</span>-&gt;{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span>
92 79 <span class="i">$This</span>-&gt;{<span class="w">Name</span>} = <span class="q">&quot;Atom ${ObjectID}&quot;</span><span class="sc">;</span>
93 80 <span class="i">$This</span>-&gt;{<span class="w">AtomSymbol</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
94 81 <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} = <span class="n">0</span><span class="sc">;</span>
95 82 <span class="i">$This</span>-&gt;{<span class="w">XYZ</span>} = <span class="w">Vector::ZeroVector</span><span class="sc">;</span>
96 83 <span class="s">}</span>
97 84
98 85 <span class="c"># Initialize atom properties...</span>
99 <a name="_InitializeAtomProperties-"></a> 86 <span class="k">sub </span><span class="m">_InitializeAtomProperties</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">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
105 92 <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
106 93 <span class="s">}</span>
107 94 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">&#39;AtomSymbol&#39;</span>}<span class="s">)</span> <span class="s">{</span>
108 95 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;new: Atom object instantiated without setting atom symbol...&quot;</span><span class="sc">;</span>
109 96 <span class="s">}</span>
110 97
111 98 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
112 99 <span class="s">}</span>
113 100
114 101 <span class="c"># Initialize class ...</span>
115 <a name="_InitializeClass-"></a> 102 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
116 103 <span class="c">#Class name...</span>
117 104 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
118 105
119 106 <span class="c"># ID to keep track of objects...</span>
120 107 <span class="i">$ObjectID</span> = <span class="n">0</span><span class="sc">;</span>
121 108
122 109 <span class="c"># Load atom class data...</span>
123 110 <span class="i">_LoadAtomClassData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
124 111 <span class="s">}</span>
125 112
126 113 <span class="c"># Setup an explicit SetID method to block setting of ID by AUTOLOAD function...</span>
127 <a name="SetID-"></a> 114 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span>
128 115 <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>
129 116
130 117 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetID: Object ID can&#39;t be changed: it&#39;s used for internal tracking...&quot;</span><span class="sc">;</span>
131 118
132 119 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
133 120 <span class="s">}</span>
134 121
135 122 <span class="c"># Setup an explicit SetMolecule method to block setting of ID by AUTOLOAD function...</span>
136 <a name="SetMolecule-"></a> 123 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span>
137 124 <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>
138 125
139 126 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetMolecule: Molecule property can&#39;t be changed: it&#39;s used for internal tracking...&quot;</span><span class="sc">;</span>
140 127
141 128 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
142 129 <span class="s">}</span>
143 130
144 131 <span class="c"># Assign atom to molecule...</span>
145 <a name="_SetMolecule-"></a> 132 <span class="k">sub </span><span class="m">_SetMolecule</span> <span class="s">{</span>
146 133 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
147 134
148 135 <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span>
149 136
150 137 <span class="c"># Weaken the reference to disable increment of reference count; otherwise,</span>
151 138 <span class="c"># it it becomes a circular reference and destruction of Molecule object doesn&#39;t</span>
152 139 <span class="c"># get initiated which in turn disables destruction of atom object.</span>
153 140 <span class="c">#</span>
154 141 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
155 142
156 143 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
157 144 <span class="s">}</span>
158 145
159 146 <span class="c"># Setup atom symbol and atomic number for the element...</span>
160 147 <span class="c">#</span>
161 148 <span class="c"># Possible atom symbol values:</span>
162 149 <span class="c"># . An element symbol or some other type of atom: L - Atom list; LP - Lone pair; R# - R group;</span>
163 150 <span class="c"># A, Q, * - unknown atom; or something else?</span>
164 151 <span class="c">#</span>
165 152 <span class="c"># Default mass number corresponds to the most abundant natural isotope unless it&#39;s explicity</span>
166 153 <span class="c"># set using &quot;MassNumber&quot; property.</span>
167 154 <span class="c">#</span>
168 <a name="SetAtomSymbol-"></a> 155 <span class="k">sub </span><span class="m">SetAtomSymbol</span> <span class="s">{</span>
169 156 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
170 157 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
171 158
172 159 <span class="i">$This</span>-&gt;{<span class="w">AtomSymbol</span>} = <span class="i">$AtomSymbol</span><span class="sc">;</span>
173 160
174 161 <span class="i">$AtomicNumber</span> = <span class="i">PeriodicTable::GetElementAtomicNumber</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span>
175 162 <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} = <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicNumber</span><span class="s">)</span> ? <span class="i">$AtomicNumber</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
176 163
177 164 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
178 165 <span class="s">}</span>
179 166
180 167 <span class="c"># Setup atom symbol and atomic number for the element...</span>
181 <a name="SetAtomicNumber-"></a> 168 <span class="k">sub </span><span class="m">SetAtomicNumber</span> <span class="s">{</span>
182 169 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
183 170 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span>
184 171
185 172 <span class="i">$AtomSymbol</span> = <span class="i">PeriodicTable::GetElementAtomSymbol</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
186 173 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$AtomSymbol</span><span class="s">)</span> <span class="s">{</span>
187 174 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetAtomicNumber: Didn&#39;t set atomic number: Invalid atomic number, $AtomicNumber, specified...&quot;</span><span class="sc">;</span>
188 175 <span class="k">return</span><span class="sc">;</span>
189 176 <span class="s">}</span>
190 177 <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} = <span class="i">$AtomicNumber</span><span class="sc">;</span>
191 178 <span class="i">$This</span>-&gt;{<span class="w">AtomSymbol</span>} = <span class="i">$AtomSymbol</span><span class="sc">;</span>
192 179
193 180 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
194 181 <span class="s">}</span>
195 182
196 183 <span class="c"># Set atom as stereo center...</span>
197 184 <span class="c">#</span>
198 <a name="SetStereoCenter-"></a> 185 <span class="k">sub </span><span class="m">SetStereoCenter</span> <span class="s">{</span>
199 186 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StereoCenter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
200 187
201 188 <span class="i">$This</span><span class="i">-&gt;SetProperty</span><span class="s">(</span><span class="q">&#39;StereoCenter&#39;</span><span class="cm">,</span> <span class="i">$StereoCenter</span><span class="s">)</span><span class="sc">;</span>
202 189
203 190 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
204 191 <span class="s">}</span>
205 192
206 193 <span class="c"># Is it a stereo center?</span>
207 194 <span class="c">#</span>
208 <a name="IsStereoCenter-"></a> 195 <span class="k">sub </span><span class="m">IsStereoCenter</span> <span class="s">{</span>
209 196 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
210 197 <span class="k">my</span><span class="s">(</span><span class="i">$StereoCenter</span><span class="s">)</span><span class="sc">;</span>
211 198
212 199 <span class="i">$StereoCenter</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;StereoCenter&#39;</span><span class="s">)</span><span class="sc">;</span>
213 200
214 201 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$StereoCenter</span><span class="s">)</span> &amp;&amp; <span class="i">$StereoCenter</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
215 202 <span class="s">}</span>
216 203
217 204 <span class="c"># Set atom stereochemistry.</span>
218 205 <span class="c">#</span>
219 206 <span class="c"># Supported values are: R, S.</span>
220 207 <span class="c">#</span>
221 208 <span class="c"># Notes:</span>
222 209 <span class="c">#</span>
223 210 <span class="c"># . After the ligands around a central stereocenter has been ranked using CIP priority scheme and</span>
224 211 <span class="c"># the lowest ranked ligand lies behind the center atom, then R and S values correspond to:</span>
225 212 <span class="c">#</span>
226 213 <span class="c"># R: Clockwise arrangement of remaining ligands around the central atom going from highest to lowest ranked ligand</span>
227 214 <span class="c"># S: CounterClockwise arrangement of remaining ligands around the central atom going from highest to lowest ranked ligand</span>
228 215 <span class="c">#</span>
229 216 <span class="c"># . Assignment of any other arbitray values besides R and S is also allowed; however, a warning is printed.</span>
230 217 <span class="c">#</span>
231 <a name="SetStereochemistry-"></a> 218 <span class="k">sub </span><span class="m">SetStereochemistry</span> <span class="s">{</span>
232 219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Stereochemistry</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
233 220
234 221 <span class="k">if</span> <span class="s">(</span><span class="i">$Stereochemistry</span> !~ <span class="q">/^(R|S)$/i</span><span class="s">)</span> <span class="s">{</span>
235 222 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetStereochemistry: Assigning non-supported Stereochemistry value of $Stereochemistry. Supported values: R, S...&quot;</span><span class="sc">;</span>
236 223 <span class="s">}</span>
237 224
238 225 <span class="i">$This</span><span class="i">-&gt;SetProperty</span><span class="s">(</span><span class="q">&#39;StereoCenter&#39;</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
239 226 <span class="i">$This</span><span class="i">-&gt;SetProperty</span><span class="s">(</span><span class="q">&#39;Stereochemistry&#39;</span><span class="cm">,</span> <span class="i">$Stereochemistry</span><span class="s">)</span><span class="sc">;</span>
240 227
241 228 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
242 229 <span class="s">}</span>
243 230
244 231 <span class="c"># Setup mass number for atom...</span>
245 <a name="SetMassNumber-"></a> 232 <span class="k">sub </span><span class="m">SetMassNumber</span> <span class="s">{</span>
246 233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
247 234 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span>
248 235
249 236 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
250 237 <span class="i">$AtomSymbol</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomSymbol</span>}<span class="sc">;</span>
251 238 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
252 239 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetMassNumber: Didn&#39;t set mass number: Non standard atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol...&quot;</span><span class="sc">;</span>
253 240 <span class="k">return</span><span class="sc">;</span>
254 241 <span class="s">}</span>
255 242 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
256 243 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetMassNumber: Unknown mass number, $MassNumber, specified for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. Don&#39;t forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope...&quot;</span><span class="sc">;</span>
257 244 <span class="s">}</span>
258 245 <span class="i">$This</span><span class="i">-&gt;SetProperty</span><span class="s">(</span><span class="q">&#39;MassNumber&#39;</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span>
259 246
260 247 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
261 248 <span class="s">}</span>
262 249
263 250 <span class="c"># Get mass number...</span>
264 251 <span class="c">#</span>
265 <a name="GetMassNumber-"></a> 252 <span class="k">sub </span><span class="m">GetMassNumber</span> <span class="s">{</span>
266 253 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
267 254
268 255 <span class="c"># Is mass number explicity set?</span>
269 256 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;MassNumber&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
270 257 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;MassNumber&#39;</span><span class="s">)</span><span class="sc">;</span>
271 258 <span class="s">}</span>
272 259
273 260 <span class="c"># Is it an element symbol?</span>
274 261 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
275 262 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
276 263 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
277 264 <span class="s">}</span>
278 265
279 266 <span class="c"># Return most abundant mass number...</span>
280 267 <span class="k">return</span> <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
281 268 <span class="s">}</span>
282 269
283 270 <span class="c"># Get atomic weight:</span>
284 271 <span class="c"># . Explicitly set by the caller</span>
285 272 <span class="c"># . Using atomic number</span>
286 273 <span class="c">#</span>
287 <a name="GetAtomicWeight-"></a> 274 <span class="k">sub </span><span class="m">GetAtomicWeight</span> <span class="s">{</span>
288 275 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
289 276
290 277 <span class="c"># Is atomic weight explicity set?</span>
291 278 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;AtomicWeight&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
292 279 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;AtomicWeight&#39;</span><span class="s">)</span><span class="sc">;</span>
293 280 <span class="s">}</span>
294 281
295 282 <span class="c"># Is it an element symbol?</span>
296 283 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
297 284 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
298 285 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
299 286 <span class="s">}</span>
300 287
301 288 <span class="c"># Return its atomic weight...</span>
302 289 <span class="k">return</span> <span class="i">PeriodicTable::GetElementAtomicWeight</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
303 290 <span class="s">}</span>
304 291
305 292 <span class="c"># Get exact mass weight:</span>
306 293 <span class="c"># . Explicitly set by the caller</span>
307 294 <span class="c"># . Using atomic number and mass number explicity set by the caller</span>
308 295 <span class="c"># . Using atomic number and most abundant isotope</span>
309 296 <span class="c">#</span>
310 <a name="GetExactMass-"></a> 297 <span class="k">sub </span><span class="m">GetExactMass</span> <span class="s">{</span>
311 298 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
312 299
313 300 <span class="c"># Is exact mass explicity set?</span>
314 301 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;ExactMass&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
315 302 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;ExactMass&#39;</span><span class="s">)</span><span class="sc">;</span>
316 303 <span class="s">}</span>
317 304
318 305 <span class="c"># Is it an element symbol?</span>
319 306 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
320 307 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
321 308 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
322 309 <span class="s">}</span>
323 310
324 311 <span class="c"># Is mass number explicitly set?</span>
325 312 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;MassNumber&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
326 313 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;MassNumber&#39;</span><span class="s">)</span><span class="sc">;</span>
327 314 <span class="k">if</span> <span class="s">(</span><span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
328 315 <span class="k">return</span> <span class="i">PeriodicTable::GetElementNaturalIsotopeMass</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$MassNumber</span><span class="s">)</span><span class="sc">;</span>
329 316 <span class="s">}</span>
330 317 <span class="s">}</span>
331 318
332 319 <span class="c"># Return most abundant isotope mass...</span>
333 320 <span class="k">return</span> <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMass</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
334 321 <span class="s">}</span>
335 322
336 323 <span class="c"># Get formal charge:</span>
337 324 <span class="c"># . Explicitly set by the caller</span>
338 325 <span class="c"># . Or return zero insetad of undef</span>
339 326 <span class="c">#</span>
340 <a name="GetFormalCharge-"></a> 327 <span class="k">sub </span><span class="m">GetFormalCharge</span> <span class="s">{</span>
341 328 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
342 329 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span>
343 330
344 331 <span class="i">$FormalCharge</span> = <span class="n">0</span><span class="sc">;</span>
345 332 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;FormalCharge&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
346 333 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;FormalCharge&#39;</span><span class="s">)</span><span class="sc">;</span>
347 334 <span class="s">}</span>
348 335
349 336 <span class="k">return</span> <span class="k">defined</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> ? <span class="i">$FormalCharge</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
350 337 <span class="s">}</span>
351 338
352 339 <span class="c"># Get spin multiplicity:</span>
353 340 <span class="c"># . Explicitly set by the caller</span>
354 341 <span class="c"># . From FreeRadicalElectrons value explicitly set by the caller</span>
355 342 <span class="c"># . Or return zero insetad of undef</span>
356 343 <span class="c">#</span>
357 <a name="GetSpinMultiplicity-"></a> 344 <span class="k">sub </span><span class="m">GetSpinMultiplicity</span> <span class="s">{</span>
358 345 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
359 346 <span class="k">my</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span>
360 347
361 348 <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span>
362 349 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;SpinMultiplicity&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
363 350 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;SpinMultiplicity&#39;</span><span class="s">)</span><span class="sc">;</span>
364 351 <span class="k">return</span> <span class="k">defined</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span> ? <span class="i">$SpinMultiplicity</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
365 352 <span class="s">}</span>
366 353
367 354 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;FreeRadicalElectrons&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
368 355 <span class="k">my</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span><span class="sc">;</span>
369 356 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;FreeRadicalElectrons&#39;</span><span class="s">)</span><span class="sc">;</span>
370 357
371 358 <span class="j">SPINMULTIPLICITY:</span> <span class="s">{</span>
372 359 <span class="k">if</span> <span class="s">(</span><span class="i">$FreeRadicalElectrons</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> <span class="i">$SpinMultiplicity</span> = <span class="n">2</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span>
373 360 <span class="k">if</span> <span class="s">(</span><span class="i">$FreeRadicalElectrons</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> <span class="i">$SpinMultiplicity</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span>
374 361 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GetSpinMultiplicity: It&#39;s not possible to determine spin multiplicity from the specified free radical electrons value, $FreeRadicalElectrons. It has been set to 0...&quot;</span><span class="sc">;</span>
375 362 <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span>
376 363 <span class="s">}</span>
377 364 <span class="s">}</span>
378 365
379 366 <span class="k">return</span> <span class="i">$SpinMultiplicity</span><span class="sc">;</span>
380 367 <span class="s">}</span>
381 368
382 369 <span class="c"># Get number of free radical electrons:</span>
383 370 <span class="c"># . Explicitly set by the caller</span>
384 371 <span class="c"># . From SpinMultiplicity value explicitly set by the caller</span>
385 372 <span class="c"># . Or return zero insetad of undef</span>
386 373 <span class="c">#</span>
387 374 <span class="c"># Notes:</span>
388 375 <span class="c"># . For atoms with explicit assignment of SpinMultiplicity property values corresponding to</span>
389 376 <span class="c"># Singlet (two unpaired electrons corresponding to one spin state), Doublet (free radical; an unpaired</span>
390 377 <span class="c"># electron corresponding to two spin states), and Triplet (two unparied electrons corresponding to</span>
391 378 <span class="c"># three spin states; divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:</span>
392 379 <span class="c">#</span>
393 380 <span class="c"># SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1</span>
394 381 <span class="c"># SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2</span>
395 382 <span class="c">#</span>
396 <a name="GetFreeRadicalElectrons-"></a> 383 <span class="k">sub </span><span class="m">GetFreeRadicalElectrons</span> <span class="s">{</span>
397 384 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
398 385 <span class="k">my</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span><span class="sc">;</span>
399 386
400 387 <span class="i">$FreeRadicalElectrons</span> = <span class="n">0</span><span class="sc">;</span>
401 388
402 389 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;FreeRadicalElectrons&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
403 390 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;FreeRadicalElectrons&#39;</span><span class="s">)</span><span class="sc">;</span>
404 391 <span class="k">return</span> <span class="k">defined</span><span class="s">(</span><span class="i">$FreeRadicalElectrons</span><span class="s">)</span> ? <span class="i">$FreeRadicalElectrons</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
405 392 <span class="s">}</span>
406 393
407 394 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;SpinMultiplicity&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
408 395 <span class="k">my</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span><span class="sc">;</span>
409 396 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;SpinMultiplicity&#39;</span><span class="s">)</span><span class="sc">;</span>
410 397
411 398 <span class="j">SPINMULTIPLICITY:</span> <span class="s">{</span>
412 399 <span class="k">if</span> <span class="s">(</span><span class="i">$SpinMultiplicity</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FreeRadicalElectrons</span> = <span class="n">2</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span>
413 400 <span class="k">if</span> <span class="s">(</span><span class="i">$SpinMultiplicity</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FreeRadicalElectrons</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span>
414 401 <span class="k">if</span> <span class="s">(</span><span class="i">$SpinMultiplicity</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FreeRadicalElectrons</span> = <span class="n">2</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SPINMULTIPLICITY</span><span class="sc">;</span><span class="s">}</span>
415 402 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GetFreeRadicalElectrons: It&#39;s not possible to determine free radical electrons from the specified spin multiplicity value, $FreeRadicalElectrons. It has been set to 0...&quot;</span><span class="sc">;</span>
416 403 <span class="i">$FreeRadicalElectrons</span> = <span class="n">0</span><span class="sc">;</span>
417 404 <span class="s">}</span>
418 405 <span class="s">}</span>
419 406
420 407 <span class="k">return</span> <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span>
421 408 <span class="s">}</span>
422 409
423 410 <span class="c"># Set atom coordinates using:</span>
424 411 <span class="c"># . An array reference with three values</span>
425 412 <span class="c"># . An array containg three values</span>
426 413 <span class="c"># . A 3D vector</span>
427 414 <span class="c">#</span>
428 <a name="SetXYZ-"></a> 415 <span class="k">sub </span><span class="m">SetXYZ</span> <span class="s">{</span>
429 416 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
430 417
431 418 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
432 419 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetXYZ: No values specified...&quot;</span><span class="sc">;</span>
433 420 <span class="k">return</span><span class="sc">;</span>
434 421 <span class="s">}</span>
435 422
436 423 <span class="i">$This</span>-&gt;{<span class="w">XYZ</span>}<span class="i">-&gt;SetXYZ</span><span class="s">(</span><span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
437 424 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
438 425 <span class="s">}</span>
439 426
440 427 <span class="c"># Set X value...</span>
441 <a name="SetX-"></a> 428 <span class="k">sub </span><span class="m">SetX</span> <span class="s">{</span>
442 429 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
443 430
444 431 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span>
445 432 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetX: Undefined X value...&quot;</span><span class="sc">;</span>
446 433 <span class="k">return</span><span class="sc">;</span>
447 434 <span class="s">}</span>
448 435 <span class="i">$This</span>-&gt;{<span class="w">XYZ</span>}<span class="i">-&gt;SetX</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
449 436 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
450 437 <span class="s">}</span>
451 438
452 439 <span class="c"># Set Y value...</span>
453 <a name="SetY-"></a> 440 <span class="k">sub </span><span class="m">SetY</span> <span class="s">{</span>
454 441 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
455 442
456 443 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span>
457 444 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetY: Undefined Y value...&quot;</span><span class="sc">;</span>
458 445 <span class="k">return</span><span class="sc">;</span>
459 446 <span class="s">}</span>
460 447 <span class="i">$This</span>-&gt;{<span class="w">XYZ</span>}<span class="i">-&gt;SetY</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
461 448 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
462 449 <span class="s">}</span>
463 450
464 451 <span class="c"># Set Z value...</span>
465 <a name="SetZ-"></a> 452 <span class="k">sub </span><span class="m">SetZ</span> <span class="s">{</span>
466 453 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</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="k">defined</span> <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span>
469 456 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetZ: Undefined Z value...&quot;</span><span class="sc">;</span>
470 457 <span class="k">return</span><span class="sc">;</span>
471 458 <span class="s">}</span>
472 459 <span class="i">$This</span>-&gt;{<span class="w">XYZ</span>}<span class="i">-&gt;SetZ</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
473 460 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
474 461 <span class="s">}</span>
475 462
476 463 <span class="c"># Return XYZ as:</span>
477 464 <span class="c"># . Reference to an array</span>
478 465 <span class="c"># . An array</span>
479 466 <span class="c">#</span>
480 <a name="GetXYZ-"></a> 467 <span class="k">sub </span><span class="m">GetXYZ</span> <span class="s">{</span>
481 468 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
482 469
483 470 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">XYZ</span>}<span class="i">-&gt;GetXYZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
484 471 <span class="s">}</span>
485 472
486 473 <span class="c"># Return XYZ as a vector object...</span>
487 474 <span class="c">#</span>
488 <a name="GetXYZVector-"></a> 475 <span class="k">sub </span><span class="m">GetXYZVector</span> <span class="s">{</span>
489 476 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
490 477
491 478 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">XYZ</span>}<span class="sc">;</span>
492 479 <span class="s">}</span>
493 480
494 481 <span class="c"># Get X value...</span>
495 <a name="GetX-"></a> 482 <span class="k">sub </span><span class="m">GetX</span> <span class="s">{</span>
496 483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
497 484
498 485 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">XYZ</span>}<span class="i">-&gt;GetX</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
499 486 <span class="s">}</span>
500 487
501 488 <span class="c"># Get Y value...</span>
502 <a name="GetY-"></a> 489 <span class="k">sub </span><span class="m">GetY</span> <span class="s">{</span>
503 490 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
504 491
505 492 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">XYZ</span>}<span class="i">-&gt;GetY</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
506 493 <span class="s">}</span>
507 494
508 495 <span class="c"># Get Z value...</span>
509 <a name="GetZ-"></a> 496 <span class="k">sub </span><span class="m">GetZ</span> <span class="s">{</span>
510 497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
511 498
512 499 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">XYZ</span>}<span class="i">-&gt;GetZ</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
513 500 <span class="s">}</span>
514 501
515 502 <span class="c"># Delete atom...</span>
516 <a name="DeleteAtom-"></a> 503 <span class="k">sub </span><span class="m">DeleteAtom</span> <span class="s">{</span>
517 504 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
518 505
519 506 <span class="c"># Is this atom in a molecule?</span>
520 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
521 508 <span class="c"># Nothing to do...</span>
522 509 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
523 510 <span class="s">}</span>
524 511 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
525 512
526 513 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_DeleteAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
527 514 <span class="s">}</span>
528 515
529 516 <span class="c"># Get atom neighbor objects as array. In scalar conetxt, return number of neighbors...</span>
530 <a name="GetNeighbors-"></a> 517 <span class="k">sub </span><span class="m">GetNeighbors</span> <span class="s">{</span>
531 518 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@ExcludeNeighbors</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
532 519
533 520 <span class="c"># Is this atom in a molecule?</span>
534 521 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
535 522 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
536 523 <span class="s">}</span>
537 524 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
538 525
539 526 <span class="k">if</span> <span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span>
540 527 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetAtomNeighbors</span><span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span><span class="sc">;</span>
541 528 <span class="s">}</span>
542 529 <span class="k">else</span> <span class="s">{</span>
543 530 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
544 531 <span class="s">}</span>
545 532 <span class="s">}</span>
546 533
547 534 <span class="c"># Get atom neighbor objects as array. In scalar conetxt, return number of neighbors...</span>
548 <a name="_GetAtomNeighbors-"></a> 535 <span class="k">sub </span><span class="m">_GetAtomNeighbors</span> <span class="s">{</span>
549 536 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@ExcludeNeighbors</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
550 537 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
551 538
552 539 <span class="k">if</span> <span class="s">(</span>!<span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span>
553 540 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetAtomNeighbors</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
554 541 <span class="s">}</span>
555 542
556 543 <span class="c"># Setup a map for neigbhors to exclude...</span>
557 544 <span class="k">my</span><span class="s">(</span><span class="i">$ExcludeNeighbor</span><span class="cm">,</span> <span class="i">$ExcludeNeighborID</span><span class="cm">,</span> <span class="i">%ExcludeNeighborsIDsMap</span><span class="s">)</span><span class="sc">;</span>
558 545
559 546 <span class="i">%ExcludeNeighborsIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
560 547 <span class="k">for</span> <span class="i">$ExcludeNeighbor</span> <span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span>
561 548 <span class="i">$ExcludeNeighborID</span> = <span class="i">$ExcludeNeighbor</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
562 549 <span class="i">$ExcludeNeighborsIDsMap</span>{<span class="i">$ExcludeNeighborID</span>} = <span class="i">$ExcludeNeighborID</span><span class="sc">;</span>
563 550 <span class="s">}</span>
564 551
565 552 <span class="c"># Generate a filtered neighbors list...</span>
566 553 <span class="k">my</span><span class="s">(</span><span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">$NeighborID</span><span class="cm">,</span> <span class="i">@FilteredAtomNeighbors</span><span class="s">)</span><span class="sc">;</span>
567 554 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
568 555 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">-&gt;_GetAtomNeighbors</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
569 556 <span class="i">$NeighborID</span> = <span class="i">$Neighbor</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
570 557 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ExcludeNeighborsIDsMap</span>{<span class="i">$NeighborID</span>}<span class="s">)</span> <span class="s">{</span>
571 558 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
572 559 <span class="s">}</span>
573 560 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$Neighbor</span><span class="sc">;</span>
574 561 <span class="s">}</span>
575 562
576 563 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtomNeighbors</span><span class="sc">;</span>
577 564 <span class="s">}</span>
578 565
579 566 <span class="c"># Get specific atom neighbor objects as array. In scalar conetxt, return number of neighbors.</span>
580 567 <span class="c">#</span>
581 568 <span class="c"># Notes:</span>
582 569 <span class="c"># . AtomSpecification correspond to any valid AtomicInvariant based atomic specifications</span>
583 570 <span class="c"># as implemented in DoesAtomNeighborhoodMatch method.</span>
584 571 <span class="c"># . Multiple atom specifications can be used in a string delimited by comma.</span>
585 572 <span class="c">#</span>
586 <a name="GetNeighborsUsingAtomSpecification-"></a> 573 <span class="k">sub </span><span class="m">GetNeighborsUsingAtomSpecification</span> <span class="s">{</span>
587 574 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomSpecification</span><span class="cm">,</span> <span class="i">@ExcludeNeighbors</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
588 575 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span><span class="sc">;</span>
589 576
590 577 <span class="i">@AtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
591 578 <span class="i">@AtomNeighbors</span> = <span class="i">$This</span><span class="i">-&gt;GetNeighbors</span><span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span><span class="sc">;</span>
592 579
593 580 <span class="c"># Does atom has any neighbors and do they need to be filtered?</span>
594 581 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">@AtomNeighbors</span> &amp;&amp; <span class="k">defined</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="s">)</span> &amp;&amp; <span class="i">$AtomSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
595 582 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@AtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@AtomNeighbors</span><span class="sc">;</span>
596 583 <span class="s">}</span>
597 584
598 585 <span class="c"># Filter neighbors using atom specification...</span>
599 586 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="cm">,</span> <span class="i">@FilteredAtomNeighbors</span><span class="s">)</span><span class="sc">;</span>
600 587
601 588 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
602 589 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span> <span class="s">{</span>
603 590 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomNeighbor</span><span class="i">-&gt;_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
604 591 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
605 592 <span class="s">}</span>
606 593 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$AtomNeighbor</span><span class="sc">;</span>
607 594 <span class="s">}</span>
608 595
609 596 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtomNeighbors</span><span class="sc">;</span>
610 597 <span class="s">}</span>
611 598
612 599
613 600 <span class="c"># Get non-hydrogen atom neighbor objects as array. In scalar context, return number of neighbors...</span>
614 <a name="GetHeavyAtomNeighbors-"></a> 601 <span class="k">sub </span><span class="m">GetHeavyAtomNeighbors</span> <span class="s">{</span>
615 602 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
616 603
617 604 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
618 605 <span class="s">}</span>
619 606
620 607 <span class="c"># Get non-hydrogen atom neighbor objects as array. In scalar context, return number of neighbors...</span>
621 <a name="GetNonHydrogenAtomNeighbors-"></a> 608 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighbors</span> <span class="s">{</span>
622 609 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
623 610
624 611 <span class="c"># Is this atom in a molecule?</span>
625 612 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
626 613 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
627 614 <span class="s">}</span>
628 615 <span class="k">my</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
629 616
630 617 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetFilteredAtomNeighbors</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
631 618 <span class="s">}</span>
632 619
633 620 <span class="c"># Get hydrogen atom neighbor objects as array. In scalar context, return numbe of neighbors...</span>
634 <a name="GetHydrogenAtomNeighbors-"></a> 621 <span class="k">sub </span><span class="m">GetHydrogenAtomNeighbors</span> <span class="s">{</span>
635 622 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
636 623
637 624 <span class="c"># Is this atom in a molecule?</span>
638 625 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
639 626 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
640 627 <span class="s">}</span>
641 628 <span class="k">my</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
642 629
643 630 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetFilteredAtomNeighbors</span><span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
644 631 <span class="s">}</span>
645 632
646 633 <span class="c"># Get non-hydrogen neighbor of hydrogen atom...</span>
647 634 <span class="c">#</span>
648 <a name="GetNonHydrogenNeighborOfHydrogenAtom-"></a> 635 <span class="k">sub </span><span class="m">GetNonHydrogenNeighborOfHydrogenAtom</span> <span class="s">{</span>
649 636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
650 637
651 638 <span class="c"># Is it Hydrogen?</span>
652 639 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
653 640 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
654 641 <span class="s">}</span>
655 642 <span class="k">my</span><span class="s">(</span><span class="i">@Neighbors</span><span class="s">)</span><span class="sc">;</span>
656 643
657 644 <span class="i">@Neighbors</span> = <span class="i">$This</span><span class="i">-&gt;GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
658 645
659 646 <span class="k">return</span> <span class="s">(</span><span class="i">@Neighbors</span> == <span class="n">1</span><span class="s">)</span> ? <span class="i">$Neighbors</span>[<span class="n">0</span>] <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
660 647 <span class="s">}</span>
661 648
662 649 <span class="c"># Get filtered atom atom neighbors</span>
663 <a name="_GetFilteredAtomNeighbors-"></a> 650 <span class="k">sub </span><span class="m">_GetFilteredAtomNeighbors</span> <span class="s">{</span>
664 651 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
665 652
666 653 <span class="c"># Check flags...</span>
667 654 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
668 655 <span class="i">$NonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
669 656 <span class="s">}</span>
670 657 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$HydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
671 658 <span class="i">$HydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
672 659 <span class="s">}</span>
673 660 <span class="k">my</span><span class="s">(</span><span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">@FilteredAtomNeighbors</span><span class="s">)</span><span class="sc">;</span>
674 661
675 662 <span class="i">@FilteredAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
676 663 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
677 664 <span class="k">if</span> <span class="s">(</span><span class="i">$NonHydrogenAtomsOnly</span> &amp;&amp; <span class="i">$Neighbor</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
678 665 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
679 666 <span class="s">}</span>
680 667 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenAtomsOnly</span> &amp;&amp; <span class="s">(</span>!<span class="i">$Neighbor</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
681 668 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
682 669 <span class="s">}</span>
683 670 <span class="k">push</span> <span class="i">@FilteredAtomNeighbors</span><span class="cm">,</span> <span class="i">$Neighbor</span><span class="sc">;</span>
684 671 <span class="s">}</span>
685 672
686 673 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtomNeighbors</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtomNeighbors</span><span class="sc">;</span>
687 674 <span class="s">}</span>
688 675
689 676 <span class="c"># Get number of neighbors...</span>
690 677 <span class="c">#</span>
691 <a name="GetNumOfNeighbors-"></a> 678 <span class="k">sub </span><span class="m">GetNumOfNeighbors</span> <span class="s">{</span>
692 679 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
693 680 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span>
694 681
695 682 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">-&gt;GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
696 683
697 684 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
698 685 <span class="s">}</span>
699 686
700 687 <span class="c"># Get number of neighbors which are non-hydrogen atoms...</span>
701 <a name="GetNumOfHeavyAtomNeighbors-"></a> 688 <span class="k">sub </span><span class="m">GetNumOfHeavyAtomNeighbors</span> <span class="s">{</span>
702 689 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
703 690
704 691 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
705 692 <span class="s">}</span>
706 693
707 694 <span class="c"># Get number of neighbors which are non-hydrogen atoms...</span>
708 <a name="GetNumOfNonHydrogenAtomNeighbors-"></a> 695 <span class="k">sub </span><span class="m">GetNumOfNonHydrogenAtomNeighbors</span> <span class="s">{</span>
709 696 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
710 697 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span>
711 698
712 699 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">-&gt;GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
713 700
714 701 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
715 702 <span class="s">}</span>
716 703
717 704 <span class="c"># Get number of neighbors which are hydrogen atoms...</span>
718 <a name="GetNumOfHydrogenAtomNeighbors-"></a> 705 <span class="k">sub </span><span class="m">GetNumOfHydrogenAtomNeighbors</span> <span class="s">{</span>
719 706 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
720 707 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNeighbors</span><span class="s">)</span><span class="sc">;</span>
721 708
722 709 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">-&gt;GetHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
723 710
724 711 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> ? <span class="i">$NumOfNeighbors</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
725 712 <span class="s">}</span>
726 713
727 714 <span class="c"># Get bond objects as array. In scalar context, return number of bonds...</span>
728 <a name="GetBonds-"></a> 715 <span class="k">sub </span><span class="m">GetBonds</span> <span class="s">{</span>
729 716 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
730 717
731 718 <span class="c"># Is this atom in a molecule?</span>
732 719 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
733 720 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
734 721 <span class="s">}</span>
735 722 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
736 723
737 724 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetAtomBonds</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
738 725 <span class="s">}</span>
739 726
740 727 <span class="c"># Get bond to specified atom...</span>
741 <a name="GetBondToAtom-"></a> 728 <span class="k">sub </span><span class="m">GetBondToAtom</span> <span class="s">{</span>
742 729 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
743 730
744 731 <span class="c"># Is this atom in a molecule?</span>
745 732 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
746 733 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
747 734 <span class="s">}</span>
748 735 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
749 736
750 737 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetBondToAtom</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span><span class="sc">;</span>
751 738 <span class="s">}</span>
752 739
753 740 <span class="c"># It it bonded to a specified atom?</span>
754 <a name="IsBondedToAtom-"></a> 741 <span class="k">sub </span><span class="m">IsBondedToAtom</span> <span class="s">{</span>
755 742 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
756 743
757 744 <span class="c"># Is this atom in a molecule?</span>
758 745 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
759 746 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
760 747 <span class="s">}</span>
761 748 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
762 749
763 750 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_IsBondedToAtom</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span><span class="sc">;</span>
764 751 <span class="s">}</span>
765 752
766 753 <span class="c"># Get bond objects to non-hydrogen atoms as array. In scalar context, return number of bonds...</span>
767 <a name="GetBondsToHeavyAtoms-"></a> 754 <span class="k">sub </span><span class="m">GetBondsToHeavyAtoms</span> <span class="s">{</span>
768 755 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
769 756
770 757 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
771 758 <span class="s">}</span>
772 759
773 760 <span class="c"># Get bond objects to non-hydrogen atoms as array. In scalar context, return number of bonds...</span>
774 <a name="GetBondsToNonHydrogenAtoms-"></a> 761 <span class="k">sub </span><span class="m">GetBondsToNonHydrogenAtoms</span> <span class="s">{</span>
775 762 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
776 763
777 764 <span class="c"># Is this atom in a molecule?</span>
778 765 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
779 766 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
780 767 <span class="s">}</span>
781 768 <span class="k">my</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
782 769
783 770 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetFilteredBonds</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
784 771 <span class="s">}</span>
785 772
786 773 <span class="c"># Get bond objects to hydrogen atoms as array. In scalar context, return number of bonds...</span>
787 <a name="GetBondsToHydrogenAtoms-"></a> 774 <span class="k">sub </span><span class="m">GetBondsToHydrogenAtoms</span> <span class="s">{</span>
788 775 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
789 776
790 777 <span class="c"># Is this atom in a molecule?</span>
791 778 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
792 779 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
793 780 <span class="s">}</span>
794 781 <span class="k">my</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
795 782
796 783 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetFilteredBonds</span><span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
797 784 <span class="s">}</span>
798 785
799 786 <span class="c"># Get filtered bonds...</span>
800 <a name="_GetFilteredBonds-"></a> 787 <span class="k">sub </span><span class="m">_GetFilteredBonds</span> <span class="s">{</span>
801 788 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
802 789
803 790 <span class="c"># Check flags...</span>
804 791 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondsToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
805 792 <span class="i">$BondsToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
806 793 <span class="s">}</span>
807 794 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondsToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
808 795 <span class="i">$BondsToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
809 796 <span class="s">}</span>
810 797
811 798 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">@FilteredBonds</span><span class="s">)</span><span class="sc">;</span>
812 799
813 800 <span class="i">@FilteredBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
814 801 <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">-&gt;GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
815 802 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">-&gt;GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
816 803 <span class="k">if</span> <span class="s">(</span><span class="i">$BondsToNonHydrogenAtomsOnly</span> &amp;&amp; <span class="i">$BondedAtom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
817 804 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
818 805 <span class="s">}</span>
819 806 <span class="k">if</span> <span class="s">(</span><span class="i">$BondsToHydrogenAtomsOnly</span> &amp;&amp; <span class="s">(</span>!<span class="i">$BondedAtom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
820 807 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
821 808 <span class="s">}</span>
822 809 <span class="k">push</span> <span class="i">@FilteredBonds</span><span class="cm">,</span> <span class="i">$Bond</span><span class="sc">;</span>
823 810 <span class="s">}</span>
824 811
825 812 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredBonds</span> <span class="co">:</span> <span class="s">(</span><span class="k">scalar</span> <span class="i">@FilteredBonds</span><span class="s">)</span><span class="sc">;</span>
826 813 <span class="s">}</span>
827 814
828 815 <span class="c"># Get number of bonds...</span>
829 816 <span class="c">#</span>
830 <a name="GetNumOfBonds-"></a> 817 <span class="k">sub </span><span class="m">GetNumOfBonds</span> <span class="s">{</span>
831 818 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
832 819 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span>
833 820
834 821 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
835 822
836 823 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
837 824 <span class="s">}</span>
838 825
839 826 <span class="c"># Get number of bonds to non-hydrogen atoms...</span>
840 <a name="GetNumOfBondsToHeavyAtoms-"></a> 827 <span class="k">sub </span><span class="m">GetNumOfBondsToHeavyAtoms</span> <span class="s">{</span>
841 828 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
842 829
843 830 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
844 831 <span class="s">}</span>
845 832
846 833 <span class="c"># Get number of bonds to non-hydrogen atoms...</span>
847 <a name="GetNumOfBondsToNonHydrogenAtoms-"></a> 834 <span class="k">sub </span><span class="m">GetNumOfBondsToNonHydrogenAtoms</span> <span class="s">{</span>
848 835 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
849 836 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span>
850 837
851 838 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
852 839
853 840 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
854 841 <span class="s">}</span>
855 842
856 843 <span class="c"># Get number of single bonds to heavy atoms...</span>
857 <a name="GetNumOfSingleBondsToHeavyAtoms-"></a> 844 <span class="k">sub </span><span class="m">GetNumOfSingleBondsToHeavyAtoms</span> <span class="s">{</span>
858 845 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
859 846
860 847 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
861 848 <span class="s">}</span>
862 849
863 850 <span class="c"># Get number of single bonds to non-hydrogen atoms...</span>
864 <a name="GetNumOfSingleBondsToNonHydrogenAtoms-"></a> 851 <span class="k">sub </span><span class="m">GetNumOfSingleBondsToNonHydrogenAtoms</span> <span class="s">{</span>
865 852 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
866 853
867 854 <span class="c"># Is this atom in a molecule?</span>
868 855 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
869 856 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
870 857 <span class="s">}</span>
871 858 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span>
872 859 <span class="s">}</span>
873 860
874 861 <span class="c"># Get number of double bonds to heavy atoms...</span>
875 <a name="GetNumOfDoubleBondsToHeavyAtoms-"></a> 862 <span class="k">sub </span><span class="m">GetNumOfDoubleBondsToHeavyAtoms</span> <span class="s">{</span>
876 863 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
877 864
878 865 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfDoubleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
879 866 <span class="s">}</span>
880 867
881 868 <span class="c"># Get number of double bonds to non-hydrogen atoms...</span>
882 <a name="GetNumOfDoubleBondsToNonHydrogenAtoms-"></a> 869 <span class="k">sub </span><span class="m">GetNumOfDoubleBondsToNonHydrogenAtoms</span> <span class="s">{</span>
883 870 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
884 871
885 872 <span class="c"># Is this atom in a molecule?</span>
886 873 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
887 874 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
888 875 <span class="s">}</span>
889 876 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">2</span><span class="s">)</span><span class="sc">;</span>
890 877 <span class="s">}</span>
891 878
892 879 <span class="c"># Get number of triple bonds to heavy atoms...</span>
893 <a name="GetNumOfTripleBondsToHeavyAtoms-"></a> 880 <span class="k">sub </span><span class="m">GetNumOfTripleBondsToHeavyAtoms</span> <span class="s">{</span>
894 881 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
895 882
896 883 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfTripleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
897 884 <span class="s">}</span>
898 885
899 886 <span class="c"># Get number of triple bonds to non-hydrogen atoms...</span>
900 <a name="GetNumOfTripleBondsToNonHydrogenAtoms-"></a> 887 <span class="k">sub </span><span class="m">GetNumOfTripleBondsToNonHydrogenAtoms</span> <span class="s">{</span>
901 888 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
902 889
903 890 <span class="c"># Is this atom in a molecule?</span>
904 891 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
905 892 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
906 893 <span class="s">}</span>
907 894 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">3</span><span class="s">)</span><span class="sc">;</span>
908 895 <span class="s">}</span>
909 896
910 897 <span class="c"># Get number of bonds of specified bond order to non-hydrogen atoms...</span>
911 <a name="_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms-"></a> 898 <span class="k">sub </span><span class="m">_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span> <span class="s">{</span>
912 899 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$SpecifiedBondOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
913 900 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
914 901
915 902 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span>
916 903 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
917 904 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
918 905 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">-&gt;GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
919 906 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedBondOrder</span> == <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span>
920 907 <span class="i">$NumOfBonds</span>++<span class="sc">;</span>
921 908 <span class="s">}</span>
922 909 <span class="s">}</span>
923 910 <span class="k">return</span> <span class="i">$NumOfBonds</span><span class="sc">;</span>
924 911 <span class="s">}</span>
925 912
926 913 <span class="c"># Get number of aromatic bonds to heavy atoms...</span>
927 <a name="GetNumOfAromaticBondsToHeavyAtoms-"></a> 914 <span class="k">sub </span><span class="m">GetNumOfAromaticBondsToHeavyAtoms</span> <span class="s">{</span>
928 915 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
929 916
930 917 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfAromaticBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
931 918 <span class="s">}</span>
932 919
933 920 <span class="c"># Get number of aromatic bonds to non-hydrogen atoms...</span>
934 <a name="GetNumOfAromaticBondsToNonHydrogenAtoms-"></a> 921 <span class="k">sub </span><span class="m">GetNumOfAromaticBondsToNonHydrogenAtoms</span> <span class="s">{</span>
935 922 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
936 923 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
937 924
938 925 <span class="c"># Is this atom in a molecule?</span>
939 926 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
940 927 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
941 928 <span class="s">}</span>
942 929
943 930 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span>
944 931 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
945 932 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
946 933 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">-&gt;IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfBonds</span>++<span class="sc">;</span> <span class="s">}</span>
947 934 <span class="s">}</span>
948 935 <span class="k">return</span> <span class="i">$NumOfBonds</span><span class="sc">;</span>
949 936 <span class="s">}</span>
950 937
951 938 <span class="c"># Get number of different bond types to non-hydrogen atoms...</span>
952 939 <span class="c">#</span>
953 <a name="GetNumOfBondTypesToHeavyAtoms-"></a> 940 <span class="k">sub </span><span class="m">GetNumOfBondTypesToHeavyAtoms</span> <span class="s">{</span>
954 941 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$CountAromaticBonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
955 942
956 943 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfBondTypesToNonHydrogenAtoms</span><span class="s">(</span><span class="i">$CountAromaticBonds</span><span class="s">)</span><span class="sc">;</span>
957 944 <span class="s">}</span>
958 945
959 946 <span class="c"># Get number of single, double, triple, and aromatic bonds from an atom to all other</span>
960 947 <span class="c"># non-hydrogen atoms. Value of CountAtomaticBonds parameter controls whether</span>
961 948 <span class="c"># number of aromatic bonds is returned; default is not to count aromatic bonds. During</span>
962 949 <span class="c"># counting of aromatic bonds, the bond marked aromatic is not included in the count</span>
963 950 <span class="c"># of other bond types.</span>
964 951 <span class="c">#</span>
965 <a name="GetNumOfBondTypesToNonHydrogenAtoms-"></a> 952 <span class="k">sub </span><span class="m">GetNumOfBondTypesToNonHydrogenAtoms</span> <span class="s">{</span>
966 953 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$CountAromaticBonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
967 954 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="cm">,</span> <span class="i">$None</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
968 955
969 956 <span class="i">$CountAromaticBonds</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$CountAromaticBonds</span><span class="s">)</span> ? <span class="i">$CountAromaticBonds</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
970 957
971 958 <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="s">)</span> = <span class="s">(</span><span class="q">&#39;0&#39;</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
972 959 <span class="i">$NumOfAromaticBonds</span> = <span class="i">$CountAromaticBonds</span> ? <span class="n">0</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
973 960
974 961 <span class="c"># Is this atom in a molecule?</span>
975 962 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
976 963 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span><span class="sc">;</span>
977 964 <span class="s">}</span>
978 965
979 966 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
980 967
981 968 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
982 969 <span class="j">BONDTYPE:</span> <span class="s">{</span>
983 970 <span class="k">if</span> <span class="s">(</span><span class="i">$CountAromaticBonds</span><span class="s">)</span> <span class="s">{</span>
984 971 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">-&gt;IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfAromaticBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span>
985 972 <span class="s">}</span>
986 973 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">-&gt;IsSingle</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfSingleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span>
987 974 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">-&gt;IsDouble</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfDoubleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span>
988 975 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">-&gt;IsTriple</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$NumOfTripleBonds</span>++<span class="sc">;</span> <span class="k">last</span> <span class="j">BONDTYPE</span><span class="sc">;</span> <span class="s">}</span>
989 976 <span class="i">$None</span> = <span class="n">1</span><span class="sc">;</span>
990 977 <span class="s">}</span>
991 978 <span class="s">}</span>
992 979 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span><span class="sc">;</span>
993 980 <span class="s">}</span>
994 981
995 982 <span class="c"># Get number of sigma and pi bonds to heavy atoms...</span>
996 983 <span class="c">#</span>
997 <a name="GetNumOfSigmaAndPiBondsToHeavyAtoms-"></a> 984 <span class="k">sub </span><span class="m">GetNumOfSigmaAndPiBondsToHeavyAtoms</span> <span class="s">{</span>
998 985 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
999 986
1000 987 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1001 988 <span class="s">}</span>
1002 989
1003 990 <span class="c"># Get number of sigma and pi bonds from an atom to all other non-hydrogen atoms.</span>
1004 991 <span class="c"># Sigma and pi bonds are counted using the following methodology: a single bond</span>
1005 992 <span class="c"># correspond to one sigma bond; a double bond contributes one to sigma bond count</span>
1006 993 <span class="c"># and one to pi bond count; a triple bond contributes one to sigma bond count and</span>
1007 994 <span class="c"># two to pi bond count.</span>
1008 995 <span class="c">#</span>
1009 <a name="GetNumOfSigmaAndPiBondsToNonHydrogenAtoms-"></a> 996 <span class="k">sub </span><span class="m">GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</span> <span class="s">{</span>
1010 997 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1011 998 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfSigmaBonds</span><span class="cm">,</span> <span class="i">$NumOfPiBonds</span><span class="s">)</span><span class="sc">;</span>
1012 999
1013 1000 <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfBondTypesToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1014 1001
1015 1002 <span class="i">$NumOfSigmaBonds</span> = <span class="i">$NumOfSingleBonds</span> + <span class="i">$NumOfDoubleBonds</span> + <span class="i">$NumOfTripleBonds</span><span class="sc">;</span>
1016 1003 <span class="i">$NumOfPiBonds</span> = <span class="i">$NumOfDoubleBonds</span> + <span class="n">2</span>*<span class="i">$NumOfTripleBonds</span><span class="sc">;</span>
1017 1004
1018 1005 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfSigmaBonds</span><span class="cm">,</span> <span class="i">$NumOfPiBonds</span><span class="s">)</span><span class="sc">;</span>
1019 1006 <span class="s">}</span>
1020 1007
1021 1008 <span class="c"># Get information related to atoms for all heavy atoms attached to an atom..</span>
1022 1009 <span class="c">#</span>
1023 <a name="GetHeavyAtomNeighborsAtomInformation-"></a>1010 <span class="k">sub </span><span class="m">GetHeavyAtomNeighborsAtomInformation</span> <span class="s">{</span>
1024 1011 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1025 1012
1026 1013 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNonHydrogenAtomNeighborsAtomInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1027 1014 <span class="s">}</span>
1028 1015
1029 1016 <span class="c"># Get information related to atoms for all non-hydrogen atoms attached to an atom..</span>
1030 1017 <span class="c">#</span>
1031 1018 <span class="c"># The following values are returned:</span>
1032 1019 <span class="c"># . Number of non-hydrogen atom neighbors</span>
1033 1020 <span class="c"># . A reference to an array containing atom objects correpsonding to non-hydrogen</span>
1034 1021 <span class="c"># atom neighbors</span>
1035 1022 <span class="c"># . Number of different types of non-hydrogen atom neighbors</span>
1036 1023 <span class="c"># . A reference to a hash containing atom symbol as key with value corresponding</span>
1037 1024 <span class="c"># to its count for non-hydrogen atom neighbors</span>
1038 1025 <span class="c">#</span>
1039 <a name="GetNonHydrogenAtomNeighborsAtomInformation-"></a>1026 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighborsAtomInformation</span> <span class="s">{</span>
1040 1027 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1041 1028
1042 1029 <span class="c"># Is this atom in a molecule?</span>
1043 1030 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1044 1031 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
1045 1032 <span class="s">}</span>
1046 1033 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomNeighbor</span><span class="cm">,</span> <span class="i">$NumOfAtomNeighbors</span><span class="cm">,</span> <span class="i">$NumOfAtomNeighborsType</span><span class="cm">,</span> <span class="i">@AtomNeighbors</span><span class="cm">,</span> <span class="i">%AtomNeighborsTypeMap</span><span class="s">)</span><span class="sc">;</span>
1047 1034
1048 1035 <span class="i">$NumOfAtomNeighbors</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">@AtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1049 1036 <span class="i">$NumOfAtomNeighborsType</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">%AtomNeighborsTypeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1050 1037
1051 1038 <span class="i">@AtomNeighbors</span> = <span class="i">$This</span><span class="i">-&gt;GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1052 1039 <span class="i">$NumOfAtomNeighbors</span> = <span class="k">scalar</span> <span class="i">@AtomNeighbors</span><span class="sc">;</span>
1053 1040
1054 1041 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">@AtomNeighbors</span><span class="s">)</span> <span class="s">{</span>
1055 1042 <span class="i">$AtomSymbol</span> = <span class="i">$AtomNeighbor</span>-&gt;{<span class="w">AtomSymbol</span>}<span class="sc">;</span>
1056 1043 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomNeighborsTypeMap</span>{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span>
1057 1044 <span class="i">$AtomNeighborsTypeMap</span>{<span class="i">$AtomSymbol</span>} += <span class="n">1</span><span class="sc">;</span>
1058 1045 <span class="s">}</span>
1059 1046 <span class="k">else</span> <span class="s">{</span>
1060 1047 <span class="i">$AtomNeighborsTypeMap</span>{<span class="i">$AtomSymbol</span>} = <span class="n">1</span><span class="sc">;</span>
1061 1048 <span class="i">$NumOfAtomNeighborsType</span>++<span class="sc">;</span>
1062 1049 <span class="s">}</span>
1063 1050 <span class="s">}</span>
1064 1051
1065 1052 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfAtomNeighbors</span><span class="cm">,</span> \<span class="i">@AtomNeighbors</span><span class="cm">,</span> <span class="i">$NumOfAtomNeighborsType</span><span class="cm">,</span> \<span class="i">%AtomNeighborsTypeMap</span><span class="s">)</span><span class="sc">;</span>
1066 1053 <span class="s">}</span>
1067 1054
1068 1055 <span class="c"># Get information related to bonds for all heavy atoms attached to an atom..</span>
1069 1056 <span class="c">#</span>
1070 <a name="GetHeavyAtomNeighborsBondformation-"></a>1057 <span class="k">sub </span><span class="m">GetHeavyAtomNeighborsBondformation</span> <span class="s">{</span>
1071 1058 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1072 1059
1073 1060 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNonHydrogenAtomNeighborsBondInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1074 1061 <span class="s">}</span>
1075 1062
1076 1063 <span class="c"># Get information related to bonds for all non-hydrogen atoms attached to an atom..</span>
1077 1064 <span class="c">#</span>
1078 1065 <span class="c"># The following values are returned:</span>
1079 1066 <span class="c"># . Number of bonds to non-hydrogen atom neighbors</span>
1080 1067 <span class="c"># . A reference to an array containing bond objects correpsonding to non-hydrogen</span>
1081 1068 <span class="c"># atom neighbors</span>
1082 1069 <span class="c"># . A reference to a hash containing bond type as key with value corresponding</span>
1083 1070 <span class="c"># to its count for non-hydrogen atom neighbors. Bond types are: Single, Double or Triple</span>
1084 1071 <span class="c"># . A reference to a hash containing atom symbol as key pointing to bond type as second</span>
1085 1072 <span class="c"># key with values correponding to count of bond types for atom symbol for non-hydrogen</span>
1086 1073 <span class="c"># atom neighbors</span>
1087 1074 <span class="c"># . A reference to a hash containing atom symbol as key pointing to bond type as second</span>
1088 1075 <span class="c"># key with values correponding to atom objects array involved in corresponding bond type for</span>
1089 1076 <span class="c"># atom symbol for non-hydrogen atom neighbors</span>
1090 1077 <span class="c">#</span>
1091 <a name="GetNonHydrogenAtomNeighborsBondInformation-"></a>1078 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighborsBondInformation</span> <span class="s">{</span>
1092 1079 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1093 1080
1094 1081 <span class="c"># Is this atom in a molecule?</span>
1095 1082 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1096 1083 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
1097 1084 <span class="s">}</span>
1098 1085 <span class="k">my</span><span class="s">(</span><span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondedAtomSymbol</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$None</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="cm">,</span> <span class="i">%BondTypeCountMap</span><span class="cm">,</span> <span class="i">%AtomsBondTypesCountMap</span><span class="cm">,</span> <span class="i">%AtomsBondTypeAtomsMap</span><span class="s">)</span><span class="sc">;</span>
1099 1086
1100 1087 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1101 1088 <span class="i">%BondTypeCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1102 1089 <span class="i">%AtomsBondTypesCountMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">%AtomsBondTypeAtomsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1103 1090
1104 1091 <span class="i">$BondTypeCountMap</span>{<span class="w">Single</span>} = <span class="n">0</span><span class="sc">;</span>
1105 1092 <span class="i">$BondTypeCountMap</span>{<span class="w">Double</span>} = <span class="n">0</span><span class="sc">;</span>
1106 1093 <span class="i">$BondTypeCountMap</span>{<span class="w">Triple</span>} = <span class="n">0</span><span class="sc">;</span>
1107 1094
1108 1095 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1109 1096 <span class="i">$NumOfBonds</span> = <span class="k">scalar</span> <span class="i">@Bonds</span><span class="sc">;</span>
1110 1097
1111 1098 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
1112 1099 <span class="i">$BondType</span> = <span class="i">$Bond</span><span class="i">-&gt;IsSingle</span><span class="s">(</span><span class="s">)</span> ? <span class="q">&quot;Single&quot;</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">-&gt;IsDouble</span><span class="s">(</span><span class="s">)</span> ? <span class="q">&quot;Double&quot;</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">-&gt;IsTriple</span><span class="s">(</span><span class="s">)</span> ? <span class="q">&quot;Triple&quot;</span> <span class="co">:</span> <span class="q">&quot;&quot;</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
1113 1100 <span class="k">if</span> <span class="s">(</span>!<span class="i">$BondType</span><span class="s">)</span> <span class="s">{</span>
1114 1101 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
1115 1102 <span class="s">}</span>
1116 1103
1117 1104 <span class="c"># Track bond types...</span>
1118 1105 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>}<span class="s">)</span> <span class="s">{</span>
1119 1106 <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>} += <span class="n">1</span><span class="sc">;</span>
1120 1107 <span class="s">}</span>
1121 1108 <span class="k">else</span> <span class="s">{</span>
1122 1109 <span class="i">$BondTypeCountMap</span>{<span class="i">$BondType</span>} = <span class="n">1</span><span class="sc">;</span>
1123 1110 <span class="s">}</span>
1124 1111
1125 1112 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">-&gt;GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
1126 1113 <span class="i">$BondedAtomSymbol</span> = <span class="i">$BondedAtom</span>-&gt;{<span class="w">AtomSymbol</span>}<span class="sc">;</span>
1127 1114
1128 1115 <span class="c"># Track bond types count for atom types involved in specific bond types...</span>
1129 1116 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}<span class="s">)</span> <span class="s">{</span>
1130 1117 <span class="i">%</span>{<span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1131 1118 <span class="s">}</span>
1132 1119 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}<span class="s">)</span> <span class="s">{</span>
1133 1120 <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>} += <span class="n">1</span><span class="sc">;</span>
1134 1121 <span class="s">}</span>
1135 1122 <span class="k">else</span> <span class="s">{</span>
1136 1123 <span class="i">$AtomsBondTypesCountMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>} = <span class="n">1</span><span class="sc">;</span>
1137 1124 <span class="s">}</span>
1138 1125
1139 1126 <span class="c"># Track atoms involved in specific bond types for specific atom types...</span>
1140 1127 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}<span class="s">)</span> <span class="s">{</span>
1141 1128 <span class="i">%</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1142 1129 <span class="s">}</span>
1143 1130 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}<span class="s">)</span> <span class="s">{</span>
1144 1131 <span class="i">@</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1145 1132 <span class="s">}</span>
1146 1133 <span class="k">push</span> <span class="i">@</span>{<span class="i">$AtomsBondTypeAtomsMap</span>{<span class="i">$BondedAtomSymbol</span>}{<span class="i">$BondType</span>}}<span class="cm">,</span> <span class="i">$BondedAtom</span><span class="sc">;</span>
1147 1134 <span class="s">}</span>
1148 1135
1149 1136 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfBonds</span><span class="cm">,</span> \<span class="i">@Bonds</span><span class="cm">,</span> \<span class="i">%BondTypeCountMap</span><span class="cm">,</span> \<span class="i">%AtomsBondTypesCountMap</span><span class="cm">,</span> \<span class="i">%AtomsBondTypeAtomsMap</span><span class="s">)</span><span class="sc">;</span>
1150 1137 <span class="s">}</span>
1151 1138
1152 1139 <span class="c"># Get number of bonds to hydrogen atoms...</span>
1153 <a name="GetNumOfBondsToHydrogenAtoms-"></a>1140 <span class="k">sub </span><span class="m">GetNumOfBondsToHydrogenAtoms</span> <span class="s">{</span>
1154 1141 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1155 1142 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span>
1156 1143
1157 1144 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1158 1145
1159 1146 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
1160 1147 <span class="s">}</span>
1161 1148
1162 1149 <span class="c"># Get sum of bond orders to all bonded atoms...</span>
1163 1150 <span class="c">#</span>
1164 <a name="GetSumOfBondOrders-"></a>1151 <span class="k">sub </span><span class="m">GetSumOfBondOrders</span> <span class="s">{</span>
1165 1152 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1166 1153
1167 1154 <span class="c"># Is this atom in a molecule?</span>
1168 1155 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1169 1156 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1170 1157 <span class="s">}</span>
1171 1158
1172 1159 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1173 1160 <span class="s">}</span>
1174 1161
1175 1162 <span class="c"># Get sum of bond orders to non-hydrogen atoms only...</span>
1176 1163 <span class="c">#</span>
1177 <a name="GetSumOfBondOrdersToHeavyAtoms-"></a>1164 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToHeavyAtoms</span> <span class="s">{</span>
1178 1165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1179 1166
1180 1167 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1181 1168 <span class="s">}</span>
1182 1169
1183 1170 <span class="c"># Get sum of bond orders to non-hydrogen atoms only...</span>
1184 1171 <span class="c">#</span>
1185 <a name="GetSumOfBondOrdersToNonHydrogenAtoms-"></a>1172 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToNonHydrogenAtoms</span> <span class="s">{</span>
1186 1173 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1187 1174
1188 1175 <span class="c"># Is this atom in a molecule?</span>
1189 1176 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1190 1177 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1191 1178 <span class="s">}</span>
1192 1179 <span class="k">my</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
1193 1180
1194 1181 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetSumOfBondOrders</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
1195 1182 <span class="s">}</span>
1196 1183
1197 1184 <span class="c"># Get sum of bond orders to hydrogen atoms only...</span>
1198 1185 <span class="c">#</span>
1199 <a name="GetSumOfBondOrdersToHydrogenAtoms-"></a>1186 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToHydrogenAtoms</span> <span class="s">{</span>
1200 1187 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1201 1188
1202 1189 <span class="c"># Is this atom in a molecule?</span>
1203 1190 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1204 1191 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1205 1192 <span class="s">}</span>
1206 1193 <span class="k">my</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
1207 1194
1208 1195 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetSumOfBondOrders</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
1209 1196 <span class="s">}</span>
1210 1197
1211 1198 <span class="c"># Get sum of bond orders to all bonded atoms, non-hydrogen or hydrogen bonded atoms...</span>
1212 1199 <span class="c">#</span>
1213 <a name="_GetSumOfBondOrders-"></a>1200 <span class="k">sub </span><span class="m">_GetSumOfBondOrders</span> <span class="s">{</span>
1214 1201 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1215 1202
1216 1203 <span class="c"># Check flags...</span>
1217 1204 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
1218 1205 <span class="i">$ToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
1219 1206 <span class="s">}</span>
1220 1207 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
1221 1208 <span class="i">$ToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
1222 1209 <span class="s">}</span>
1223 1210 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
1224 1211 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1225 1212
1226 1213 <span class="k">if</span> <span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
1227 1214 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1228 1215 <span class="s">}</span>
1229 1216 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
1230 1217 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1231 1218 <span class="s">}</span>
1232 1219 <span class="k">else</span> <span class="s">{</span>
1233 1220 <span class="c"># All bonds...</span>
1234 1221 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1235 1222 <span class="s">}</span>
1236 1223
1237 1224 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span>
1238 1225 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
1239 1226 <span class="i">$SumOfBondOrders</span> += <span class="i">$Bond</span><span class="i">-&gt;GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1240 1227 <span class="s">}</span>
1241 1228
1242 1229 <span class="k">if</span> <span class="s">(</span><span class="i">$SumOfBondOrders</span> =~ <span class="q">/\./</span><span class="s">)</span> <span class="s">{</span>
1243 1230 <span class="c">#</span>
1244 1231 <span class="c"># Change any fractional bond order to next largest integer...</span>
1245 1232 <span class="c">#</span>
1246 1233 <span class="c"># As long as aromatic bond orders in a ring are correctly using using 4n + 2 Huckel rule</span>
1247 1234 <span class="c"># (BondOrder: 1.5) or explicity set as Kekule bonds (alternate single/double),</span>
1248 1235 <span class="c"># SumOfBondOrders should add up to an integer.</span>
1249 1236 <span class="c">#</span>
1250 1237 <span class="i">$SumOfBondOrders</span> = <span class="i">ceil</span><span class="s">(</span><span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="sc">;</span>
1251 1238 <span class="s">}</span>
1252 1239
1253 1240 <span class="k">return</span> <span class="i">$SumOfBondOrders</span><span class="sc">;</span>
1254 1241 <span class="s">}</span>
1255 1242
1256 1243 <span class="c"># Get largest bond order to any bonded atoms...</span>
1257 1244 <span class="c">#</span>
1258 <a name="GetLargestBondOrder-"></a>1245 <span class="k">sub </span><span class="m">GetLargestBondOrder</span> <span class="s">{</span>
1259 1246 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1260 1247
1261 1248 <span class="c"># Is this atom in a molecule?</span>
1262 1249 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1263 1250 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1264 1251 <span class="s">}</span>
1265 1252
1266 1253 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetLargestBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1267 1254 <span class="s">}</span>
1268 1255
1269 1256 <span class="c"># Get largest bond order to bonded non-hydrogen atoms...</span>
1270 1257 <span class="c">#</span>
1271 <a name="GetLargestBondOrderToHeavyAtoms-"></a>1258 <span class="k">sub </span><span class="m">GetLargestBondOrderToHeavyAtoms</span> <span class="s">{</span>
1272 1259 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1273 1260
1274 1261 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetLargestBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1275 1262 <span class="s">}</span>
1276 1263
1277 1264 <span class="c"># Get largest bond order to bonded non-hydrogen atoms...</span>
1278 1265 <span class="c">#</span>
1279 <a name="GetLargestBondOrderToNonHydrogenAtoms-"></a>1266 <span class="k">sub </span><span class="m">GetLargestBondOrderToNonHydrogenAtoms</span> <span class="s">{</span>
1280 1267 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1281 1268
1282 1269 <span class="c"># Is this atom in a molecule?</span>
1283 1270 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1284 1271 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1285 1272 <span class="s">}</span>
1286 1273
1287 1274 <span class="k">my</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> = <span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span>
1288 1275
1289 1276 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetLargestBondOrder</span><span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span><span class="sc">;</span>
1290 1277 <span class="s">}</span>
1291 1278
1292 1279 <span class="c"># Get largest bond order to all bonded atoms, non-hydrogen or hydrogen bonded atoms...</span>
1293 1280 <span class="c">#</span>
1294 <a name="_GetLargestBondOrder-"></a>1281 <span class="k">sub </span><span class="m">_GetLargestBondOrder</span> <span class="s">{</span>
1295 1282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="cm">,</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1296 1283
1297 1284 <span class="c"># Check flags...</span>
1298 1285 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
1299 1286 <span class="i">$ToNonHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
1300 1287 <span class="s">}</span>
1301 1288 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
1302 1289 <span class="i">$ToHydrogenAtomsOnly</span> = <span class="n">0</span><span class="sc">;</span>
1303 1290 <span class="s">}</span>
1304 1291 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$LargestBondOrder</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
1305 1292 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1306 1293
1307 1294 <span class="k">if</span> <span class="s">(</span><span class="i">$ToNonHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
1308 1295 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1309 1296 <span class="s">}</span>
1310 1297 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span>
1311 1298 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1312 1299 <span class="s">}</span>
1313 1300 <span class="k">else</span> <span class="s">{</span>
1314 1301 <span class="c"># All bonds...</span>
1315 1302 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1316 1303 <span class="s">}</span>
1317 1304
1318 1305 <span class="i">$LargestBondOrder</span> = <span class="n">0</span><span class="sc">;</span>
1319 1306 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
1320 1307 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">-&gt;GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1321 1308 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> &gt; <span class="i">$LargestBondOrder</span><span class="s">)</span> <span class="s">{</span>
1322 1309 <span class="i">$LargestBondOrder</span> = <span class="i">$BondOrder</span><span class="sc">;</span>
1323 1310 <span class="s">}</span>
1324 1311 <span class="s">}</span>
1325 1312
1326 1313 <span class="k">return</span> <span class="i">$LargestBondOrder</span><span class="sc">;</span>
1327 1314 <span class="s">}</span>
1328 1315
1329 1316 <span class="c"># Get number of implicit hydrogen for atom...</span>
1330 1317 <span class="c">#</span>
1331 <a name="GetImplicitHydrogens-"></a>1318 <span class="k">sub </span><span class="m">GetImplicitHydrogens</span> <span class="s">{</span>
1332 1319 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1333 1320
1334 1321 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1335 1322 <span class="s">}</span>
1336 1323
1337 1324 <span class="c"># Get number of implicit hydrogen for atom...</span>
1338 1325 <span class="c">#</span>
1339 <a name="GetNumOfImplicitHydrogens-"></a>1326 <span class="k">sub </span><span class="m">GetNumOfImplicitHydrogens</span> <span class="s">{</span>
1340 1327 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1341 1328
1342 1329 <span class="c"># Is this atom in a molecule?</span>
1343 1330 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1344 1331 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1345 1332 <span class="s">}</span>
1346 1333
1347 1334 <span class="c"># Is ImplicitHydrogens property explicitly set?</span>
1348 1335 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;ImplicitHydrogens&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1349 1336 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;ImplicitHydrogens&#39;</span><span class="s">)</span><span class="sc">;</span>
1350 1337 <span class="s">}</span>
1351 1338
1352 1339 <span class="c"># Is it an element symbol?</span>
1353 1340 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
1354 1341 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1355 1342 <span class="s">}</span>
1356 1343
1357 1344 <span class="k">my</span><span class="s">(</span><span class="i">$ImplicitHydrogens</span><span class="cm">,</span> <span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="sc">;</span>
1358 1345
1359 1346 <span class="i">$ImplicitHydrogens</span> = <span class="n">0</span><span class="sc">;</span>
1360 1347 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">-&gt;GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1361 1348 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">-&gt;GetPotentialTotalCommonValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1362 1349
1363 1350 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="s">)</span> &amp;&amp; <span class="k">defined</span><span class="s">(</span><span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1364 1351 <span class="c"># Subtract sum of bond orders to non-hydrogen and hydrogen atom neighbors...</span>
1365 1352 <span class="i">$ImplicitHydrogens</span> = <span class="i">$PotentialTotalValence</span> - <span class="i">$SumOfBondOrders</span><span class="sc">;</span>
1366 1353 <span class="s">}</span>
1367 1354
1368 1355 <span class="k">return</span> <span class="i">$ImplicitHydrogens</span> &gt; <span class="n">0</span> ? <span class="i">$ImplicitHydrogens</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
1369 1356 <span class="s">}</span>
1370 1357
1371 1358 <span class="c"># Get number of bonds available to form additional bonds with heavy atoms, excluding</span>
1372 1359 <span class="c"># any implicit bonds to hydrogens set using ImplicitHydrogens property.</span>
1373 1360 <span class="c">#</span>
1374 1361 <span class="c"># It&#39;s different from number of implicit or missing hydrogens, both of which are equivalent.</span>
1375 1362 <span class="c">#</span>
1376 1363 <span class="c"># For example, in a SMILES string, [nH] ring atom corresponds to an aromatic nitrogen.</span>
1377 1364 <span class="c"># Although the hydrogen specified for n is treated internally as implicit hydrogen and shows</span>
1378 1365 <span class="c"># up in missing hydrogen count, it&#39;s not available to participate in double bonds to additional</span>
1379 1366 <span class="c"># heavy atoms.</span>
1380 1367 <span class="c">#</span>
1381 <a name="GetNumOfBondsAvailableForHeavyAtoms-"></a>1368 <span class="k">sub </span><span class="m">GetNumOfBondsAvailableForHeavyAtoms</span> <span class="s">{</span>
1382 1369 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1383 1370
1384 1371 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfBondsAvailableForNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1385 1372 <span class="s">}</span>
1386 1373
1387 1374 <span class="c"># It&#39;s another name for GetNumOfBondsAvailableForHeavyAtoms</span>
1388 1375 <span class="c">#</span>
1389 <a name="GetNumOfBondsAvailableForNonHydrogenAtoms-"></a>1376 <span class="k">sub </span><span class="m">GetNumOfBondsAvailableForNonHydrogenAtoms</span> <span class="s">{</span>
1390 1377 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1391 1378 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfAvailableBonds</span><span class="cm">,</span> <span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="sc">;</span>
1392 1379
1393 1380 <span class="i">$NumOfAvailableBonds</span> = <span class="n">0</span><span class="sc">;</span>
1394 1381
1395 1382 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">-&gt;GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1396 1383 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">-&gt;GetPotentialTotalCommonValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1397 1384
1398 1385 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="s">)</span> &amp;&amp; <span class="k">defined</span><span class="s">(</span><span class="i">$SumOfBondOrders</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1399 1386 <span class="c"># Subtract sum of bond orders to non-hydrogen and hydrogen atom neighbors...</span>
1400 1387 <span class="i">$NumOfAvailableBonds</span> = <span class="i">$PotentialTotalValence</span> - <span class="i">$SumOfBondOrders</span><span class="sc">;</span>
1401 1388 <span class="s">}</span>
1402 1389
1403 1390 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;ImplicitHydrogens&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1404 1391 <span class="i">$NumOfAvailableBonds</span> -= <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;ImplicitHydrogens&#39;</span><span class="s">)</span><span class="sc">;</span>
1405 1392 <span class="s">}</span>
1406 1393
1407 1394 <span class="k">return</span> <span class="i">$NumOfAvailableBonds</span> &gt; <span class="n">0</span> ? <span class="i">$NumOfAvailableBonds</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
1408 1395 <span class="s">}</span>
1409 1396
1410 1397 <span class="c"># Disable setting of explicit hydrogens property...</span>
1411 <a name="SetExplicitHydrogens-"></a>1398 <span class="k">sub </span><span class="m">SetExplicitHydrogens</span> <span class="s">{</span>
1412 1399 <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>
1413 1400
1414 1401 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetExplicitHydrogens: Setting of explicit hydrogens is not supported...&quot;</span><span class="sc">;</span>
1415 1402
1416 1403 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
1417 1404 <span class="s">}</span>
1418 1405
1419 1406 <span class="c"># Get number of explicit hydrogens for atom...</span>
1420 1407 <span class="c">#</span>
1421 <a name="GetExplicitHydrogens-"></a>1408 <span class="k">sub </span><span class="m">GetExplicitHydrogens</span> <span class="s">{</span>
1422 1409 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1423 1410
1424 1411 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1425 1412 <span class="s">}</span>
1426 1413
1427 1414 <span class="c"># Get number of explicit hydrogens for atom...</span>
1428 1415 <span class="c">#</span>
1429 <a name="GetNumOfExplicitHydrogens-"></a>1416 <span class="k">sub </span><span class="m">GetNumOfExplicitHydrogens</span> <span class="s">{</span>
1430 1417 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1431 1418 <span class="k">my</span><span class="s">(</span><span class="i">$HydrogenAtomNbrs</span><span class="s">)</span><span class="sc">;</span>
1432 1419
1433 1420 <span class="c"># Is this atom in a molecule?</span>
1434 1421 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1435 1422 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1436 1423 <span class="s">}</span>
1437 1424
1438 1425 <span class="i">$HydrogenAtomNbrs</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1439 1426
1440 1427 <span class="k">return</span> <span class="k">defined</span> <span class="i">$HydrogenAtomNbrs</span> ? <span class="i">$HydrogenAtomNbrs</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
1441 1428 <span class="s">}</span>
1442 1429
1443 1430 <span class="c"># Get num of missing hydrogens...</span>
1444 1431 <span class="c">#</span>
1445 <a name="GetMissingHydrogens-"></a>1432 <span class="k">sub </span><span class="m">GetMissingHydrogens</span> <span class="s">{</span>
1446 1433 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1447 1434
1448 1435 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1449 1436 <span class="s">}</span>
1450 1437
1451 1438 <span class="c"># Get num of missing hydrogens...</span>
1452 1439 <span class="c">#</span>
1453 <a name="GetNumOfMissingHydrogens-"></a>1440 <span class="k">sub </span><span class="m">GetNumOfMissingHydrogens</span> <span class="s">{</span>
1454 1441 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1455 1442
1456 1443 <span class="c"># Is this atom in a molecule?</span>
1457 1444 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1458 1445 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1459 1446 <span class="s">}</span>
1460 1447
1461 1448 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1462 1449 <span class="s">}</span>
1463 1450
1464 1451 <span class="c"># Get total number of hydrogens...</span>
1465 1452 <span class="c">#</span>
1466 <a name="GetHydrogens-"></a>1453 <span class="k">sub </span><span class="m">GetHydrogens</span> <span class="s">{</span>
1467 1454 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1468 1455
1469 1456 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1470 1457 <span class="s">}</span>
1471 1458
1472 1459 <span class="c"># Get total number of hydrogens...</span>
1473 1460 <span class="c">#</span>
1474 <a name="GetNumOfHydrogens-"></a>1461 <span class="k">sub </span><span class="m">GetNumOfHydrogens</span> <span class="s">{</span>
1475 1462 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1476 1463
1477 1464 <span class="c"># Is this atom in a molecule?</span>
1478 1465 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1479 1466 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1480 1467 <span class="s">}</span>
1481 1468
1482 1469 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">-&gt;GetNumOfExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1483 1470 <span class="s">}</span>
1484 1471
1485 1472 <span class="c"># Valence corresponds to the number of electrons used by an atom in bonding:</span>
1486 1473 <span class="c">#</span>
1487 1474 <span class="c"># Valence = ValenceElectrons - ValenceFreeElectrons = BondingElectrons</span>
1488 1475 <span class="c">#</span>
1489 1476 <span class="c"># Single, double, triple bonds with bond orders of 1, 2 and 3 correspond to contribution of</span>
1490 1477 <span class="c"># 1, 2, and 3 bonding electrons. So Valence can be computed using:</span>
1491 1478 <span class="c">#</span>
1492 1479 <span class="c"># Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge</span>
1493 1480 <span class="c">#</span>
1494 1481 <span class="c"># where positive and negative values of FormalCharge increase and decrease the number</span>
1495 1482 <span class="c"># of bonding electrons respectively.</span>
1496 1483 <span class="c">#</span>
1497 1484 <span class="c"># The current release of MayaChemTools supports the following three valence models, which</span>
1498 1485 <span class="c"># are used during calculation of implicit hydrogens: MDLValenceModel, DaylightValenceModel,</span>
1499 1486 <span class="c"># InternalValenceModel or MayaChemToolsValenceModel.</span>
1500 1487 <span class="c">#</span>
1501 1488 <span class="c"># Notes:</span>
1502 1489 <span class="c"># . This doesn&#39;t always corresponds to explicit valence.</span>
1503 1490 <span class="c"># . Missing hydrogens are included in the valence.</span>
1504 1491 <span class="c"># . For neutral molecules, valence and sum of bond order are equal.</span>
1505 1492 <span class="c"># . For molecules containing only single bonds, SumOfBondOrders and NumOfBonds are equal.</span>
1506 1493 <span class="c"># . Free radical electrons lead to the decrease in valence. For atoms with explicit assignment</span>
1507 1494 <span class="c"># of SpinMultiplicity property values corresponding to Singlet (two unparied electrons</span>
1508 1495 <span class="c"># corresponding to one spin state), Doublet (free radical; an unpaired electron corresponding</span>
1509 1496 <span class="c"># to two spin states), and Triplet (two unparied electrons corresponding to three spin states;</span>
1510 1497 <span class="c"># divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:</span>
1511 1498 <span class="c">#</span>
1512 1499 <span class="c"># SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1 (one valence electron not available for bonding)</span>
1513 1500 <span class="c"># SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2 (two valence electrons not available for bonding)</span>
1514 1501 <span class="c">#</span>
1515 <a name="GetValence-"></a>1502 <span class="k">sub </span><span class="m">GetValence</span> <span class="s">{</span>
1516 1503 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1517 1504
1518 1505 <span class="c"># Is this atom in a molecule?</span>
1519 1506 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1520 1507 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1521 1508 <span class="s">}</span>
1522 1509
1523 1510 <span class="c"># Is Valence property explicitly set?</span>
1524 1511 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Valence&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1525 1512 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Valence&#39;</span><span class="s">)</span><span class="sc">;</span>
1526 1513 <span class="s">}</span>
1527 1514 <span class="k">my</span><span class="s">(</span><span class="i">$Valence</span><span class="s">)</span><span class="sc">;</span>
1528 1515
1529 1516 <span class="i">$Valence</span> = <span class="i">$This</span><span class="i">-&gt;GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">-&gt;GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">-&gt;GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1530 1517
1531 1518 <span class="k">return</span> <span class="i">$Valence</span> &gt; <span class="n">0</span> ? <span class="i">$Valence</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
1532 1519 <span class="s">}</span>
1533 1520
1534 1521 <span class="c"># Get free non-bodning valence electrons left on atom after taking into account</span>
1535 1522 <span class="c"># sum of bond orders, missing hydrogens and formal charged on the atom. Free</span>
1536 1523 <span class="c"># radical electrons are included in the valence free electrons count by default.</span>
1537 1524 <span class="c">#</span>
1538 1525 <span class="c"># Valence corresponds to number of electrons used by atom in bonding:</span>
1539 1526 <span class="c">#</span>
1540 1527 <span class="c"># Valence = ValenceElectrons - ValenceFreeElectrons</span>
1541 1528 <span class="c">#</span>
1542 1529 <span class="c"># Additionally, valence can also be calculated by:</span>
1543 1530 <span class="c">#</span>
1544 1531 <span class="c"># Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge</span>
1545 1532 <span class="c">#</span>
1546 1533 <span class="c"># Valence and SumOfBondOrders are equal for neutral molecules.</span>
1547 1534 <span class="c">#</span>
1548 1535 <span class="c"># From two formulas for Valence described above, non-bonding free electrons</span>
1549 1536 <span class="c"># left can be computed by:</span>
1550 1537 <span class="c">#</span>
1551 1538 <span class="c"># ValenceFreeElectrons = ValenceElectrons - Valence</span>
1552 1539 <span class="c"># = ValenceElectrons - SumOfBondOrders -</span>
1553 1540 <span class="c"># NumOfMissingHydrogens - FormalCharge</span>
1554 1541 <span class="c">#</span>
1555 1542 <span class="c"># . Notes:</span>
1556 1543 <span class="c"># . Missing hydrogens are excluded from the valence free electrons.</span>
1557 1544 <span class="c"># . Any free radical electrons are considered part of the valence free electrons</span>
1558 1545 <span class="c"># by default.</span>
1559 1546 <span class="c">#</span>
1560 1547 <span class="c"># Examples:</span>
1561 1548 <span class="c">#</span>
1562 1549 <span class="c"># o NH3: ValenceFreeElectrons = 5 - 3 = 5 - 3 - 0 - 0 = 2</span>
1563 1550 <span class="c"># o NH2: ValenceFreeElectrons = 5 - 3 = 5 - 2 - 1 - 0 = 2</span>
1564 1551 <span class="c"># o NH4+; ValenceFreeElectrons = 5 - 5 = 5 - 4 - 0 - 1 = 0</span>
1565 1552 <span class="c"># o NH3+; ValenceFreeElectrons = 5 - 5 = 5 - 3 - 1 - 1 = 0</span>
1566 1553 <span class="c"># o C(=O)O- : ValenceFreeElectrons on O- = 6 - 0 = 6 - 1 - 0 - (-1) = 6</span>
1567 1554 <span class="c"># o C(=O)O- : ValenceFreeElectrons on =O = 6 - 2 = 6 - 2 - 0 - 0 = 4</span>
1568 1555 <span class="c">#</span>
1569 1556 <span class="c">#</span>
1570 <a name="GetValenceFreeElectrons-"></a>1557 <span class="k">sub </span><span class="m">GetValenceFreeElectrons</span> <span class="s">{</span>
1571 1558 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1572 1559
1573 1560 <span class="c"># Is this atom in a molecule?</span>
1574 1561 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1575 1562 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1576 1563 <span class="s">}</span>
1577 1564
1578 1565 <span class="c"># Is ValenceFreeElectrons property explicitly set?</span>
1579 1566 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;ValenceFreeElectrons&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1580 1567 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;ValenceFreeElectrons&#39;</span><span class="s">)</span><span class="sc">;</span>
1581 1568 <span class="s">}</span>
1582 1569
1583 1570 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
1584 1571 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1585 1572 <span class="s">}</span>
1586 1573
1587 1574 <span class="k">my</span><span class="s">(</span><span class="i">$ValenceFreeElectrons</span><span class="s">)</span><span class="sc">;</span>
1588 1575
1589 1576 <span class="i">$ValenceFreeElectrons</span> = <span class="i">$This</span><span class="i">-&gt;GetValenceElectrons</span><span class="s">(</span><span class="s">)</span> - <span class="i">$This</span><span class="i">-&gt;GetValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1590 1577 <span class="k">if</span> <span class="s">(</span><span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> <span class="s">{</span>
1591 1578 <span class="i">$ValenceFreeElectrons</span> -= <span class="i">$This</span><span class="i">-&gt;GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1592 1579 <span class="s">}</span>
1593 1580
1594 1581 <span class="k">return</span> <span class="i">$ValenceFreeElectrons</span> &gt; <span class="n">0</span> ? <span class="i">$ValenceFreeElectrons</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
1595 1582 <span class="s">}</span>
1596 1583
1597 1584 <span class="c"># Get potential total common valence for calculating the number of implicit hydrogens</span>
1598 1585 <span class="c"># using the specified common valence model or default internal model for a molecule...</span>
1599 1586 <span class="c">#</span>
1600 <a name="GetPotentialTotalCommonValence-"></a>1587 <span class="k">sub </span><span class="m">GetPotentialTotalCommonValence</span> <span class="s">{</span>
1601 1588 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1602 1589
1603 1590 <span class="c"># Is this atom in a molecule?</span>
1604 1591 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1605 1592 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1606 1593 <span class="s">}</span>
1607 1594 <span class="k">my</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$ValenceModel</span><span class="s">)</span><span class="sc">;</span>
1608 1595
1609 1596 <span class="i">$PotentialTotalValence</span> = <span class="n">0</span><span class="sc">;</span>
1610 1597 <span class="i">$ValenceModel</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="i">-&gt;GetValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1611 1598
1612 1599 <span class="j">VALENCEMODEL:</span> <span class="s">{</span>
1613 1600 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> =~ <span class="q">/^MDLValenceModel$/i</span><span class="s">)</span> <span class="s">{</span>
1614 1601 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">-&gt;_GetPotentialTotalCommonValenceUsingMDLValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1615 1602 <span class="k">last</span> <span class="j">VALENCEMODEL</span><span class="sc">;</span>
1616 1603 <span class="s">}</span>
1617 1604 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> =~ <span class="q">/^DaylightValenceModel$/i</span><span class="s">)</span> <span class="s">{</span>
1618 1605 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">-&gt;_GetPotentialTotalCommonValenceUsingDaylightValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1619 1606 <span class="k">last</span> <span class="j">VALENCEMODEL</span><span class="sc">;</span>
1620 1607 <span class="s">}</span>
1621 1608 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> !~ <span class="q">/^(InternalValenceModel|MayaChemToolsValenceModel)$/i</span><span class="s">)</span> <span class="s">{</span>
1622 1609 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GetPotentialTotalCommonValence: The current release of MayaChemTools doesn&#39;t support the specified valence model $ValenceModel. Supported valence models: MDLValenceModel, DaylightValenceModel, InternalValenceModel. Using internal valence model...&quot;</span><span class="sc">;</span>
1623 1610 <span class="s">}</span>
1624 1611 <span class="c"># Use internal valence model as the default valence model...</span>
1625 1612 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">-&gt;_GetPotentialTotalCommonValenceUsingInternalValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1626 1613 <span class="s">}</span>
1627 1614
1628 1615 <span class="k">return</span> <span class="i">$PotentialTotalValence</span><span class="sc">;</span>
1629 1616 <span class="s">}</span>
1630 1617
1631 1618 <span class="c"># Get potential total common valence using data for MDL valence model available in file,</span>
1632 1619 <span class="c"># lib/data/MDLValenceModelData.csv, distributed with the package...</span>
1633 1620 <span class="c">#</span>
1634 <a name="_GetPotentialTotalCommonValenceUsingMDLValenceModel-"></a>1621 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingMDLValenceModel</span> <span class="s">{</span>
1635 1622 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1636 1623
1637 1624 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetPotentialTotalCommonValenceUsingValenceModelData</span><span class="s">(</span>\<span class="i">%MDLValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span>
1638 1625
1639 1626 <span class="s">}</span>
1640 1627
1641 1628 <span class="c"># Get potential total common valence using data for Daylight valence model available in file,</span>
1642 1629 <span class="c"># lib/data/DaylightValenceModelData.csv, distributed with the release...</span>
1643 1630 <span class="c">#</span>
1644 <a name="_GetPotentialTotalCommonValenceUsingDaylightValenceModel-"></a>1631 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingDaylightValenceModel</span> <span class="s">{</span>
1645 1632 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1646 1633
1647 1634 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetPotentialTotalCommonValenceUsingValenceModelData</span><span class="s">(</span>\<span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span>
1648 1635 <span class="s">}</span>
1649 1636
1650 1637 <span class="c"># Get potential total common valence using data for a specific valence model...</span>
1651 1638 <span class="c">#</span>
1652 <a name="_GetPotentialTotalCommonValenceUsingValenceModelData-"></a>1639 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingValenceModelData</span> <span class="s">{</span>
1653 1640 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ValenceModelDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1654 1641 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span>
1655 1642
1656 1643 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
1657 1644 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
1658 1645 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1659 1646 <span class="s">}</span>
1660 1647
1661 1648 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">-&gt;GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1662 1649
1663 1650 <span class="c"># Is any valence model data available for atomic number and formal charge?</span>
1664 1651 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ValenceModelDataRef</span>-&gt;{<span class="i">$AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
1665 1652 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1666 1653 <span class="s">}</span>
1667 1654 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ValenceModelDataRef</span>-&gt;{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}<span class="s">)</span> <span class="s">{</span>
1668 1655 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1669 1656 <span class="s">}</span>
1670 1657
1671 1658 <span class="k">my</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="cm">,</span> <span class="i">$CurrentEffectiveValence</span><span class="cm">,</span> <span class="i">$AvailableCommonValence</span><span class="s">)</span><span class="sc">;</span>
1672 1659
1673 1660 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">-&gt;GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1674 1661 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span> <span class="s">{</span>
1675 1662 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span>
1676 1663 <span class="s">}</span>
1677 1664 <span class="i">$CurrentEffectiveValence</span> = <span class="i">$SumOfBondOrders</span> + <span class="i">$This</span><span class="i">-&gt;GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1678 1665
1679 1666 <span class="i">$PotentialTotalValence</span> = <span class="n">0</span><span class="sc">;</span>
1680 1667 <span class="j">VALENCE:</span> <span class="k">for</span> <span class="i">$AvailableCommonValence</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ValenceModelDataRef</span>-&gt;{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">CommonValences</span>}}<span class="s">)</span> <span class="s">{</span>
1681 1668 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentEffectiveValence</span> &lt;= <span class="i">$AvailableCommonValence</span><span class="s">)</span> <span class="s">{</span>
1682 1669 <span class="i">$PotentialTotalValence</span> = <span class="i">$AvailableCommonValence</span><span class="sc">;</span>
1683 1670 <span class="k">last</span> <span class="j">VALENCE</span><span class="sc">;</span>
1684 1671 <span class="s">}</span>
1685 1672 <span class="s">}</span>
1686 1673
1687 1674 <span class="k">return</span> <span class="i">$PotentialTotalValence</span><span class="sc">;</span>
1688 1675 <span class="s">}</span>
1689 1676
1690 1677 <span class="c">#</span>
1691 1678 <span class="c"># For elements with one one common valence, potential total common valence used</span>
1692 1679 <span class="c"># during the calculation for number of implicit hydrogens during InternalValenceMode</span>
1693 1680 <span class="c"># corresponds to:</span>
1694 1681 <span class="c">#</span>
1695 1682 <span class="c"># CommonValence + FormalCharge - FreeRadicalElectrons</span>
1696 1683 <span class="c">#</span>
1697 1684 <span class="c"># For elements with multiple common valences, each common valence is used to</span>
1698 1685 <span class="c"># calculate total potential common valence as shown above, and the first total potential</span>
1699 1686 <span class="c"># common valence gerater than the sum of bond orderes is selected as the final total</span>
1700 1687 <span class="c"># common valence.</span>
1701 1688 <span class="c">#</span>
1702 1689 <span class="c"># Group numbers &gt; 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He)</span>
1703 1690 <span class="c">#</span>
1704 1691 <span class="c"># Formal charge sign is not adjusted. Positive and negative values result in the</span>
1705 1692 <span class="c"># increase and decrease of valence.</span>
1706 1693 <span class="c">#</span>
1707 1694 <span class="c"># Group 14 containing C, Si, Ge, Sn, Pb...</span>
1708 1695 <span class="c">#</span>
1709 1696 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
1710 1697 <span class="c"># values result in the decrease of valence.</span>
1711 1698 <span class="c">#</span>
1712 1699 <span class="c"># Group 13 containing B, Al, Ga, In, Tl...</span>
1713 1700 <span class="c">#</span>
1714 1701 <span class="c"># Formal charge sign is always reversed. Positive and negative values result in the</span>
1715 1702 <span class="c"># decrease and increase of valence.</span>
1716 1703 <span class="c">#</span>
1717 1704 <span class="c"># Groups 1 (H) through 12 (Zn)...</span>
1718 1705 <span class="c">#</span>
1719 1706 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
1720 1707 <span class="c"># values result in the decrease of valence.</span>
1721 1708 <span class="c">#</span>
1722 1709 <span class="c"># Lanthanides and actinides...</span>
1723 1710 <span class="c">#</span>
1724 1711 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
1725 1712 <span class="c"># values result in the decrease of valence.</span>
1726 1713 <span class="c">#</span>
1727 1714 <span class="c"># Notes:</span>
1728 1715 <span class="c"># . CommonValence and HighestCommonValence available from PeriodicTable module</span>
1729 1716 <span class="c"># are equivalent to most common and highest sum of bond orders for an element. For</span>
1730 1717 <span class="c"># neutral atoms involved only in single bonds, it corresponds to highest number of</span>
1731 1718 <span class="c"># allowed bonds for the atom.</span>
1732 1719 <span class="c"># . FormalCharge sign is reversed for electropositive elements with positive formal charge</span>
1733 1720 <span class="c"># during common valence calculations. Electropositive elements, metals and transition elements,</span>
1734 1721 <span class="c"># have usually plus formal charge and it leads to decrease in common valence; the negative</span>
1735 1722 <span class="c"># formal charge should result in the decrease of common valence.</span>
1736 1723 <span class="c"># . For carbon, both plus/minus formal charge cause decrease in common valence</span>
1737 1724 <span class="c"># . For elements on the right of carbon in periodic table, electronegative elements, plus formal</span>
1738 1725 <span class="c"># charge causes common valence to increase and minus formal charge cause it to decrease.</span>
1739 1726 <span class="c">#</span>
1740 <a name="_GetPotentialTotalCommonValenceUsingInternalValenceModel-"></a>1727 <span class="k">sub </span><span class="m">_GetPotentialTotalCommonValenceUsingInternalValenceModel</span> <span class="s">{</span>
1741 1728 <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>
1742 1729 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="s">)</span><span class="sc">;</span>
1743 1730
1744 1731 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
1745 1732 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
1746 1733 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1747 1734 <span class="s">}</span>
1748 1735
1749 1736 <span class="i">$CommonValences</span> = <span class="i">PeriodicTable::GetElementCommonValences</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
1750 1737 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CommonValences</span><span class="s">)</span> <span class="s">{</span>
1751 1738 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1752 1739 <span class="s">}</span>
1753 1740
1754 1741 <span class="k">my</span><span class="s">(</span><span class="i">$PotentialTotalValence</span><span class="cm">,</span> <span class="i">$AdjustedFormalCharge</span><span class="cm">,</span> <span class="i">$FreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$SumOfBondOrders</span><span class="cm">,</span> <span class="i">$AvailableCommonValence</span><span class="cm">,</span> <span class="i">@AvailableCommonValences</span><span class="s">)</span><span class="sc">;</span>
1755 1742
1756 1743 <span class="i">$AdjustedFormalCharge</span> = <span class="i">$This</span><span class="i">-&gt;_GetFormalChargeAdjustedForInternalValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1757 1744 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">-&gt;GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1758 1745
1759 1746 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">-&gt;GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1760 1747 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SumOfBondOrders</span><span class="s">)</span> <span class="s">{</span>
1761 1748 <span class="i">$SumOfBondOrders</span> = <span class="n">0</span><span class="sc">;</span>
1762 1749 <span class="s">}</span>
1763 1750
1764 1751 <span class="i">@AvailableCommonValences</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="sc">;</span>
1765 1752
1766 1753 <span class="k">if</span> <span class="s">(</span><span class="i">@AvailableCommonValences</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
1767 1754 <span class="c"># Calculate potential total valence using the only available common valence...</span>
1768 1755 <span class="i">$PotentialTotalValence</span> = <span class="i">$AvailableCommonValences</span>[<span class="n">0</span>] + <span class="i">$AdjustedFormalCharge</span> - <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span>
1769 1756 <span class="s">}</span>
1770 1757 <span class="k">else</span> <span class="s">{</span>
1771 1758 <span class="c"># Calculate potential total valence using common valence from a list of available valences</span>
1772 1759 <span class="c"># that makes it higher than sum of bond orders or using the highest common valence...</span>
1773 1760 <span class="j">VALENCE:</span> <span class="k">for</span> <span class="i">$AvailableCommonValence</span> <span class="s">(</span><span class="i">@AvailableCommonValences</span><span class="s">)</span> <span class="s">{</span>
1774 1761 <span class="i">$PotentialTotalValence</span> = <span class="i">$AvailableCommonValence</span> + <span class="i">$AdjustedFormalCharge</span> - <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span>
1775 1762
1776 1763 <span class="k">if</span> <span class="s">(</span><span class="i">$PotentialTotalValence</span> &lt; <span class="n">0</span> || <span class="i">$PotentialTotalValence</span> &gt;= <span class="i">$SumOfBondOrders</span><span class="s">)</span> <span class="s">{</span>
1777 1764 <span class="k">last</span> <span class="j">VALENCE</span><span class="sc">;</span>
1778 1765 <span class="s">}</span>
1779 1766 <span class="s">}</span>
1780 1767 <span class="s">}</span>
1781 1768
1782 1769 <span class="k">return</span> <span class="i">$PotentialTotalValence</span> &gt; <span class="n">0</span> ? <span class="i">$PotentialTotalValence</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
1783 1770 <span class="s">}</span>
1784 1771
1785 1772 <span class="c"># Adjust sign of the formal charge for potential total common valence calculation</span>
1786 1773 <span class="c"># used during internal valence model to figure out number of implicit hydrogens.</span>
1787 1774 <span class="c">#</span>
1788 <a name="_GetFormalChargeAdjustedForInternalValenceModel-"></a>1775 <span class="k">sub </span><span class="m">_GetFormalChargeAdjustedForInternalValenceModel</span> <span class="s">{</span>
1789 1776 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1790 1777 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$GroupNumber</span><span class="cm">,</span> <span class="i">$SwitchSign</span><span class="s">)</span><span class="sc">;</span>
1791 1778
1792 1779 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">-&gt;GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1793 1780 <span class="k">if</span> <span class="s">(</span><span class="i">$FormalCharge</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
1794 1781 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1795 1782 <span class="s">}</span>
1796 1783
1797 1784 <span class="i">$GroupNumber</span> = <span class="i">$This</span><span class="i">-&gt;GetGroupNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1798 1785 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$GroupNumber</span><span class="s">)</span> <span class="s">{</span>
1799 1786 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span>
1800 1787 <span class="s">}</span>
1801 1788
1802 1789 <span class="c"># Group numbers &gt; 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He)</span>
1803 1790 <span class="c">#</span>
1804 1791 <span class="c"># Formal charge sign is not adjusted. Positive and negative values result in the</span>
1805 1792 <span class="c"># increase and decrease of valence.</span>
1806 1793 <span class="c">#</span>
1807 1794 <span class="c"># Group 14 containing C, Si, Ge, Sn, Pb...</span>
1808 1795 <span class="c">#</span>
1809 1796 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
1810 1797 <span class="c"># values result in the decrease of valence.</span>
1811 1798 <span class="c">#</span>
1812 1799 <span class="c"># Group 13 containing B, Al, Ga, In, Tl...</span>
1813 1800 <span class="c">#</span>
1814 1801 <span class="c"># Formal charge sign is always reversed. Positive and negative values result in the</span>
1815 1802 <span class="c"># decrease and increase of valence.</span>
1816 1803 <span class="c">#</span>
1817 1804 <span class="c"># Groups 1 (H) through 12 (Zn)...</span>
1818 1805 <span class="c">#</span>
1819 1806 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
1820 1807 <span class="c"># values result in the decrease of valence.</span>
1821 1808 <span class="c">#</span>
1822 1809 <span class="c"># Lanthanides and actinides...</span>
1823 1810 <span class="c">#</span>
1824 1811 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span>
1825 1812 <span class="c"># values result in the decrease of valence.</span>
1826 1813 <span class="c">#</span>
1827 1814
1828 1815 <span class="i">$SwitchSign</span> = <span class="n">0</span><span class="sc">;</span>
1829 1816 <span class="k">if</span> <span class="s">(</span><span class="k">length</span> <span class="i">$GroupNumber</span><span class="s">)</span> <span class="s">{</span>
1830 1817 <span class="j">GROUPNUMBER:</span> <span class="s">{</span>
1831 1818 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> &gt; <span class="n">14</span><span class="s">)</span> <span class="s">{</span>
1832 1819 <span class="c"># Groups on the right side of C group in the periodic table...</span>
1833 1820 <span class="i">$SwitchSign</span> = <span class="n">0</span><span class="sc">;</span>
1834 1821 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span>
1835 1822 <span class="s">}</span>
1836 1823 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> == <span class="n">14</span><span class="s">)</span> <span class="s">{</span>
1837 1824 <span class="c"># Group containing C, Si, Ge, Sn, Pb...</span>
1838 1825 <span class="i">$SwitchSign</span> = <span class="s">(</span><span class="i">$FormalCharge</span> &gt; <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
1839 1826 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span>
1840 1827 <span class="s">}</span>
1841 1828 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> == <span class="n">13</span><span class="s">)</span> <span class="s">{</span>
1842 1829 <span class="c"># Group containing B, Al, Ga, In, Tl...</span>
1843 1830 <span class="i">$SwitchSign</span> = <span class="n">1</span><span class="sc">;</span>
1844 1831 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span>
1845 1832 <span class="s">}</span>
1846 1833 <span class="c"># Groups 1 (H) through 12 (Zn)...</span>
1847 1834 <span class="k">if</span> <span class="s">(</span><span class="i">$GroupNumber</span> &gt;=<span class="n">1</span> &amp;&amp; <span class="i">$GroupNumber</span> &lt;= <span class="n">12</span><span class="s">)</span> <span class="s">{</span>
1848 1835 <span class="c"># Groups 1 (H) through 12 (Zn)...</span>
1849 1836 <span class="i">$SwitchSign</span> = <span class="s">(</span><span class="i">$FormalCharge</span> &gt; <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
1850 1837 <span class="k">last</span> <span class="j">GROUPNUMBER</span><span class="sc">;</span>
1851 1838 <span class="s">}</span>
1852 1839 <span class="s">}</span>
1853 1840 <span class="s">}</span>
1854 1841 <span class="k">else</span> <span class="s">{</span>
1855 1842 <span class="c"># Lanthanides and actinides...</span>
1856 1843 <span class="i">$SwitchSign</span> = <span class="s">(</span><span class="i">$FormalCharge</span> &gt; <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
1857 1844 <span class="s">}</span>
1858 1845
1859 1846 <span class="k">if</span> <span class="s">(</span><span class="i">$SwitchSign</span><span class="s">)</span> <span class="s">{</span>
1860 1847 <span class="i">$FormalCharge</span> *= <span class="n">-1.0</span><span class="sc">;</span>
1861 1848 <span class="s">}</span>
1862 1849
1863 1850 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span>
1864 1851 <span class="s">}</span>
1865 1852
1866 1853 <span class="c"># Get lowest common valence...</span>
1867 <a name="GetLowestCommonValence-"></a>1854 <span class="k">sub </span><span class="m">GetLowestCommonValence</span> <span class="s">{</span>
1868 1855 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1869 1856
1870 1857 <span class="c"># Is LowestCommonValence property explicitly set?</span>
1871 1858 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;LowestCommonValence&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1872 1859 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;LowestCommonValence&#39;</span><span class="s">)</span><span class="sc">;</span>
1873 1860 <span class="s">}</span>
1874 1861 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$LowestCommonValence</span><span class="s">)</span><span class="sc">;</span>
1875 1862
1876 1863 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
1877 1864 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
1878 1865 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1879 1866 <span class="s">}</span>
1880 1867 <span class="c"># Any need to differentiate between internal and other valence models...</span>
1881 1868
1882 1869 <span class="c"># LowestCommonValence is not set for all elements...</span>
1883 1870 <span class="i">$LowestCommonValence</span> = <span class="i">PeriodicTable::GetElementLowestCommonValence</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
1884 1871 <span class="k">if</span> <span class="s">(</span>!<span class="i">$LowestCommonValence</span><span class="s">)</span> <span class="s">{</span>
1885 1872 <span class="i">$LowestCommonValence</span> = <span class="k">undef</span><span class="sc">;</span>
1886 1873 <span class="s">}</span>
1887 1874
1888 1875 <span class="k">return</span> <span class="i">$LowestCommonValence</span><span class="sc">;</span>
1889 1876 <span class="s">}</span>
1890 1877
1891 1878 <span class="c"># Get highest common valence...</span>
1892 <a name="GetHighestCommonValence-"></a>1879 <span class="k">sub </span><span class="m">GetHighestCommonValence</span> <span class="s">{</span>
1893 1880 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1894 1881
1895 1882 <span class="c"># Is HighestCommonValence property explicitly set?</span>
1896 1883 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;HighestCommonValence&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1897 1884 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;HighestCommonValence&#39;</span><span class="s">)</span><span class="sc">;</span>
1898 1885 <span class="s">}</span>
1899 1886 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$HighestCommonValence</span><span class="s">)</span><span class="sc">;</span>
1900 1887
1901 1888 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
1902 1889 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
1903 1890 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1904 1891 <span class="s">}</span>
1905 1892
1906 1893 <span class="c"># Any need to differentiate between internal and other valence models...</span>
1907 1894
1908 1895 <span class="c"># HighestCommonValence is not set for all elements...</span>
1909 1896 <span class="i">$HighestCommonValence</span> = <span class="i">PeriodicTable::GetElementHighestCommonValence</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
1910 1897 <span class="k">if</span> <span class="s">(</span>!<span class="i">$HighestCommonValence</span><span class="s">)</span> <span class="s">{</span>
1911 1898 <span class="i">$HighestCommonValence</span> = <span class="k">undef</span><span class="sc">;</span>
1912 1899 <span class="s">}</span>
1913 1900
1914 1901 <span class="k">return</span> <span class="i">$HighestCommonValence</span><span class="sc">;</span>
1915 1902 <span class="s">}</span>
1916 1903
1917 1904 <span class="c"># Get valence electrons...</span>
1918 <a name="GetValenceElectrons-"></a>1905 <span class="k">sub </span><span class="m">GetValenceElectrons</span> <span class="s">{</span>
1919 1906 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1920 1907
1921 1908 <span class="c"># Is ValenceElectrons property explicitly set?</span>
1922 1909 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;ValenceElectrons&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1923 1910 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;ValenceElectrons&#39;</span><span class="s">)</span><span class="sc">;</span>
1924 1911 <span class="s">}</span>
1925 1912 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$ValenceElectrons</span><span class="s">)</span><span class="sc">;</span>
1926 1913
1927 1914 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
1928 1915 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
1929 1916 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1930 1917 <span class="s">}</span>
1931 1918
1932 1919 <span class="i">$ValenceElectrons</span> = <span class="i">PeriodicTable::GetElementValenceElectrons</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
1933 1920
1934 1921 <span class="k">return</span> <span class="i">$ValenceElectrons</span><span class="sc">;</span>
1935 1922 <span class="s">}</span>
1936 1923
1937 1924 <span class="c"># Add hydrogens to specified atom in molecule and return number of hydrogens added:</span>
1938 1925 <span class="c">#</span>
1939 1926 <span class="c"># o HydrogensToAdd = ImplicitHydrogenCount - ExplicitHydrogenCount</span>
1940 1927 <span class="c">#</span>
1941 1928 <span class="c"># o XYZ are set to ZeroVector</span>
1942 1929 <span class="c">#</span>
1943 <a name="AddHydrogens-"></a>1930 <span class="k">sub </span><span class="m">AddHydrogens</span> <span class="s">{</span>
1944 1931 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenPositionsWarning</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1945 1932
1946 1933 <span class="c"># Is this atom in a molecule?</span>
1947 1934 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1948 1935 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1949 1936 <span class="s">}</span>
1950 1937 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$HydrogenPositionsWarning</span><span class="s">)</span> <span class="s">{</span>
1951 1938 <span class="i">$HydrogenPositionsWarning</span> = <span class="n">1</span><span class="sc">;</span>
1952 1939 <span class="s">}</span>
1953 1940 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenPositionsWarning</span><span class="s">)</span> <span class="s">{</span>
1954 1941 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;AddHydrogens: The current release of MayaChemTools doesn&#39;t assign any hydrogen positions...&quot;</span><span class="sc">;</span>
1955 1942 <span class="s">}</span>
1956 1943
1957 1944 <span class="c"># Is it an element symbol?</span>
1958 1945 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
1959 1946 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1960 1947 <span class="s">}</span>
1961 1948
1962 1949 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$HydrogensAdded</span><span class="cm">,</span> <span class="i">$HydrogensToAdd</span><span class="s">)</span><span class="sc">;</span>
1963 1950
1964 1951 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
1965 1952 <span class="i">$HydrogensAdded</span> = <span class="n">0</span><span class="sc">;</span>
1966 1953 <span class="i">$HydrogensToAdd</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1967 1954 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogensToAdd</span> &lt;= <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
1968 1955 <span class="k">return</span> <span class="i">$HydrogensAdded</span><span class="sc">;</span>
1969 1956 <span class="s">}</span>
1970 1957
1971 1958 <span class="k">my</span><span class="s">(</span><span class="i">$Count</span><span class="cm">,</span> <span class="i">$Hydrogen</span><span class="s">)</span><span class="sc">;</span>
1972 1959
1973 1960 <span class="k">for</span> <span class="i">$Count</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$HydrogensToAdd</span><span class="s">)</span> <span class="s">{</span>
1974 1961 <span class="i">$HydrogensAdded</span>++<span class="sc">;</span>
1975 1962
1976 1963 <span class="i">$Hydrogen</span> = <span class="i">$Molecule</span><span class="i">-&gt;NewAtom</span><span class="s">(</span><span class="q">&#39;AtomSymbol&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;H&#39;</span><span class="cm">,</span> <span class="q">&#39;XYZ&#39;</span> <span class="cm">=&gt;</span> <span class="s">[</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
1977 1964 <span class="i">$Molecule</span><span class="i">-&gt;NewBond</span><span class="s">(</span><span class="q">&#39;Atoms&#39;</span> <span class="cm">=&gt;</span> <span class="s">[</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Hydrogen</span><span class="s">]</span><span class="cm">,</span> <span class="q">&#39;BondOrder&#39;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
1978 1965 <span class="s">}</span>
1979 1966
1980 1967 <span class="k">return</span> <span class="i">$HydrogensAdded</span><span class="sc">;</span>
1981 1968 <span class="s">}</span>
1982 1969
1983 1970 <span class="c"># Delete hydrogens attached to atom in molecule and return total number of hydrogens deleted...</span>
1984 <a name="DeleteHydrogens-"></a>1971 <span class="k">sub </span><span class="m">DeleteHydrogens</span> <span class="s">{</span>
1985 1972 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1986 1973
1987 1974 <span class="c"># Is this atom in a molecule?</span>
1988 1975 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1989 1976 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
1990 1977 <span class="s">}</span>
1991 1978
1992 1979 <span class="c"># Is it an element symbol?</span>
1993 1980 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
1994 1981 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
1995 1982 <span class="s">}</span>
1996 1983
1997 1984 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">$HydrogensDeleted</span><span class="cm">,</span> <span class="i">@Neighbors</span><span class="s">)</span><span class="sc">;</span>
1998 1985
1999 1986 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
2000 1987 <span class="i">$HydrogensDeleted</span> = <span class="n">0</span><span class="sc">;</span>
2001 1988 <span class="i">@Neighbors</span> = <span class="i">$This</span><span class="i">-&gt;GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2002 1989
2003 1990 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">@Neighbors</span><span class="s">)</span> <span class="s">{</span>
2004 1991 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Neighbor</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2005 1992 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
2006 1993 <span class="s">}</span>
2007 1994 <span class="i">$Molecule</span><span class="i">-&gt;_DeleteAtom</span><span class="s">(</span><span class="i">$Neighbor</span><span class="s">)</span><span class="sc">;</span>
2008 1995 <span class="i">$HydrogensDeleted</span>++<span class="sc">;</span>
2009 1996 <span class="s">}</span>
2010 1997
2011 1998 <span class="k">return</span> <span class="i">$HydrogensDeleted</span><span class="sc">;</span>
2012 1999 <span class="s">}</span>
2013 2000
2014 2001 <span class="c"># Copy atom and all its associated data...</span>
2015 <a name="Copy-"></a>2002 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span>
2016 2003 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2017 2004 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
2018 2005
2019 2006 <span class="i">$Atom</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
2020 2007
2021 2008 <span class="k">return</span> <span class="i">$Atom</span><span class="sc">;</span>
2022 2009 <span class="s">}</span>
2023 2010
2024 2011 <span class="c"># Get atomic invariant value...</span>
2025 2012 <span class="c">#</span>
2026 <a name="GetAtomicInvariantValue-"></a>2013 <span class="k">sub </span><span class="m">GetAtomicInvariantValue</span> <span class="s">{</span>
2027 2014 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2028 2015 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
2029 2016
2030 2017 <span class="i">$Value</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
2031 2018
2032 2019 <span class="j">ATOMICVARIANT:</span> <span class="s">{</span>
2033 2020 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AS|AtomSymbol|ElementSymbol)$/i</span><span class="s">)</span> <span class="s">{</span>
2034 2021 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2035 2022 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2036 2023 <span class="s">}</span>
2037 2024 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(X|NumOfNonHydrogenAtomNeighbors|NumOfHeavyAtomNeighbors)$/i</span><span class="s">)</span> <span class="s">{</span>
2038 2025 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2039 2026 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2040 2027 <span class="s">}</span>
2041 2028 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(BO|SumOfBondOrdersToNonHydrogenAtoms|SumOfBondOrdersToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
2042 2029 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2043 2030 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2044 2031 <span class="s">}</span>
2045 2032 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(LBO|LargestBondOrderToNonHydrogenAtoms|LargestBondOrderToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
2046 2033 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetLargestBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2047 2034 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2048 2035 <span class="s">}</span>
2049 2036 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(H|NumOfImplicitAndExplicitHydrogens)$/i</span><span class="s">)</span> <span class="s">{</span>
2050 2037 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2051 2038 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2052 2039 <span class="s">}</span>
2053 2040 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(SB|NumOfSingleBondsToNonHydrogenAtoms|NumOfSingleBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
2054 2041 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2055 2042 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2056 2043 <span class="s">}</span>
2057 2044 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(DB|NumOfDoubleBondsToNonHydrogenAtoms|NumOfDoubleBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
2058 2045 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfDoubleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2059 2046 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2060 2047 <span class="s">}</span>
2061 2048 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(TB|NumOfTripleBondsToNonHydrogenAtoms|NumOfTripleBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
2062 2049 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfTripleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2063 2050 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2064 2051 <span class="s">}</span>
2065 2052 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AB|NumOfAromaticBondsToNonHydrogenAtoms|NumOfAromaticBondsToHeavyAtoms)$/i</span><span class="s">)</span> <span class="s">{</span>
2066 2053 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfAromaticBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2067 2054 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2068 2055 <span class="s">}</span>
2069 2056 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(FC|FormalCharge)$/i</span><span class="s">)</span> <span class="s">{</span>
2070 2057 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2071 2058 <span class="i">$Value</span> = <span class="k">defined</span> <span class="i">$Value</span> ? <span class="i">$Value</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2072 2059 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2073 2060 <span class="s">}</span>
2074 2061 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(T|TotalNumOfAtomNeighbors)$/i</span><span class="s">)</span> <span class="s">{</span>
2075 2062 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">-&gt;GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2076 2063 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2077 2064 <span class="s">}</span>
2078 2065 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(TSB|TotalNumOfSingleBonds)$/i</span><span class="s">)</span> <span class="s">{</span>
2079 2066 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">-&gt;GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2080 2067 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2081 2068 <span class="s">}</span>
2082 2069 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(Ar|Aromatic)$/i</span><span class="s">)</span> <span class="s">{</span>
2083 2070 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2084 2071 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2085 2072 <span class="s">}</span>
2086 2073 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(RA|RingAtom)$/i</span><span class="s">)</span> <span class="s">{</span>
2087 2074 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;IsInRing</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2088 2075 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2089 2076 <span class="s">}</span>
2090 2077 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(Str|Stereochemistry)$/i</span><span class="s">)</span> <span class="s">{</span>
2091 2078 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetStereochemistry</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2092 2079 <span class="i">$Value</span>= <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$Value</span> =~ <span class="q">/^(R|S)$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="i">$Value</span> <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
2093 2080 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2094 2081 <span class="s">}</span>
2095 2082 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AN|AtomicNumber)$/i</span><span class="s">)</span> <span class="s">{</span>
2096 2083 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2097 2084 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2098 2085 <span class="s">}</span>
2099 2086 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AM|AtomicMass)$/i</span><span class="s">)</span> <span class="s">{</span>
2100 2087 <span class="i">$Value</span> = <span class="i">round</span><span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="n">4</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
2101 2088 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2102 2089 <span class="s">}</span>
2103 2090 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(MN|MassNumber)$/i</span><span class="s">)</span> <span class="s">{</span>
2104 2091 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetMassNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2105 2092 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2106 2093 <span class="s">}</span>
2107 2094 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(SM|SpinMultiplicity)$/i</span><span class="s">)</span> <span class="s">{</span>
2108 2095 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2109 2096 <span class="i">$Value</span> = <span class="k">defined</span> <span class="i">$Value</span> ? <span class="i">$Value</span> <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
2110 2097 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span>
2111 2098 <span class="s">}</span>
2112 2099 <span class="i">$Value</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
2113 2100 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GetAtomicInvariantValue: Unknown atomic invariant $AtomicInvariant...&quot;</span><span class="sc">;</span>
2114 2101 <span class="s">}</span>
2115 2102
2116 2103 <span class="k">return</span> <span class="i">$Value</span><span class="sc">;</span>
2117 2104 <span class="s">}</span>
2118 2105
2119 2106 <span class="c"># Get period number of the atom..</span>
2120 2107 <span class="c">#</span>
2121 <a name="GetPeriodNumber-"></a>2108 <span class="k">sub </span><span class="m">GetPeriodNumber</span> <span class="s">{</span>
2122 2109 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2123 2110
2124 2111 <span class="c"># Is PeriodNumber property explicitly set?</span>
2125 2112 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;PeriodNumber&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2126 2113 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;PeriodNumber&#39;</span><span class="s">)</span><span class="sc">;</span>
2127 2114 <span class="s">}</span>
2128 2115 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$PeriodNumber</span><span class="s">)</span><span class="sc">;</span>
2129 2116
2130 2117 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
2131 2118 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
2132 2119 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2133 2120 <span class="s">}</span>
2134 2121
2135 2122 <span class="i">$PeriodNumber</span> = <span class="i">PeriodicTable::GetElementPeriodNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
2136 2123
2137 2124 <span class="k">return</span> <span class="i">$PeriodNumber</span><span class="sc">;</span>
2138 2125 <span class="s">}</span>
2139 2126
2140 2127 <span class="c"># Get group number of the atom..</span>
2141 2128 <span class="c">#</span>
2142 <a name="GetGroupNumber-"></a>2129 <span class="k">sub </span><span class="m">GetGroupNumber</span> <span class="s">{</span>
2143 2130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2144 2131
2145 2132 <span class="c"># Is GroupNumber property explicitly set?</span>
2146 2133 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;GroupNumber&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2147 2134 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;GroupNumber&#39;</span><span class="s">)</span><span class="sc">;</span>
2148 2135 <span class="s">}</span>
2149 2136 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$GroupNumber</span><span class="s">)</span><span class="sc">;</span>
2150 2137
2151 2138 <span class="i">$AtomicNumber</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
2152 2139 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
2153 2140 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2154 2141 <span class="s">}</span>
2155 2142
2156 2143 <span class="i">$GroupNumber</span> = <span class="i">PeriodicTable::GetElementGroupNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
2157 2144
2158 2145 <span class="k">return</span> <span class="i">$GroupNumber</span><span class="sc">;</span>
2159 2146 <span class="s">}</span>
2160 2147
2161 2148 <span class="c"># Is it a specified topological pharmacophore atom type?</span>
2162 2149 <span class="c">#</span>
2163 <a name="IsTopologicalPharmacophoreType-"></a>2150 <span class="k">sub </span><span class="m">IsTopologicalPharmacophoreType</span> <span class="s">{</span>
2164 2151 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2165 2152
2166 2153 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_IsFunctionalClassType</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span><span class="sc">;</span>
2167 2154 <span class="s">}</span>
2168 2155
2169 2156 <span class="c"># Is it a specified functional class atom type?</span>
2170 2157 <span class="c">#</span>
2171 <a name="IsFunctionalClassType-"></a>2158 <span class="k">sub </span><span class="m">IsFunctionalClassType</span> <span class="s">{</span>
2172 2159 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2173 2160
2174 2161 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_IsFunctionalClassType</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span><span class="sc">;</span>
2175 2162 <span class="s">}</span>
2176 2163
2177 2164 <span class="c"># Is it a specified functional/topological pharmacophore atom type?</span>
2178 2165 <span class="c">#</span>
2179 <a name="_IsFunctionalClassType-"></a>2166 <span class="k">sub </span><span class="m">_IsFunctionalClassType</span> <span class="s">{</span>
2180 2167 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2181 2168 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
2182 2169
2183 2170 <span class="i">$Value</span> = <span class="n">0</span><span class="sc">;</span>
2184 2171
2185 2172 <span class="j">TYPE:</span> <span class="s">{</span>
2186 2173 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(HBD|HydrogenBondDonor)$/i</span><span class="s">)</span> <span class="s">{</span>
2187 2174 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;IsHydrogenBondDonor</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2188 2175 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
2189 2176 <span class="s">}</span>
2190 2177 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(HBA|HydrogenBondAcceptor)$/i</span><span class="s">)</span> <span class="s">{</span>
2191 2178 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;IsHydrogenBondAcceptor</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2192 2179 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
2193 2180 <span class="s">}</span>
2194 2181 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(PI|PositivelyIonizable)$/i</span><span class="s">)</span> <span class="s">{</span>
2195 2182 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;IsPositivelyIonizable</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2196 2183 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
2197 2184 <span class="s">}</span>
2198 2185 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(NI|NegativelyIonizable)$/i</span><span class="s">)</span> <span class="s">{</span>
2199 2186 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;IsNegativelyIonizable</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2200 2187 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
2201 2188 <span class="s">}</span>
2202 2189 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(H|Hydrophobic)$/i</span><span class="s">)</span> <span class="s">{</span>
2203 2190 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;IsHydrophobic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2204 2191 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
2205 2192 <span class="s">}</span>
2206 2193 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(Ar|Aromatic)$/i</span><span class="s">)</span> <span class="s">{</span>
2207 2194 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2208 2195 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
2209 2196 <span class="s">}</span>
2210 2197 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(Hal|Halogen)$/i</span><span class="s">)</span> <span class="s">{</span>
2211 2198 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;IsHalogen</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2212 2199 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
2213 2200 <span class="s">}</span>
2214 2201 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(RA|RingAtom)$/i</span><span class="s">)</span> <span class="s">{</span>
2215 2202 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;IsInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2216 2203 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
2217 2204 <span class="s">}</span>
2218 2205 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^(CA|ChainAtom)$/i</span><span class="s">)</span> <span class="s">{</span>
2219 2206 <span class="i">$Value</span> = <span class="i">$This</span><span class="i">-&gt;IsNotInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2220 2207 <span class="k">last</span> <span class="j">TYPE</span><span class="sc">;</span>
2221 2208 <span class="s">}</span>
2222 2209 <span class="i">$Value</span> = <span class="n">0</span><span class="sc">;</span>
2223 2210 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;_IsType: Unknown functional/pharmacohore type $Type...&quot;</span><span class="sc">;</span>
2224 2211 <span class="s">}</span>
2225 2212 <span class="k">return</span> <span class="i">$Value</span><span class="sc">;</span>
2226 2213 <span class="s">}</span>
2227 2214
2228 2215 <span class="c"># Is it a Hydrogen atom?</span>
2229 <a name="IsHydrogen-"></a>2216 <span class="k">sub </span><span class="m">IsHydrogen</span> <span class="s">{</span>
2230 2217 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2231 2218
2232 2219 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">1</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2233 2220 <span class="s">}</span>
2234 2221
2235 2222 <span class="c"># Is it a Carbon atom?</span>
2236 <a name="IsCarbon-"></a>2223 <span class="k">sub </span><span class="m">IsCarbon</span> <span class="s">{</span>
2237 2224 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2238 2225
2239 2226 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">6</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2240 2227 <span class="s">}</span>
2241 2228
2242 2229 <span class="c"># Is it a Nitrogen atom?</span>
2243 <a name="IsNitrogen-"></a>2230 <span class="k">sub </span><span class="m">IsNitrogen</span> <span class="s">{</span>
2244 2231 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2245 2232
2246 2233 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">7</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2247 2234 <span class="s">}</span>
2248 2235
2249 2236 <span class="c"># Is it a Oxygen atom?</span>
2250 <a name="IsOxygen-"></a>2237 <span class="k">sub </span><span class="m">IsOxygen</span> <span class="s">{</span>
2251 2238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2252 2239
2253 2240 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">8</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2254 2241 <span class="s">}</span>
2255 2242
2256 2243 <span class="c"># Is it a Fluorine atom?</span>
2257 <a name="IsFluorine-"></a>2244 <span class="k">sub </span><span class="m">IsFluorine</span> <span class="s">{</span>
2258 2245 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2259 2246
2260 2247 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">9</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2261 2248 <span class="s">}</span>
2262 2249
2263 2250 <span class="c"># Is it a Silicon atom?</span>
2264 <a name="IsSilicon-"></a>2251 <span class="k">sub </span><span class="m">IsSilicon</span> <span class="s">{</span>
2265 2252 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2266 2253
2267 2254 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">14</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2268 2255 <span class="s">}</span>
2269 2256
2270 2257 <span class="c"># Is it a Phosphorus atom?</span>
2271 <a name="IsPhosphorus-"></a>2258 <span class="k">sub </span><span class="m">IsPhosphorus</span> <span class="s">{</span>
2272 2259 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2273 2260
2274 2261 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">15</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2275 2262 <span class="s">}</span>
2276 2263
2277 2264 <span class="c"># Is it a Sulphur atom?</span>
2278 <a name="IsSulphur-"></a>2265 <span class="k">sub </span><span class="m">IsSulphur</span> <span class="s">{</span>
2279 2266 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2280 2267
2281 2268 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;IsSulfur</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2282 2269 <span class="s">}</span>
2283 2270
2284 2271 <span class="c"># Is it a Sulfur atom?</span>
2285 <a name="IsSulfur-"></a>2272 <span class="k">sub </span><span class="m">IsSulfur</span> <span class="s">{</span>
2286 2273 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2287 2274
2288 2275 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">16</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2289 2276 <span class="s">}</span>
2290 2277
2291 2278 <span class="c"># Is it a Chlorine atom?</span>
2292 <a name="IsChlorine-"></a>2279 <span class="k">sub </span><span class="m">IsChlorine</span> <span class="s">{</span>
2293 2280 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2294 2281
2295 2282 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">17</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2296 2283 <span class="s">}</span>
2297 2284
2298 2285 <span class="c"># Is it a Arsenic atom?</span>
2299 <a name="IsArsenic-"></a>2286 <span class="k">sub </span><span class="m">IsArsenic</span> <span class="s">{</span>
2300 2287 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2301 2288
2302 2289 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">33</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2303 2290 <span class="s">}</span>
2304 2291
2305 2292 <span class="c"># Is it a Selenium atom?</span>
2306 <a name="IsSelenium-"></a>2293 <span class="k">sub </span><span class="m">IsSelenium</span> <span class="s">{</span>
2307 2294 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2308 2295
2309 2296 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">34</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2310 2297 <span class="s">}</span>
2311 2298
2312 2299 <span class="c"># Is it a Bromine atom?</span>
2313 <a name="IsBromine-"></a>2300 <span class="k">sub </span><span class="m">IsBromine</span> <span class="s">{</span>
2314 2301 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2315 2302
2316 2303 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">35</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2317 2304 <span class="s">}</span>
2318 2305
2319 2306 <span class="c"># Is it a Tellurium atom?</span>
2320 <a name="IsTellurium-"></a>2307 <span class="k">sub </span><span class="m">IsTellurium</span> <span class="s">{</span>
2321 2308 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2322 2309
2323 2310 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">52</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2324 2311 <span class="s">}</span>
2325 2312
2326 2313 <span class="c"># Is it a Iodine atom?</span>
2327 <a name="IsIodine-"></a>2314 <span class="k">sub </span><span class="m">IsIodine</span> <span class="s">{</span>
2328 2315 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2329 2316
2330 2317 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">53</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2331 2318 <span class="s">}</span>
2332 2319
2333 2320 <span class="c"># Is it a hetro atom? (N, O, F, P, S, Cl, Br, I)</span>
2334 <a name="IsHeteroAtom-"></a>2321 <span class="k">sub </span><span class="m">IsHeteroAtom</span> <span class="s">{</span>
2335 2322 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2336 2323
2337 2324 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8|9|15|16|17|35|53)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2338 2325 <span class="s">}</span>
2339 2326
2340 2327 <span class="c"># Is it a halogen atom? (F, Cl, Br, I)</span>
2341 <a name="IsHalogen-"></a>2328 <span class="k">sub </span><span class="m">IsHalogen</span> <span class="s">{</span>
2342 2329 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2343 2330
2344 2331 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(9|17|35|53)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2345 2332 <span class="s">}</span>
2346 2333
2347 2334 <span class="c"># Is it classified as metallic?</span>
2348 <a name="IsMetallic-"></a>2335 <span class="k">sub </span><span class="m">IsMetallic</span> <span class="s">{</span>
2349 2336 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2350 2337 <span class="k">my</span><span class="s">(</span><span class="i">$Classification</span><span class="s">)</span><span class="sc">;</span>
2351 2338
2352 2339 <span class="i">$Classification</span> = <span class="i">PeriodicTable::GetElementClassification</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="s">)</span><span class="sc">;</span>
2353 2340
2354 2341 <span class="k">return</span> <span class="s">(</span><span class="i">$Classification</span> =~ <span class="q">/^Metallic$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2355 2342 <span class="s">}</span>
2356 2343
2357 2344 <span class="c"># Is it a non carbon or hydrogen atom? (C, H)</span>
2358 <a name="IsNonCarbonOrHydrogen-"></a>2345 <span class="k">sub </span><span class="m">IsNonCarbonOrHydrogen</span> <span class="s">{</span>
2359 2346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2360 2347
2361 2348 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(1|6)$/</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
2362 2349 <span class="s">}</span>
2363 2350
2364 2351 <span class="c"># Is it a polar atom? ( N, O, P, S)</span>
2365 <a name="IsPolarAtom-"></a>2352 <span class="k">sub </span><span class="m">IsPolarAtom</span> <span class="s">{</span>
2366 2353 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2367 2354
2368 2355 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8|15|16)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2369 2356 <span class="s">}</span>
2370 2357
2371 2358 <span class="c"># Is it an isotope?</span>
2372 <a name="IsIsotope-"></a>2359 <span class="k">sub </span><span class="m">IsIsotope</span> <span class="s">{</span>
2373 2360 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2374 2361
2375 2362 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>}<span class="sc">;</span>
2376 2363 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
2377 2364 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2378 2365 <span class="s">}</span>
2379 2366
2380 2367 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;MassNumber&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2381 2368 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2382 2369 <span class="s">}</span>
2383 2370 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="cm">,</span> <span class="i">$MostAbundantMassNumber</span><span class="s">)</span><span class="sc">;</span>
2384 2371
2385 2372 <span class="i">$MassNumber</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;MassNumber&#39;</span><span class="s">)</span><span class="sc">;</span>
2386 2373 <span class="i">$MostAbundantMassNumber</span> = <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
2387 2374
2388 2375 <span class="k">return</span> <span class="s">(</span><span class="i">$MassNumber</span> == <span class="i">$MostAbundantMassNumber</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
2389 2376 <span class="s">}</span>
2390 2377
2391 2378 <span class="c"># Is it a terminal atom?</span>
2392 <a name="IsTerminal-"></a>2379 <span class="k">sub </span><span class="m">IsTerminal</span> <span class="s">{</span>
2393 2380 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2394 2381
2395 2382 <span class="c"># Is this atom in a molecule?</span>
2396 2383 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2397 2384 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
2398 2385 <span class="s">}</span>
2399 2386
2400 2387 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> &lt;= <span class="n">1</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span>
2401 2388
2402 2389 <span class="s">}</span>
2403 2390
2404 2391 <span class="c"># Is aromatic property set for the atom?</span>
2405 <a name="IsAromatic-"></a>2392 <span class="k">sub </span><span class="m">IsAromatic</span> <span class="s">{</span>
2406 2393 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2407 2394 <span class="k">my</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span><span class="sc">;</span>
2408 2395
2409 2396 <span class="i">$Aromatic</span> = <span class="i">$This</span><span class="i">-&gt;GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2410 2397
2411 2398 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span> &amp;&amp; <span class="i">$Aromatic</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2412 2399 <span class="s">}</span>
2413 2400
2414 2401 <span class="c"># Is this a hydrogen atom and attached to one of these atoms: N, O, P, S</span>
2415 <a name="IsPolarHydrogen-"></a>2402 <span class="k">sub </span><span class="m">IsPolarHydrogen</span> <span class="s">{</span>
2416 2403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2417 2404
2418 2405 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2419 2406 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2420 2407 <span class="s">}</span>
2421 2408
2422 2409 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
2423 2410 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">-&gt;GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2424 2411 <span class="k">if</span> <span class="s">(</span><span class="i">@Bonds</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
2425 2412 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2426 2413 <span class="s">}</span>
2427 2414
2428 2415 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="s">)</span><span class="sc">;</span>
2429 2416 <span class="s">(</span><span class="i">$Bond</span><span class="s">)</span> = <span class="i">@Bonds</span><span class="sc">;</span>
2430 2417 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">-&gt;GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
2431 2418
2432 2419 <span class="k">return</span> <span class="i">$BondedAtom</span><span class="i">-&gt;IsPolarAtom</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>
2433 2420 <span class="s">}</span>
2434 2421
2435 2422 <span class="c"># Is it a hydrogen bond donor atom?</span>
2436 2423 <span class="c">#</span>
2437 <a name="IsHBondDonor-"></a>2424 <span class="k">sub </span><span class="m">IsHBondDonor</span> <span class="s">{</span>
2438 2425 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2439 2426
2440 2427 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;IsHydrogenBondDonor</span><span class="s">(</span><span class="i">$HydrogenBondsType</span><span class="s">)</span><span class="sc">;</span>
2441 2428 <span class="s">}</span>
2442 2429
2443 2430 <span class="c"># The currrent release of MayaChemTools supports identification of two types of</span>
2444 2431 <span class="c"># hydrogen bond donor and acceptor atoms with these names:</span>
2445 2432 <span class="c">#</span>
2446 2433 <span class="c"># HBondsType1 or HydrogenBondsType1</span>
2447 2434 <span class="c"># HBondsType2 or HydrogenBondsType2</span>
2448 2435 <span class="c">#</span>
2449 2436 <span class="c"># The names of these hydrogen bond types are rather arbitrary. However, their</span>
2450 2437 <span class="c"># definitions have specific meaning and are as follows:</span>
2451 2438 <span class="c">#</span>
2452 2439 <span class="c"># HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</span>
2453 2440 <span class="c"># . Donor: NH, NH2, NH3, OH - Any N and O with available H</span>
2454 2441 <span class="c"># . Acceptor: N[!H], O - Any N without available H and any O</span>
2455 2442 <span class="c">#</span>
2456 2443 <span class="c"># HydrogenBondsType2 [ Ref 91 ]:</span>
2457 2444 <span class="c"># . Donor: NH, NH2, NH3, OH - Any N and O with availabe H</span>
2458 2445 <span class="c"># . Acceptor: N, O - Any N and O</span>
2459 2446 <span class="c">#</span>
2460 2447 <span class="c"># Note:</span>
2461 2448 <span class="c"># . HydrogenBondsType2 definition corresponds to Rule of 5.</span>
2462 2449 <span class="c">#</span>
2463 2450
2464 2451 <span class="c"># Is it a hydrogen bond donor atom?</span>
2465 2452 <span class="c">#</span>
2466 2453 <span class="c"># The currrent release of MayaChemTools supports identification of two types of</span>
2467 <a name="IsHydrogenBondDonor-"></a>2454 <span class="k">sub </span><span class="m">IsHydrogenBondDonor</span> <span class="s">{</span>
2468 2455 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2469 2456 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
2470 2457
2471 2458 <span class="i">$HydrogenBondsType</span> = <span class="k">defined</span> <span class="i">$HydrogenBondsType</span> ? <span class="i">$HydrogenBondsType</span> <span class="co">:</span> <span class="q">&#39;HBondsType1&#39;</span><span class="sc">;</span>
2472 2459 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
2473 2460
2474 2461 <span class="j">HYDROGENBONDSTYPE:</span> <span class="s">{</span>
2475 2462
2476 2463 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType1|HydrogenBondsType1)$/i</span><span class="s">)</span> <span class="s">{</span>
2477 2464 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">-&gt;_IsHydrogenBondDonorOfType1</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2478 2465 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span>
2479 2466 <span class="s">}</span>
2480 2467
2481 2468 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType2|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span>
2482 2469 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">-&gt;_IsHydrogenBondDonorOfType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2483 2470 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span>
2484 2471 <span class="s">}</span>
2485 2472
2486 2473 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
2487 2474 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;IsHydrogenBondDonor: The current release of MayaChemTools doesn&#39;t support specified value, $HydrogenBondsType, for HydrogenBondsType. Valid values: HBondsType1, HydrogenBondsType1, HBondsType2 HydrogenBondsType2 ...&quot;</span><span class="sc">;</span>
2488 2475 <span class="s">}</span>
2489 2476
2490 2477 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
2491 2478 <span class="s">}</span>
2492 2479
2493 2480 <span class="c"># Is it a MayaChemTools HBondType1 hydrogen bond donor atom?</span>
2494 2481 <span class="c">#</span>
2495 <a name="_IsHydrogenBondDonorOfType1-"></a>2482 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType1</span> <span class="s">{</span>
2496 2483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2497 2484
2498 2485 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_IsHydrogenBondDonorOfType1OrType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2499 2486 <span class="s">}</span>
2500 2487
2501 2488 <span class="c"># Is it a MayaChemTools HBondType2 hydrogen bond donor atom?</span>
2502 2489 <span class="c">#</span>
2503 <a name="_IsHydrogenBondDonorOfType2-"></a>2490 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType2</span> <span class="s">{</span>
2504 2491 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2505 2492
2506 2493 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_IsHydrogenBondDonorOfType1OrType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2507 2494 <span class="s">}</span>
2508 2495
2509 2496 <span class="c"># Is it a hydrogen bond donor atom of MayaChemTools Type1 or Type2?</span>
2510 2497 <span class="c">#</span>
2511 2498 <span class="c"># HydrogenBondDonor definition [ Ref 60-61, Ref 65-66, Ref 91 ]: NH, NH2, OH</span>
2512 2499 <span class="c">#</span>
2513 2500 <span class="c"># In other words:</span>
2514 2501 <span class="c"># . NH, NH2 - Nitrogen atom with available hydrogen</span>
2515 2502 <span class="c"># . OH - Oxygen atom with avilable hydrogen</span>
2516 2503 <span class="c">#</span>
2517 <a name="_IsHydrogenBondDonorOfType1OrType2-"></a>2504 <span class="k">sub </span><span class="m">_IsHydrogenBondDonorOfType1OrType2</span> <span class="s">{</span>
2518 2505 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2519 2506
2520 2507 <span class="c"># Is this atom in a molecule?</span>
2521 2508 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2522 2509 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2523 2510 <span class="s">}</span>
2524 2511
2525 2512 <span class="c"># Is it N or O?</span>
2526 2513 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(7|8)$/</span><span class="s">)</span> <span class="s">{</span>
2527 2514 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2528 2515 <span class="s">}</span>
2529 2516
2530 2517 <span class="c"># Any explicitly attached hydrogens?</span>
2531 2518 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2532 2519 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2533 2520 <span class="s">}</span>
2534 2521
2535 2522 <span class="c"># Any missing hydrogens?</span>
2536 2523 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfMissingHydrogens</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>
2537 2524 <span class="s">}</span>
2538 2525
2539 2526 <span class="c"># Is it a hydrogen bond acceptor atom?</span>
2540 2527 <span class="c">#</span>
2541 <a name="IsHBondAcceptor-"></a>2528 <span class="k">sub </span><span class="m">IsHBondAcceptor</span> <span class="s">{</span>
2542 2529 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2543 2530
2544 2531 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;IsHydrogenBondAcceptor</span><span class="s">(</span><span class="i">$HydrogenBondsType</span><span class="s">)</span><span class="sc">;</span>
2545 2532 <span class="s">}</span>
2546 2533
2547 2534 <span class="c"># Is it a hydrogen bond acceptor atom?</span>
2548 2535 <span class="c">#</span>
2549 <a name="IsHydrogenBondAcceptor-"></a>2536 <span class="k">sub </span><span class="m">IsHydrogenBondAcceptor</span> <span class="s">{</span>
2550 2537 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2551 2538 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
2552 2539
2553 2540 <span class="i">$HydrogenBondsType</span> = <span class="k">defined</span> <span class="i">$HydrogenBondsType</span> ? <span class="i">$HydrogenBondsType</span> <span class="co">:</span> <span class="q">&#39;HBondsType1&#39;</span><span class="sc">;</span>
2554 2541 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
2555 2542
2556 2543 <span class="j">HYDROGENBONDSTYPE:</span> <span class="s">{</span>
2557 2544
2558 2545 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType1|HydrogenBondsType1)$/i</span><span class="s">)</span> <span class="s">{</span>
2559 2546 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">-&gt;_IsHydrogenBondAcceptorOfType1</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2560 2547 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span>
2561 2548 <span class="s">}</span>
2562 2549
2563 2550 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> =~ <span class="q">/^(HBondsType2|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span>
2564 2551 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">-&gt;_IsHydrogenBondAcceptorOfType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2565 2552 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span>
2566 2553 <span class="s">}</span>
2567 2554
2568 2555 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
2569 2556 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;IsHydrogenBondAcceptor: The current release of MayaChemTools doesn&#39;t support specified value, $HydrogenBondsType, for HydrogenBondsType. Valid values: HBondsType1, HydrogenBondsType1, HBondsType2 HydrogenBondsType2 ...&quot;</span><span class="sc">;</span>
2570 2557 <span class="s">}</span>
2571 2558
2572 2559 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
2573 2560 <span class="s">}</span>
2574 2561
2575 2562 <span class="c"># Is it a MayaChemTools HBondType1 hydrogen bond acceptor atom?</span>
2576 2563 <span class="c">#</span>
2577 2564 <span class="c"># HydrogenBondAcceptor definition [ Ref 60-61, Ref 65-66 ]: N[!H], O</span>
2578 2565 <span class="c">#</span>
2579 2566 <span class="c"># In other words:</span>
2580 2567 <span class="c"># . N[!H] - Nitrogen atom with no hydrogen</span>
2581 2568 <span class="c"># . O - Oxygen atom</span>
2582 2569 <span class="c">#</span>
2583 <a name="_IsHydrogenBondAcceptorOfType1-"></a>2570 <span class="k">sub </span><span class="m">_IsHydrogenBondAcceptorOfType1</span> <span class="s">{</span>
2584 2571 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2585 2572
2586 2573 <span class="c"># Is this atom in a molecule?</span>
2587 2574 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2588 2575 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2589 2576 <span class="s">}</span>
2590 2577
2591 2578 <span class="c"># Is it N or O?</span>
2592 2579 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(7|8)$/</span><span class="s">)</span> <span class="s">{</span>
2593 2580 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2594 2581 <span class="s">}</span>
2595 2582
2596 2583 <span class="c"># Is it O?</span>
2597 2584 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">8</span> <span class="s">)</span> <span class="s">{</span>
2598 2585 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2599 2586 <span class="s">}</span>
2600 2587
2601 2588 <span class="c"># Any explicitly attached hydrogens?</span>
2602 2589 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2603 2590 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2604 2591 <span class="s">}</span>
2605 2592
2606 2593 <span class="c"># Any missing hydrogens?</span>
2607 2594 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
2608 2595 <span class="s">}</span>
2609 2596
2610 2597 <span class="c"># Is it a MayaChemTools HBondType2 hydrogen bond acceptor atom?</span>
2611 2598 <span class="c">#</span>
2612 2599 <span class="c"># HydrogenBondAcceptor definition [ Ref 91 ]: N, O</span>
2613 2600 <span class="c">#</span>
2614 2601 <span class="c"># In other words:</span>
2615 2602 <span class="c"># . Any Nitrogen or Oxygen atom</span>
2616 2603 <span class="c">#</span>
2617 2604 <span class="c"># Note:</span>
2618 2605 <span class="c"># . HydrogenBondsType2 definition corresponds to Rule of 5.</span>
2619 2606 <span class="c">#</span>
2620 <a name="_IsHydrogenBondAcceptorOfType2-"></a>2607 <span class="k">sub </span><span class="m">_IsHydrogenBondAcceptorOfType2</span> <span class="s">{</span>
2621 2608 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2622 2609
2623 2610 <span class="c"># Is this atom in a molecule?</span>
2624 2611 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2625 2612 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2626 2613 <span class="s">}</span>
2627 2614
2628 2615 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8)$/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2629 2616 <span class="s">}</span>
2630 2617
2631 2618 <span class="c"># Is it a positively ionizable atom?</span>
2632 2619 <span class="c">#</span>
2633 2620 <span class="c"># PositivelyIonizable defintion [ Ref 60-61, Ref 65-66 ]: +, NH2</span>
2634 2621 <span class="c">#</span>
2635 2622 <span class="c"># In other words:</span>
2636 2623 <span class="c"># . Any atom with positve formal charge</span>
2637 2624 <span class="c"># . NH2 - Nitogen atom in amino group</span>
2638 2625 <span class="c">#</span>
2639 <a name="IsPositivelyIonizable-"></a>2626 <span class="k">sub </span><span class="m">IsPositivelyIonizable</span> <span class="s">{</span>
2640 2627 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2641 2628 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span>
2642 2629
2643 2630 <span class="c"># Is this atom in a molecule?</span>
2644 2631 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2645 2632 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2646 2633 <span class="s">}</span>
2647 2634
2648 2635 <span class="c"># Any explicit positive formal charge?</span>
2649 2636 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">-&gt;GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2650 2637 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> &amp;&amp; <span class="i">$FormalCharge</span> &gt; <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
2651 2638 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2652 2639 <span class="s">}</span>
2653 2640
2654 2641 <span class="c"># Is it N?</span>
2655 2642 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} != <span class="n">7</span> <span class="s">)</span> <span class="s">{</span>
2656 2643 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2657 2644 <span class="s">}</span>
2658 2645
2659 2646 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span> == <span class="n">2</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2660 2647 <span class="s">}</span>
2661 2648
2662 2649 <span class="c"># Is it a negatively ionizable atom?</span>
2663 2650 <span class="c">#</span>
2664 2651 <span class="c"># NegativelyIonizable definition [ Ref 60-61, Ref 65-66 ]: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
2665 2652 <span class="c">#</span>
2666 2653 <span class="c"># In other words:</span>
2667 2654 <span class="c"># . Any atom with negative formal charge</span>
2668 2655 <span class="c"># . Carbon atom in C(=O)OH group</span>
2669 2656 <span class="c"># . Phosphorous in P(=O)OH group</span>
2670 2657 <span class="c"># . Sulfur atom in S(=O)OH group</span>
2671 2658 <span class="c">#</span>
2672 <a name="IsNegativelyIonizable-"></a>2659 <span class="k">sub </span><span class="m">IsNegativelyIonizable</span> <span class="s">{</span>
2673 2660 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2674 2661 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span>
2675 2662
2676 2663 <span class="c"># Is this atom in a molecule?</span>
2677 2664 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2678 2665 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2679 2666 <span class="s">}</span>
2680 2667
2681 2668 <span class="c"># Any explicit negative formal charge?</span>
2682 2669 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">-&gt;GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2683 2670 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> &amp;&amp; <span class="i">$FormalCharge</span> &lt; <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
2684 2671 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2685 2672 <span class="s">}</span>
2686 2673
2687 2674 <span class="c"># Is it C, P or S?</span>
2688 2675 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(6|15|16)$/</span> <span class="s">)</span> <span class="s">{</span>
2689 2676 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2690 2677 <span class="s">}</span>
2691 2678
2692 2679 <span class="c"># Collect oxygens connected to C, P or S with single or double bonds and not connected to</span>
2693 2680 <span class="c"># any other heavy atom...</span>
2694 2681 <span class="k">my</span><span class="s">(</span><span class="i">$Neighbor</span><span class="cm">,</span> <span class="i">$NeighborOxygenBondOrder</span><span class="cm">,</span> <span class="i">$NumOfNeighborOxygensWithSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfNeighborOxygensWithDoubleBonds</span><span class="s">)</span><span class="sc">;</span>
2695 2682
2696 2683 <span class="i">$NumOfNeighborOxygensWithSingleBonds</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$NumOfNeighborOxygensWithDoubleBonds</span> = <span class="n">0</span><span class="sc">;</span>
2697 2684
2698 2685 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$Neighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2699 2686 <span class="c"># Is it an oxygen?</span>
2700 2687 <span class="k">if</span> <span class="s">(</span><span class="i">$Neighbor</span>-&gt;{<span class="w">AtomicNumber</span>} != <span class="n">8</span><span class="s">)</span> <span class="s">{</span>
2701 2688 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
2702 2689 <span class="s">}</span>
2703 2690 <span class="c"># Is oxygent connected to only heavy atom?</span>
2704 2691 <span class="k">if</span> <span class="s">(</span><span class="i">$Neighbor</span><span class="i">-&gt;GetNumOfHeavyAtomNeighbors</span><span class="s">(</span><span class="s">)</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
2705 2692 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span>
2706 2693 <span class="s">}</span>
2707 2694 <span class="i">$NeighborOxygenBondOrder</span> = <span class="i">$This</span><span class="i">-&gt;GetBondToAtom</span><span class="s">(</span><span class="i">$Neighbor</span><span class="s">)</span><span class="i">-&gt;GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2708 2695
2709 2696 <span class="k">if</span> <span class="s">(</span><span class="i">$NeighborOxygenBondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
2710 2697 <span class="i">$NumOfNeighborOxygensWithDoubleBonds</span>++<span class="sc">;</span>
2711 2698 <span class="s">}</span>
2712 2699 <span class="k">elsif</span> <span class="s">(</span><span class="i">$NeighborOxygenBondOrder</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
2713 2700 <span class="i">$NumOfNeighborOxygensWithSingleBonds</span>++<span class="sc">;</span>
2714 2701 <span class="s">}</span>
2715 2702 <span class="s">}</span>
2716 2703 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfNeighborOxygensWithDoubleBonds</span> &gt;= <span class="n">1</span> &amp;&amp; <span class="i">$NumOfNeighborOxygensWithSingleBonds</span> &gt;= <span class="n">1</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
2717 2704 <span class="s">}</span>
2718 2705
2719 2706 <span class="c"># Is it a liphophilic atom?</span>
2720 2707 <span class="c">#</span>
2721 2708 <span class="c"># Lipophilic definition [ Ref 60-61, Ref 65-66 ]: C(C)(C)(C)(C), Cl, Br, I, S(C)(C)</span>
2722 2709 <span class="c">#</span>
2723 2710 <span class="c"># In other words:</span>
2724 2711 <span class="c"># . C(C)(C)(C)(C) - Carbon atom connected to only other carbons</span>
2725 2712 <span class="c"># . Chlorine, Bromine or Iodine atom</span>
2726 2713 <span class="c"># . S(C)(C) - Sulfur connected to two carbons</span>
2727 2714 <span class="c">#</span>
2728 <a name="IsLipophilic-"></a>2715 <span class="k">sub </span><span class="m">IsLipophilic</span> <span class="s">{</span>
2729 2716 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2730 2717
2731 2718 <span class="c"># Is this atom in a molecule?</span>
2732 2719 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2733 2720 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2734 2721 <span class="s">}</span>
2735 2722
2736 2723 <span class="c"># Is it Cl, Br, I?</span>
2737 2724 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(17|35|53)$/</span><span class="s">)</span> <span class="s">{</span>
2738 2725 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2739 2726 <span class="s">}</span>
2740 2727
2741 2728 <span class="c"># Is it C, S?</span>
2742 2729 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(6|16)$/</span><span class="s">)</span> <span class="s">{</span>
2743 2730 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2744 2731 <span class="s">}</span>
2745 2732
2746 2733 <span class="c"># Are all heavy atom neighbors Carbons?</span>
2747 2734 <span class="k">my</span><span class="s">(</span><span class="i">$HeavyAtomNeighbor</span><span class="cm">,</span> <span class="i">@HeavyAtomNeighbors</span><span class="s">)</span><span class="sc">;</span>
2748 2735 <span class="i">@HeavyAtomNeighbors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2749 2736 <span class="i">@HeavyAtomNeighbors</span> = <span class="i">$This</span><span class="i">-&gt;GetHeavyAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2750 2737
2751 2738 <span class="k">for</span> <span class="i">$HeavyAtomNeighbor</span> <span class="s">(</span><span class="i">@HeavyAtomNeighbors</span><span class="s">)</span> <span class="s">{</span>
2752 2739 <span class="k">if</span> <span class="s">(</span><span class="i">$HeavyAtomNeighbor</span>-&gt;{<span class="w">AtomicNumber</span>} != <span class="n">6</span><span class="s">)</span> <span class="s">{</span>
2753 2740 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2754 2741 <span class="s">}</span>
2755 2742 <span class="s">}</span>
2756 2743
2757 2744 <span class="c"># Does sulfur has two carbon neighbors?</span>
2758 2745 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="n">16</span><span class="s">)</span> <span class="s">{</span>
2759 2746 <span class="k">if</span> <span class="s">(</span><span class="i">@HeavyAtomNeighbors</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
2760 2747 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2761 2748 <span class="s">}</span>
2762 2749 <span class="s">}</span>
2763 2750 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2764 2751 <span class="s">}</span>
2765 2752
2766 2753 <span class="c"># Is it hydrophobic?</span>
2767 2754 <span class="c">#</span>
2768 <a name="IsHydrophobic-"></a>2755 <span class="k">sub </span><span class="m">IsHydrophobic</span> <span class="s">{</span>
2769 2756 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2770 2757
2771 2758 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;IsLipophilic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
2772 2759 <span class="s">}</span>
2773 2760
2774 2761 <span class="c"># Is it a Nitrogen atom in Guadinium group?</span>
2775 2762 <span class="c">#</span>
2776 <a name="IsGuadiniumNitrogen-"></a>2763 <span class="k">sub </span><span class="m">IsGuadiniumNitrogen</span> <span class="s">{</span>
2777 2764 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2778 2765
2779 2766 <span class="c"># Is it Nitrogen?</span>
2780 2767 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2781 2768 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2782 2769 <span class="s">}</span>
2783 2770
2784 2771 <span class="c"># Is it connected to a Guadinium Carbon?</span>
2785 2772 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span>
2786 2773
2787 2774 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2788 2775 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">-&gt;IsGuadiniumCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2789 2776 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2790 2777 <span class="s">}</span>
2791 2778 <span class="s">}</span>
2792 2779
2793 2780 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2794 2781 <span class="s">}</span>
2795 2782
2796 2783 <span class="c"># Is it a Carbon atom in Guadinium group?</span>
2797 2784 <span class="c">#</span>
2798 2785 <span class="c"># Guadinium group definition:</span>
2799 2786 <span class="c">#</span>
2800 2787 <span class="c"># R2N-C(=NR)-(NR2) or R2N-C(=NR2+)-(NR2)</span>
2801 2788 <span class="c">#</span>
2802 2789 <span class="c"># where:</span>
2803 2790 <span class="c"># . R = Hydrogens or group of atoms attached through Carbon</span>
2804 2791 <span class="c"># . Only one of the three Nitrogens has a double bond to Carbon and has optional</span>
2805 2792 <span class="c"># formal charge allowing it to be neutral or charged state</span>
2806 2793 <span class="c">#</span>
2807 <a name="IsGuadiniumCarbon-"></a>2794 <span class="k">sub </span><span class="m">IsGuadiniumCarbon</span> <span class="s">{</span>
2808 2795 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2809 2796
2810 2797 <span class="c"># Is it Carbon?</span>
2811 2798 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2812 2799 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2813 2800 <span class="s">}</span>
2814 2801
2815 2802 <span class="c"># Match atom neighborhood...</span>
2816 2803 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
2817 2804
2818 2805 <span class="i">$CentralAtomSpec</span> = <span class="q">&#39;C.X3.BO4&#39;</span><span class="sc">;</span>
2819 2806 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">&#39;N.FC0&#39;</span><span class="cm">,</span> <span class="q">&#39;N.FC0&#39;</span><span class="cm">,</span> <span class="q">&#39;N.FC0,N.FC+1&#39;</span><span class="s">)</span><span class="sc">;</span>
2820 2807 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">&#39;-&#39;</span><span class="cm">,</span> <span class="q">&#39;-&#39;</span><span class="cm">,</span> <span class="q">&#39;=&#39;</span><span class="s">)</span><span class="sc">;</span>
2821 2808 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">&#39;C,H&#39;</span><span class="cm">,</span> <span class="q">&#39;C,H&#39;</span><span class="cm">,</span> <span class="q">&#39;C,H&#39;</span><span class="s">)</span><span class="sc">;</span>
2822 2809
2823 2810 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2824 2811 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2825 2812 <span class="s">}</span>
2826 2813
2827 2814 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2828 2815 <span class="s">}</span>
2829 2816
2830 2817 <span class="c"># Is it a Nitrogen atom in Amide group?</span>
2831 2818 <span class="c">#</span>
2832 <a name="IsAmideNitrogen-"></a>2819 <span class="k">sub </span><span class="m">IsAmideNitrogen</span> <span class="s">{</span>
2833 2820 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2834 2821
2835 2822 <span class="c"># Is it Nitrogen?</span>
2836 2823 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2837 2824 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2838 2825 <span class="s">}</span>
2839 2826
2840 2827 <span class="c"># Is it connected to a Amide Carbon?</span>
2841 2828 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span>
2842 2829
2843 2830 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2844 2831 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">-&gt;IsAmideCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2845 2832 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2846 2833 <span class="s">}</span>
2847 2834 <span class="s">}</span>
2848 2835
2849 2836 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2850 2837 <span class="s">}</span>
2851 2838
2852 2839 <span class="c"># Is it a Carbon atom in Amide group?</span>
2853 2840 <span class="c">#</span>
2854 2841 <span class="c"># Amide group definition: R-C(=O)-N(-R&#39;)-R&#39;&#39;</span>
2855 2842 <span class="c">#</span>
2856 2843 <span class="c"># where:</span>
2857 2844 <span class="c"># . R = Hydrogen or groups of atoms attached through Carbon</span>
2858 2845 <span class="c"># . R&#39; = Hydrogens or groups of atoms attached through Carbon or hetro atoms</span>
2859 2846 <span class="c"># . R&#39;&#39; = Hydrogens or groups of atoms attached through Carbon or hetro atoms</span>
2860 2847 <span class="c">#</span>
2861 <a name="IsAmideCarbon-"></a>2848 <span class="k">sub </span><span class="m">IsAmideCarbon</span> <span class="s">{</span>
2862 2849 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2863 2850
2864 2851 <span class="c"># Is this atom in a molecule?</span>
2865 2852 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2866 2853 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2867 2854 <span class="s">}</span>
2868 2855
2869 2856 <span class="c"># Is it Carbon?</span>
2870 2857 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2871 2858 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2872 2859 <span class="s">}</span>
2873 2860
2874 2861 <span class="c"># Match atom neighborhood...</span>
2875 2862 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
2876 2863
2877 2864 <span class="i">$CentralAtomSpec</span> = <span class="q">&#39;C.X3.BO4,C.X2.BO3&#39;</span><span class="sc">;</span>
2878 2865 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">&#39;C,H&#39;</span><span class="cm">,</span> <span class="q">&#39;O&#39;</span><span class="cm">,</span> <span class="q">&#39;N&#39;</span><span class="s">)</span><span class="sc">;</span>
2879 2866 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">&#39;-&#39;</span><span class="cm">,</span> <span class="q">&#39;=&#39;</span><span class="cm">,</span> <span class="q">&#39;-&#39;</span><span class="s">)</span><span class="sc">;</span>
2880 2867 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">&#39;C,H&#39;</span><span class="cm">,</span> <span class="q">&#39;C&#39;</span><span class="cm">,</span> <span class="q">&#39;C,H,N,O,S,P,F,Cl,Br,I&#39;</span><span class="s">)</span><span class="sc">;</span>
2881 2868
2882 2869 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2883 2870 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2884 2871 <span class="s">}</span>
2885 2872
2886 2873 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2887 2874 <span class="s">}</span>
2888 2875
2889 2876 <span class="c"># Is it a Oxygen atom in Carboxylate group?</span>
2890 2877 <span class="c">#</span>
2891 <a name="IsCarboxylateOxygen-"></a>2878 <span class="k">sub </span><span class="m">IsCarboxylateOxygen</span> <span class="s">{</span>
2892 2879 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2893 2880
2894 2881 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_MatchCarboxylateAndOrCarboxylOxygen</span><span class="s">(</span><span class="q">&#39;Carboxylate&#39;</span><span class="s">)</span><span class="sc">;</span>
2895 2882 <span class="s">}</span>
2896 2883
2897 2884 <span class="c"># Is it a Carbon atom in Carboxylate group?</span>
2898 2885 <span class="c">#</span>
2899 2886 <span class="c"># Carboxyl group definition: R-C(=O)-O-</span>
2900 2887 <span class="c">#</span>
2901 <a name="IsCarboxylateCarbon-"></a>2888 <span class="k">sub </span><span class="m">IsCarboxylateCarbon</span> <span class="s">{</span>
2902 2889 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2903 2890
2904 2891 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="q">&#39;Carboxylate&#39;</span><span class="s">)</span><span class="sc">;</span>
2905 2892 <span class="s">}</span>
2906 2893
2907 2894 <span class="c"># Is it a Oxygen atom in Carboxyl group?</span>
2908 2895 <span class="c">#</span>
2909 <a name="IsCarboxylOxygen-"></a>2896 <span class="k">sub </span><span class="m">IsCarboxylOxygen</span> <span class="s">{</span>
2910 2897 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2911 2898
2912 2899 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_MatchCarboxylateAndOrCarboxylOxygen</span><span class="s">(</span><span class="q">&#39;Carboxyl&#39;</span><span class="s">)</span><span class="sc">;</span>
2913 2900 <span class="s">}</span>
2914 2901
2915 2902 <span class="c"># Is it a Carbon atom in Carboxyl group?</span>
2916 2903 <span class="c">#</span>
2917 2904 <span class="c"># Carboxyl group definition: R-C(=O)-OH</span>
2918 2905 <span class="c">#</span>
2919 <a name="IsCarboxylCarbon-"></a>2906 <span class="k">sub </span><span class="m">IsCarboxylCarbon</span> <span class="s">{</span>
2920 2907 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2921 2908
2922 2909 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="q">&#39;Carboxyl&#39;</span><span class="s">)</span><span class="sc">;</span>
2923 2910 <span class="s">}</span>
2924 2911
2925 2912 <span class="c"># Match Carboxylate and/or Carboxyl oxygen...</span>
2926 2913 <span class="c">#</span>
2927 <a name="_MatchCarboxylateAndOrCarboxylOxygen-"></a>2914 <span class="k">sub </span><span class="m">_MatchCarboxylateAndOrCarboxylOxygen</span> <span class="s">{</span>
2928 2915 <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="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2929 2916
2930 2917 <span class="c"># Is it Oxygen?</span>
2931 2918 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;IsOxygen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2932 2919 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2933 2920 <span class="s">}</span>
2934 2921
2935 2922 <span class="c"># Is it connected to a Carboxylate Carbon?</span>
2936 2923 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span>
2937 2924
2938 2925 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2939 2926 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">-&gt;_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2940 2927 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2941 2928 <span class="s">}</span>
2942 2929 <span class="s">}</span>
2943 2930
2944 2931 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2945 2932 <span class="s">}</span>
2946 2933
2947 2934 <span class="c"># Match Carboxylate and Carboxyl Carbon</span>
2948 2935 <span class="c">#</span>
2949 2936 <span class="c"># Carboxylate group definition: R-C(=O)-O-</span>
2950 2937 <span class="c"># Carboxyl group definition: R-C(=O)-OH</span>
2951 2938 <span class="c">#</span>
2952 2939 <span class="c"># where:</span>
2953 2940 <span class="c"># . R = Hydrogens or groups of atoms attached through Carbon</span>
2954 2941 <span class="c">#</span>
2955 <a name="_MatchCarboxylateAndOrCarboxylCarbon-"></a>2942 <span class="k">sub </span><span class="m">_MatchCarboxylateAndOrCarboxylCarbon</span> <span class="s">{</span>
2956 2943 <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="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
2957 2944
2958 2945 <span class="c"># Is this atom in a molecule?</span>
2959 2946 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2960 2947 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2961 2948 <span class="s">}</span>
2962 2949
2963 2950 <span class="c"># Is it Carbon?</span>
2964 2951 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2965 2952 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2966 2953 <span class="s">}</span>
2967 2954
2968 2955 <span class="c"># Match atom neighborhood...</span>
2969 2956 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
2970 2957
2971 2958 <span class="i">$CentralAtomSpec</span> = <span class="q">&#39;C.X3.BO4,C.X2.BO3&#39;</span><span class="sc">;</span>
2972 2959 <span class="j">MODE:</span> <span class="s">{</span>
2973 2960 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Carboxylate$/i</span><span class="s">)</span> <span class="s">{</span>
2974 2961 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">&#39;C,H&#39;</span><span class="cm">,</span> <span class="q">&#39;O&#39;</span><span class="cm">,</span> <span class="q">&#39;O.X1.FC-1&#39;</span><span class="s">)</span><span class="sc">;</span>
2975 2962 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span>
2976 2963 <span class="s">}</span>
2977 2964 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Carboxyl$/i</span><span class="s">)</span> <span class="s">{</span>
2978 2965 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">&#39;C,H&#39;</span><span class="cm">,</span> <span class="q">&#39;O&#39;</span><span class="cm">,</span> <span class="q">&#39;O.X1.FC0&#39;</span><span class="s">)</span><span class="sc">;</span>
2979 2966 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span>
2980 2967 <span class="s">}</span>
2981 2968 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^CarboxylateOrCarboxyl$/i</span><span class="s">)</span> <span class="s">{</span>
2982 2969 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">&#39;C,H&#39;</span><span class="cm">,</span> <span class="q">&#39;O&#39;</span><span class="cm">,</span> <span class="q">&#39;O.X1.FC-1,O.X1.FC0&#39;</span><span class="s">)</span><span class="sc">;</span>
2983 2970 <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span>
2984 2971 <span class="s">}</span>
2985 2972 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;_MatchCarboxylateAndCarboxylCarbon.: Unknown mode $Mode...&quot;</span><span class="sc">;</span>
2986 2973 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2987 2974 <span class="s">}</span>
2988 2975 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">&#39;-&#39;</span><span class="cm">,</span> <span class="q">&#39;=&#39;</span><span class="cm">,</span> <span class="q">&#39;-&#39;</span><span class="s">)</span><span class="sc">;</span>
2989 2976 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">&#39;C,H&#39;</span><span class="cm">,</span> <span class="q">&#39;C&#39;</span><span class="cm">,</span> <span class="q">&#39;C&#39;</span><span class="s">)</span><span class="sc">;</span>
2990 2977
2991 2978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
2992 2979 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
2993 2980 <span class="s">}</span>
2994 2981
2995 2982 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
2996 2983 <span class="s">}</span>
2997 2984
2998 2985 <span class="c"># Is it a Oxygen atom in Phosphate group?</span>
2999 2986 <span class="c">#</span>
3000 <a name="IsPhosphateOxygen-"></a>2987 <span class="k">sub </span><span class="m">IsPhosphateOxygen</span> <span class="s">{</span>
3001 2988 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3002 2989
3003 2990 <span class="c"># Is it Oxygen?</span>
3004 2991 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;IsOxygen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3005 2992 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3006 2993 <span class="s">}</span>
3007 2994
3008 2995 <span class="c"># Is it connected to a Phosphate Phosphorus?</span>
3009 2996 <span class="k">my</span><span class="s">(</span><span class="i">$AtomNeighbor</span><span class="s">)</span><span class="sc">;</span>
3010 2997
3011 2998 <span class="k">for</span> <span class="i">$AtomNeighbor</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3012 2999 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomNeighbor</span><span class="i">-&gt;IsPhosphatePhosphorus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3013 3000 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
3014 3001 <span class="s">}</span>
3015 3002 <span class="s">}</span>
3016 3003
3017 3004 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3018 3005 <span class="s">}</span>
3019 3006
3020 3007 <span class="c"># Is it a Phosphorus atom in Phosphate group?</span>
3021 3008 <span class="c">#</span>
3022 3009 <span class="c"># Phosphate group definition: AO-(O=)P(-OA)-OA</span>
3023 3010 <span class="c">#</span>
3024 3011 <span class="c"># where:</span>
3025 3012 <span class="c"># . A = Any Groups of atoms including hydrogens</span>
3026 3013 <span class="c">#</span>
3027 <a name="IsPhosphatePhosphorus-"></a>3014 <span class="k">sub </span><span class="m">IsPhosphatePhosphorus</span> <span class="s">{</span>
3028 3015 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3029 3016
3030 3017 <span class="c"># Is this atom in a molecule?</span>
3031 3018 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3032 3019 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3033 3020 <span class="s">}</span>
3034 3021
3035 3022 <span class="c"># Is it Phosphorus?</span>
3036 3023 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;IsPhosphorus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3037 3024 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3038 3025 <span class="s">}</span>
3039 3026
3040 3027 <span class="c"># Match atom neighborhood...</span>
3041 3028 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
3042 3029
3043 3030 <span class="i">$CentralAtomSpec</span> = <span class="q">&#39;P.X4.BO5&#39;</span><span class="sc">;</span>
3044 3031 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">&#39;O&#39;</span><span class="cm">,</span> <span class="q">&#39;O&#39;</span><span class="cm">,</span> <span class="q">&#39;O&#39;</span><span class="cm">,</span> <span class="q">&#39;O&#39;</span><span class="s">)</span><span class="sc">;</span>
3045 3032 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">&#39;-&#39;</span><span class="cm">,</span> <span class="q">&#39;=&#39;</span><span class="cm">,</span> <span class="q">&#39;-&#39;</span><span class="cm">,</span> <span class="q">&#39;-&#39;</span><span class="s">)</span><span class="sc">;</span>
3046 3033 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
3047 3034
3048 3035 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="cm">,</span> \<span class="i">@NbrAtomSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrBondSpecsRef</span><span class="cm">,</span> \<span class="i">@NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3049 3036 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
3050 3037 <span class="s">}</span>
3051 3038
3052 3039 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3053 3040 <span class="s">}</span>
3054 3041
3055 3042
3056 3043 <span class="c"># Match central atom and its neighborhood using specified atom and bonds specifications...</span>
3057 3044 <span class="c">#</span>
3058 3045 <span class="c"># Let:</span>
3059 3046 <span class="c"># AS = Atom symbol corresponding to element symbol, atomic number (#n) or any</span>
3060 3047 <span class="c"># atom (A)</span>
3061 3048 <span class="c">#</span>
3062 3049 <span class="c"># X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
3063 3050 <span class="c"># T&lt;n&gt; = Total number of atom neighbors including implcit and explicit hydrogens</span>
3064 3051 <span class="c"># BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
3065 3052 <span class="c"># LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
3066 3053 <span class="c"># SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
3067 3054 <span class="c"># TSB&lt;n&gt; = Total number of single bonds to atom neighbors including implcit and explicit hydrogens</span>
3068 3055 <span class="c"># DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
3069 3056 <span class="c"># TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
3070 3057 <span class="c"># H&lt;n&gt; = Number of implicit and explicit hydrogens for atom</span>
3071 3058 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span>
3072 3059 <span class="c"># RA or RA&lt;n&gt; = Ring atom annotation indicating whether atom is a ring</span>
3073 3060 <span class="c"># TR&lt;n&gt; = Total number of rings containing atom</span>
3074 3061 <span class="c"># FC&lt;+n/-n&gt; = Formal charge assigned to atom</span>
3075 3062 <span class="c"># MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope</span>
3076 3063 <span class="c"># SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span>
3077 3064 <span class="c">#</span>
3078 3065 <span class="c"># Then:</span>
3079 3066 <span class="c">#</span>
3080 3067 <span class="c"># Atom specification corresponds to:</span>
3081 3068 <span class="c">#</span>
3082 3069 <span class="c"># AS.X&lt;n&gt;.T&lt;n&gt;.BO&lt;n&gt;.LBO&lt;n&gt;.&lt;SB&gt;&lt;n&gt;.TSB&lt;n&gt;.&lt;DB&gt;&lt;n&gt;.&lt;TB&gt;&lt;n&gt;.H&lt;n&gt;.Ar.RA&lt;n&gt;.TR&lt;n&gt;FC&lt;+n/-n&gt;.MN&lt;n&gt;.SM&lt;n&gt;</span>
3083 3070 <span class="c">#</span>
3084 3071 <span class="c"># Except for AS which is a required atomic invariant in atom specification, all other atomic invariants are</span>
3085 3072 <span class="c"># optional. For an atom specification to match an atom, the values of all specified atomic invariants must</span>
3086 3073 <span class="c"># match. Exclamation in from of atomic invariant can be used to negate its effect during the match.</span>
3087 3074 <span class="c">#</span>
3088 3075 <span class="c"># A comma delimited atom specification string is used to match any one of the specifed atom specification.</span>
3089 3076 <span class="c">#</span>
3090 3077 <span class="c"># Notes:</span>
3091 3078 <span class="c"># . During atom specification match to an atom, the first atomic invariant is always assumed to</span>
3092 3079 <span class="c"># atom symbol.</span>
3093 3080 <span class="c"># . Atom match specfication is based on AtomicInvariantAtomTypes implemented in</span>
3094 3081 <span class="c"># AotmTypes::AtomicInvariantAtomType.pm module</span>
3095 3082 <span class="c">#</span>
3096 3083 <span class="c"># Examples:</span>
3097 3084 <span class="c"># . (&#39;N&#39;, &#39;N&#39;, &#39;N&#39;)</span>
3098 3085 <span class="c"># . (&#39;N.FC0&#39;, &#39;N.FC0&#39;, &#39;N,N.FC+1.H1&#39;)</span>
3099 3086 <span class="c"># . (&#39;N.H2&#39;, &#39;N.H2&#39;, &#39;N.H1&#39;)</span>
3100 3087 <span class="c"># . (&#39;C,N&#39;, &#39;!N&#39;, &#39;!H&#39;)</span>
3101 3088 <span class="c"># . (&#39;C,N&#39;, &#39;N.Ar&#39;, &#39;N.R5&#39;)</span>
3102 3089 <span class="c">#</span>
3103 3090 <span class="c"># Let:</span>
3104 3091 <span class="c"># -|1|s|Single = Single bond</span>
3105 3092 <span class="c"># =|2|d|Double = Double bond</span>
3106 3093 <span class="c"># #|3|t|Triple = Triple bond</span>
3107 3094 <span class="c"># :|1.5|a|Ar|Aromatic = Aromatic bond</span>
3108 3095 <span class="c">#</span>
3109 3096 <span class="c"># @|RB|Ring = Ring bond</span>
3110 3097 <span class="c"># ~|*|Any = Any bond</span>
3111 3098 <span class="c">#</span>
3112 3099 <span class="c"># Then:</span>
3113 3100 <span class="c">#</span>
3114 3101 <span class="c"># Bond specification corresponds to:</span>
3115 3102 <span class="c">#</span>
3116 3103 <span class="c"># -.:</span>
3117 3104 <span class="c"># =.@</span>
3118 3105 <span class="c"># Double.Aromatic</span>
3119 3106 <span class="c">#</span>
3120 3107 <span class="c"># For a bond specification to match bond between two atoms, the values of all specified bond symbols must</span>
3121 3108 <span class="c"># match. Exclamation in from of bond symbol can be used to negate its effect during the match.</span>
3122 3109 <span class="c">#</span>
3123 3110 <span class="c"># A comma delimited bond specification string is used to match any one of the specifed atom specification.</span>
3124 3111 <span class="c">#</span>
3125 <a name="DoesAtomNeighborhoodMatch-"></a>3112 <span class="k">sub </span><span class="m">DoesAtomNeighborhoodMatch</span> <span class="s">{</span>
3126 3113 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="cm">,</span> <span class="i">$CentralAtomSpec</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3127 3114 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NumOfNbrBondSpecs</span><span class="cm">,</span> <span class="i">$NumOfNbrOfNbrAtomSpecs</span><span class="s">)</span><span class="sc">;</span>
3128 3115
3129 3116 <span class="c"># Is this atom in a molecule?</span>
3130 3117 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CentralAtom</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3131 3118 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3132 3119 <span class="s">}</span>
3133 3120
3134 3121 <span class="i">$NumOfNbrAtomSpecs</span> = <span class="k">defined</span> <span class="i">$NbrAtomSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrAtomSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3135 3122 <span class="i">$NumOfNbrBondSpecs</span> = <span class="k">defined</span> <span class="i">$NbrBondSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrBondSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3136 3123 <span class="i">$NumOfNbrOfNbrAtomSpecs</span> = <span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrOfNbrAtomSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3137 3124
3138 3125 <span class="c"># Validate number of specifications...</span>
3139 3126 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNbrBondSpecs</span> &amp;&amp; <span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span> != <span class="i">$NumOfNbrBondSpecs</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3140 3127 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;DoesAtomNeighborhoodMatch: Number of specified central atom, $NumOfNbrAtomSpecs, and bond, $NumOfNbrBondSpecs, specifications must be same; No neighborhood match performed ...&quot;</span><span class="sc">;</span>
3141 3128 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3142 3129 <span class="s">}</span>
3143 3130
3144 3131 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNbrOfNbrAtomSpecs</span> &amp;&amp; <span class="s">(</span><span class="i">$NumOfNbrOfNbrAtomSpecs</span> != <span class="i">$NumOfNbrAtomSpecs</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3145 3132 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;DoesAtomNeighborhoodMatch: Number of specified central atom, $NumOfNbrAtomSpecs, and neighbor of neighbor atoms specifications, $NumOfNbrOfNbrAtomSpecs, must be same; No neighborhood match performed ...&quot;</span><span class="sc">;</span>
3146 3133 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3147 3134 <span class="s">}</span>
3148 3135
3149 3136 <span class="c"># Sort atom and bond specifications in terms of being most specific to least specific..</span>
3150 3137 <span class="s">(</span><span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">$CentralAtom</span><span class="i">-&gt;_SortSpecificationsForAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
3151 3138
3152 3139 <span class="c"># Does central atom specification match?</span>
3153 3140 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CentralAtom</span><span class="i">-&gt;_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$CentralAtomSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3154 3141 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3155 3142 <span class="s">}</span>
3156 3143
3157 3144 <span class="c"># No neighbors to match...</span>
3158 3145 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfNbrAtomSpecs</span><span class="s">)</span> <span class="s">{</span>
3159 3146 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
3160 3147 <span class="s">}</span>
3161 3148
3162 3149 <span class="c"># Match neighbors...</span>
3163 3150 <span class="k">my</span><span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> <span class="i">%NbrSpecAlreadyMatchedMap</span><span class="s">)</span><span class="sc">;</span>
3164 3151
3165 3152 <span class="i">$NbrSpecCount</span> = <span class="i">$NumOfNbrAtomSpecs</span><span class="sc">;</span>
3166 3153 <span class="i">$NbrSpecMatchCount</span> = <span class="n">0</span><span class="sc">;</span>
3167 3154
3168 3155 <span class="i">%NbrSpecAlreadyMatchedMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
3169 3156 <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span> = <span class="i">$CentralAtom</span><span class="i">-&gt;_MatchAtomNeighborhoodUsingAtomBondSpecs</span><span class="s">(</span><span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> \<span class="i">%NbrSpecAlreadyMatchedMap</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
3170 3157
3171 3158 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="s">)</span> <span class="s">{</span>
3172 3159 <span class="c"># It&#39;s match...</span>
3173 3160 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
3174 3161 <span class="s">}</span>
3175 3162
3176 3163 <span class="c"># Match central atom&#39;s missing hydrogens with any unmatched atom</span>
3177 3164 <span class="c"># and bond specifications...</span>
3178 3165 <span class="c">#</span>
3179 3166 <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span> = <span class="i">$CentralAtom</span><span class="i">-&gt;_MatchAtomNeighborhoodUsingMissingHydrogens</span><span class="s">(</span><span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> \<span class="i">%NbrSpecAlreadyMatchedMap</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
3180 3167
3181 3168 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="s">)</span> <span class="s">{</span>
3182 3169 <span class="c"># It&#39;s match...</span>
3183 3170 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
3184 3171 <span class="s">}</span>
3185 3172
3186 3173 <span class="c"># No match...</span>
3187 3174 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3188 3175 <span class="s">}</span>
3189 3176
3190 3177 <span class="c"># Match central atom neighborhood atom and bond specifications...</span>
3191 3178 <span class="c">#</span>
3192 <a name="_MatchAtomNeighborhoodUsingAtomBondSpecs-"></a>3179 <span class="k">sub </span><span class="m">_MatchAtomNeighborhoodUsingAtomBondSpecs</span> <span class="s">{</span>
3193 3180 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="cm">,</span> <span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> <span class="i">$NbrSpecAlreadyMatchedRef</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3194 3181 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$NbrAtom</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="cm">,</span> <span class="i">$NbrBondSpec</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtom</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpec</span><span class="cm">,</span> <span class="i">$MatchNbrOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrSpecsMatched</span><span class="s">)</span><span class="sc">;</span>
3195 3182
3196 3183 <span class="i">$MatchNbrOfNbrAtomSpecs</span> = <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span> &amp;&amp; <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrOfNbrAtomSpecsRef</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3197 3184
3198 3185 <span class="i">$NbrSpecsMatched</span> = <span class="n">0</span><span class="sc">;</span>
3199 3186
3200 3187 <span class="c"># Match central atom&#39;s immediate neighbors atom and bond specifications...</span>
3201 3188 <span class="j">NBRATOM:</span> <span class="k">for</span> <span class="i">$NbrAtom</span> <span class="s">(</span><span class="i">$CentralAtom</span><span class="i">-&gt;GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3202 3189 <span class="j">NBRATOMSPEC:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NbrSpecCount</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3203 3190 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NbrSpecAlreadyMatchedRef</span>-&gt;{<span class="i">$Index</span>}<span class="s">)</span> <span class="s">{</span>
3204 3191 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
3205 3192 <span class="s">}</span>
3206 3193 <span class="i">$NbrAtomSpec</span> = <span class="i">$NbrAtomSpecsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
3207 3194 <span class="i">$NbrBondSpec</span> = <span class="i">$NbrBondSpecsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
3208 3195
3209 3196 <span class="i">$NbrOfNbrAtomSpec</span> = <span class="i">$MatchNbrOfNbrAtomSpecs</span> ? <span class="i">$NbrOfNbrAtomSpecsRef</span>-&gt;[<span class="i">$Index</span>] <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
3210 3197
3211 3198 <span class="c"># Match neighbor atom specification...</span>
3212 3199 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NbrAtom</span><span class="i">-&gt;_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$NbrAtomSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3213 3200 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
3214 3201 <span class="s">}</span>
3215 3202
3216 3203 <span class="c"># Match central atom to neighbor atom bond specification...</span>
3217 3204 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CentralAtom</span><span class="i">-&gt;_DoesBondSpecificationMatch</span><span class="s">(</span><span class="i">$NbrAtom</span><span class="cm">,</span> <span class="i">$NbrBondSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3218 3205 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
3219 3206 <span class="s">}</span>
3220 3207
3221 3208 <span class="c"># Match any neighbor of neighbor atom specifications...</span>
3222 3209 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span>
3223 3210 <span class="c"># Go over the neighbors of central atom skipping the central atom...</span>
3224 3211 <span class="k">for</span> <span class="i">$NbrOfNbrAtom</span> <span class="s">(</span><span class="i">$NbrAtom</span><span class="i">-&gt;GetNeighbors</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3225 3212 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NbrOfNbrAtom</span><span class="i">-&gt;_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$NbrOfNbrAtomSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3226 3213 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
3227 3214 <span class="s">}</span>
3228 3215 <span class="s">}</span>
3229 3216 <span class="s">}</span>
3230 3217
3231 3218 <span class="c"># It&#39;s a match for a neighbor atom specification...</span>
3232 3219 <span class="i">$NbrSpecAlreadyMatchedRef</span>-&gt;{<span class="i">$Index</span>} = <span class="i">$Index</span><span class="sc">;</span>
3233 3220 <span class="i">$NbrSpecMatchCount</span>++<span class="sc">;</span>
3234 3221
3235 3222 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecMatchCount</span> == <span class="i">$NbrSpecCount</span><span class="s">)</span> <span class="s">{</span>
3236 3223 <span class="c"># It&#39;s match...</span>
3237 3224 <span class="i">$NbrSpecsMatched</span> = <span class="n">1</span><span class="sc">;</span>
3238 3225 <span class="k">last</span> <span class="j">NBRATOM</span><span class="sc">;</span>
3239 3226 <span class="s">}</span>
3240 3227 <span class="c"># Match next neighbor atom...</span>
3241 3228 <span class="k">next</span> <span class="j">NBRATOM</span><span class="sc">;</span>
3242 3229 <span class="s">}</span>
3243 3230 <span class="s">}</span>
3244 3231 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span>
3245 3232 <span class="s">}</span>
3246 3233
3247 3234 <span class="c"># Match central atom&#39;s missing hydrogens with any unmatched atom and bond</span>
3248 3235 <span class="c"># specifications...</span>
3249 3236 <span class="c">#</span>
3250 <a name="_MatchAtomNeighborhoodUsingMissingHydrogens-"></a>3237 <span class="k">sub </span><span class="m">_MatchAtomNeighborhoodUsingMissingHydrogens</span> <span class="s">{</span>
3251 3238 <span class="k">my</span><span class="s">(</span><span class="i">$CentralAtom</span><span class="cm">,</span> <span class="i">$NbrSpecCount</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="cm">,</span> <span class="i">$NbrSpecAlreadyMatchedRef</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3252 3239 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$NbrAtom</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="cm">,</span> <span class="i">$NbrBondSpec</span><span class="cm">,</span> <span class="i">$NumOfMissingHydrogens</span><span class="cm">,</span> <span class="i">$MissingHydrogensIndex</span><span class="cm">,</span> <span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$AtomSpecMatched</span><span class="cm">,</span> <span class="i">$AtomSpec</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="s">)</span><span class="sc">;</span>
3253 3240
3254 3241 <span class="i">$NbrSpecsMatched</span> = <span class="n">0</span><span class="sc">;</span>
3255 3242
3256 3243 <span class="i">$NumOfMissingHydrogens</span> = <span class="i">$CentralAtom</span><span class="i">-&gt;GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
3257 3244 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$NbrSpecCount</span> - <span class="i">$NbrSpecMatchCount</span><span class="s">)</span> &gt; <span class="i">$NumOfMissingHydrogens</span><span class="s">)</span> <span class="s">{</span>
3258 3245 <span class="c"># It won&#39;t match...</span>
3259 3246 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span>
3260 3247 <span class="s">}</span>
3261 3248
3262 3249 <span class="j">MISSINGHYDROGENNBR:</span> <span class="k">for</span> <span class="i">$MissingHydrogensIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfMissingHydrogens</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3263 3250 <span class="j">NBRATOMSPEC:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NbrSpecCount</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3264 3251 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NbrSpecAlreadyMatchedRef</span>-&gt;{<span class="i">$Index</span>}<span class="s">)</span> <span class="s">{</span>
3265 3252 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
3266 3253 <span class="s">}</span>
3267 3254 <span class="i">$NbrAtomSpec</span> = <span class="i">$NbrAtomSpecsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
3268 3255 <span class="i">$NbrBondSpec</span> = <span class="i">$NbrBondSpecsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
3269 3256
3270 3257 <span class="i">$NbrAtomSpec</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
3271 3258
3272 3259 <span class="c"># Match neighbor atom specification hydrogen atom symbol...</span>
3273 3260 <span class="i">$AtomSpecMatched</span> = <span class="n">0</span><span class="sc">;</span>
3274 3261 <span class="j">ATOMSPEC:</span> <span class="k">for</span> <span class="i">$AtomSpec</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="s">)</span> <span class="s">{</span>
3275 3262 <span class="s">(</span><span class="i">$AtomSymbol</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AtomSpec</span><span class="sc">;</span>
3276 3263 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomSymbol</span> =~ <span class="q">/^(H|A|\*)$/i</span><span class="s">)</span> <span class="s">{</span>
3277 3264 <span class="i">$AtomSpecMatched</span> = <span class="n">1</span><span class="sc">;</span>
3278 3265 <span class="k">last</span> <span class="j">ATOMSPEC</span><span class="sc">;</span>
3279 3266 <span class="s">}</span>
3280 3267 <span class="s">}</span>
3281 3268 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSpecMatched</span><span class="s">)</span> <span class="s">{</span>
3282 3269 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
3283 3270 <span class="s">}</span>
3284 3271
3285 3272 <span class="c"># Match neighbor atom bond specification to singal bond...</span>
3286 3273 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrBondSpec</span><span class="s">)</span> <span class="s">{</span>
3287 3274 <span class="i">$NbrBondSpec</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
3288 3275 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrBondSpec</span> !~ <span class="q">/^(-|1|s|Single|\~|\*|Any)/i</span><span class="s">)</span> <span class="s">{</span>
3289 3276 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
3290 3277 <span class="s">}</span>
3291 3278 <span class="s">}</span>
3292 3279
3293 3280 <span class="c"># It&#39;s a match for a neighbor atom specification...</span>
3294 3281 <span class="i">$NbrSpecAlreadyMatchedRef</span>-&gt;{<span class="i">$Index</span>} = <span class="i">$Index</span><span class="sc">;</span>
3295 3282 <span class="i">$NbrSpecMatchCount</span>++<span class="sc">;</span>
3296 3283
3297 3284 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrSpecMatchCount</span> == <span class="i">$NbrSpecCount</span><span class="s">)</span> <span class="s">{</span>
3298 3285 <span class="c"># It&#39;s match...</span>
3299 3286 <span class="i">$NbrSpecsMatched</span> = <span class="n">1</span><span class="sc">;</span>
3300 3287 <span class="k">last</span> <span class="j">MISSINGHYDROGENNBR</span><span class="sc">;</span>
3301 3288 <span class="s">}</span>
3302 3289 <span class="c"># Match next missing hydrogen neighbor...</span>
3303 3290 <span class="k">next</span> <span class="j">MISSINGHYDROGENNBR</span><span class="sc">;</span>
3304 3291 <span class="s">}</span>
3305 3292 <span class="s">}</span>
3306 3293
3307 3294 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrSpecsMatched</span><span class="cm">,</span> <span class="i">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span>
3308 3295 <span class="s">}</span>
3309 3296
3310 3297 <span class="c"># Sort atom and bond specifications base on neighbor atom specifications going</span>
3311 3298 <span class="c"># from most to least specific atom specifications.</span>
3312 3299 <span class="c">#</span>
3313 3300 <span class="c"># Atom specifications are sorted at the following two levels:</span>
3314 3301 <span class="c">#</span>
3315 3302 <span class="c"># o By atom specification count with in each specification going from most specific</span>
3316 3303 <span class="c"># to least specific, where count is determined by the number of &quot;,&quot; in each</span>
3317 3304 <span class="c"># specification. Wild card containing specifications are considered least specific</span>
3318 3305 <span class="c"># and end up at the end of the sorted list.</span>
3319 3306 <span class="c"># o By atomic invariant count with in each sorted list going from most specific to</span>
3320 3307 <span class="c"># least specific, where count is determined by the number of &quot;.&quot; in each atom</span>
3321 3308 <span class="c"># specification.</span>
3322 3309 <span class="c">#</span>
3323 3310 <span class="c">#A single atom specification,</span>
3324 3311 <span class="c"># without any commas in atom specification, is is considered most specific...</span>
3325 3312 <span class="c">#</span>
3326 <a name="_SortSpecificationsForAtomNeighborhoodMatch-"></a>3313 <span class="k">sub </span><span class="m">_SortSpecificationsForAtomNeighborhoodMatch</span> <span class="s">{</span>
3327 3314 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3328 3315 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$NeedToSort</span><span class="cm">,</span> <span class="i">$NumOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrAtomSpecCount</span><span class="cm">,</span> <span class="i">$NbrAtomSpecAtomicInvarintCount</span><span class="cm">,</span> <span class="i">$NbrAtomSpecToMatch</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="cm">,</span> <span class="i">$FirstAtomicInvariant</span><span class="cm">,</span> <span class="i">$WildCardInNbrAtomSpec</span><span class="cm">,</span> <span class="i">@NbrAtomSpecs</span><span class="cm">,</span> <span class="i">@NbrAtomSpecAtomicInvariants</span><span class="cm">,</span> <span class="i">@SortedNbrAtomSpecs</span><span class="cm">,</span> <span class="i">@SortedNbrBondSpecs</span><span class="cm">,</span> <span class="i">@SortedNbrOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">%NbrAtomSpecDataMap</span><span class="s">)</span><span class="sc">;</span>
3329 3316
3330 3317 <span class="i">$NumOfNbrAtomSpecs</span> = <span class="k">defined</span> <span class="i">$NbrAtomSpecsRef</span> ? <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$NbrAtomSpecsRef</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3331 3318
3332 3319 <span class="c"># Figure out whether sorting is necessary...</span>
3333 3320 <span class="i">$NeedToSort</span> = <span class="n">0</span><span class="sc">;</span>
3334 3321 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
3335 3322 <span class="j">ATOMSPEC:</span> <span class="k">for</span> <span class="i">$NbrAtomSpecToMatch</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NbrAtomSpecsRef</span>}<span class="s">)</span> <span class="s">{</span>
3336 3323 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">/(,|\.|A|\*)/i</span><span class="s">)</span> <span class="s">{</span>
3337 3324 <span class="i">$NeedToSort</span> = <span class="n">1</span><span class="sc">;</span>
3338 3325 <span class="k">last</span> <span class="j">ATOMSPEC</span><span class="sc">;</span>
3339 3326 <span class="s">}</span>
3340 3327 <span class="s">}</span>
3341 3328 <span class="s">}</span>
3342 3329 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NeedToSort</span><span class="s">)</span> <span class="s">{</span>
3343 3330 <span class="c"># Nothing to do...</span>
3344 3331 <span class="k">return</span> <span class="s">(</span><span class="i">$NbrAtomSpecsRef</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span><span class="sc">;</span>
3345 3332 <span class="s">}</span>
3346 3333
3347 3334 <span class="i">%NbrAtomSpecDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
3348 3335
3349 3336 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfNbrAtomSpecs</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3350 3337 <span class="i">$NbrAtomSpecToMatch</span> = <span class="i">$NbrAtomSpecsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
3351 3338 <span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
3352 3339
3353 3340 <span class="i">@NbrAtomSpecs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NbrAtomSpecToMatch</span><span class="sc">;</span>
3354 3341 <span class="i">$NbrAtomSpecCount</span> = <span class="k">scalar</span> <span class="i">@NbrAtomSpecs</span><span class="sc">;</span>
3355 3342
3356 3343 <span class="c"># Does neighbor specification contains a wild card in atom symbol specification?</span>
3357 3344 <span class="c">#</span>
3358 3345 <span class="k">if</span> <span class="s">(</span><span class="i">$NbrAtomSpecToMatch</span> =~ <span class="q">/(A|\*)/i</span><span class="s">)</span> <span class="s">{</span>
3359 3346 <span class="i">$WildCardInNbrAtomSpec</span> = <span class="n">0</span><span class="sc">;</span>
3360 3347 <span class="j">NBRATOMSPEC:</span> <span class="k">for</span> <span class="i">$NbrAtomSpec</span> <span class="s">(</span><span class="i">@NbrAtomSpecs</span><span class="s">)</span> <span class="s">{</span>
3361 3348 <span class="s">(</span><span class="i">$FirstAtomicInvariant</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="sc">;</span>
3362 3349 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span>
3363 3350 <span class="i">$FirstAtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span>
3364 3351 <span class="s">}</span>
3365 3352 <span class="i">$WildCardInNbrAtomSpec</span> = <span class="i">$This</span><span class="i">-&gt;_IsWildCardAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$FirstAtomicInvariant</span><span class="s">)</span><span class="sc">;</span>
3366 3353 <span class="k">if</span> <span class="s">(</span><span class="i">$WildCardInNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span>
3367 3354 <span class="k">last</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span>
3368 3355 <span class="s">}</span>
3369 3356 <span class="s">}</span>
3370 3357 <span class="k">if</span> <span class="s">(</span><span class="i">$WildCardInNbrAtomSpec</span><span class="s">)</span> <span class="s">{</span>
3371 3358 <span class="c"># Set NbrAtomSpecCount arbitrarily high to make the spec containing wild</span>
3372 3359 <span class="c"># card last on the sorted list while maintaining its original order in the list...</span>
3373 3360 <span class="i">$NbrAtomSpecCount</span> = <span class="n">999</span><span class="sc">;</span>
3374 3361 <span class="s">}</span>
3375 3362 <span class="s">}</span>
3376 3363
3377 3364 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}<span class="s">)</span> <span class="s">{</span>
3378 3365 <span class="i">%</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
3379 3366 <span class="s">}</span>
3380 3367
3381 3368 <span class="c"># Use first NbrAtomSpec available in @NbrAtomSpecs to determine atomic invariant count</span>
3382 3369 <span class="c"># with in each NbrAtomSpecToMatch, as @NbrAtomSpecs derived from $NbrAtomSpecToMatch</span>
3383 3370 <span class="c"># simply corresponds to a list of possible matches...</span>
3384 3371 <span class="c">#</span>
3385 3372 <span class="s">(</span><span class="i">$NbrAtomSpec</span><span class="s">)</span> = <span class="i">@NbrAtomSpecs</span><span class="sc">;</span>
3386 3373 <span class="i">@NbrAtomSpecAtomicInvariants</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$NbrAtomSpec</span><span class="sc">;</span>
3387 3374 <span class="i">$NbrAtomSpecAtomicInvarintCount</span> = <span class="k">scalar</span> <span class="i">@NbrAtomSpecAtomicInvariants</span><span class="sc">;</span>
3388 3375
3389 3376 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}<span class="s">)</span> <span class="s">{</span>
3390 3377 <span class="i">@</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
3391 3378 <span class="s">}</span>
3392 3379 <span class="k">push</span> <span class="i">@</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}}<span class="cm">,</span> <span class="i">$Index</span><span class="sc">;</span>
3393 3380
3394 3381 <span class="s">}</span>
3395 3382
3396 3383 <span class="i">@SortedNbrAtomSpecs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@SortedNbrBondSpecs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
3397 3384 <span class="i">@SortedNbrOfNbrAtomSpecs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
3398 3385
3399 3386 <span class="k">for</span> <span class="i">$NbrAtomSpecCount</span> <span class="s">(</span> <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> &lt;=&gt; <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%NbrAtomSpecDataMap</span><span class="s">)</span> <span class="s">{</span>
3400 3387 <span class="k">for</span> <span class="i">$NbrAtomSpecAtomicInvarintCount</span> <span class="s">(</span> <span class="k">sort</span> <span class="s">{</span> <span class="i">$b</span> &lt;=&gt; <span class="i">$a</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}}<span class="s">)</span> <span class="s">{</span>
3401 3388 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NbrAtomSpecDataMap</span>{<span class="i">$NbrAtomSpecCount</span>}{<span class="i">$NbrAtomSpecAtomicInvarintCount</span>}}<span class="s">)</span> <span class="s">{</span>
3402 3389 <span class="k">push</span> <span class="i">@SortedNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrAtomSpecsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
3403 3390 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrBondSpecsRef</span><span class="s">)</span> <span class="s">{</span>
3404 3391 <span class="k">push</span> <span class="i">@SortedNbrBondSpecs</span><span class="cm">,</span> <span class="i">$NbrBondSpecsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
3405 3392 <span class="s">}</span>
3406 3393 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span><span class="s">)</span> <span class="s">{</span>
3407 3394 <span class="k">push</span> <span class="i">@SortedNbrOfNbrAtomSpecs</span><span class="cm">,</span> <span class="i">$NbrOfNbrAtomSpecsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
3408 3395 <span class="s">}</span>
3409 3396 <span class="s">}</span>
3410 3397 <span class="s">}</span>
3411 3398 <span class="s">}</span>
3412 3399
3413 3400 <span class="k">return</span> <span class="s">(</span>\<span class="i">@SortedNbrAtomSpecs</span><span class="cm">,</span> <span class="k">defined</span> <span class="i">$NbrBondSpecsRef</span> ? \<span class="i">@SortedNbrBondSpecs</span> <span class="co">:</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">defined</span> <span class="i">$NbrOfNbrAtomSpecsRef</span> ? \<span class="i">@SortedNbrOfNbrAtomSpecs</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
3414 3401 <span class="s">}</span>
3415 3402
3416 3403 <span class="c"># Check whether atom matches supported atom specification...</span>
3417 3404 <span class="c">#</span>
3418 <a name="_DoesAtomSpecificationMatch-"></a>3405 <span class="k">sub </span><span class="m">_DoesAtomSpecificationMatch</span> <span class="s">{</span>
3419 3406 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomSpecificationToMatch</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3420 3407 <span class="k">my</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomSpecificationMatched</span><span class="cm">,</span> <span class="i">$AtomicInvariantMatched</span><span class="cm">,</span> <span class="i">$FirstMatch</span><span class="s">)</span><span class="sc">;</span>
3421 3408
3422 3409 <span class="c"># Anything to match...</span>
3423 3410 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$AtomSpecificationToMatch</span><span class="s">)</span> &amp;&amp; <span class="i">$AtomSpecificationToMatch</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3424 3411 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
3425 3412 <span class="s">}</span>
3426 3413
3427 3414 <span class="c"># Take out any spaces...</span>
3428 3415 <span class="i">$AtomSpecificationToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
3429 3416
3430 3417 <span class="c"># Match specified atom specifications. For multiple atom specifications in a comma delimited string,</span>
3431 3418 <span class="c"># only one atom specification needs to match for a successful match. It&#39;s up to the caller to make</span>
3432 3419 <span class="c"># sure that the specificaton list is ordered from least to most specific atom specification...</span>
3433 3420 <span class="c">#</span>
3434 3421 <span class="k">for</span> <span class="i">$AtomSpecification</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$AtomSpecificationToMatch</span><span class="s">)</span> <span class="s">{</span>
3435 3422 <span class="i">$AtomSpecificationMatched</span> = <span class="n">1</span><span class="sc">;</span>
3436 3423 <span class="i">$FirstMatch</span> = <span class="n">1</span><span class="sc">;</span>
3437 3424
3438 3425 <span class="c"># Match all atom symbol atomic invariants...</span>
3439 3426 <span class="j">ATOMICINVARIANT:</span> <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$AtomSpecification</span><span class="s">)</span> <span class="s">{</span>
3440 3427 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstMatch</span><span class="s">)</span> <span class="s">{</span>
3441 3428 <span class="c"># Match atom symbol atomic invariant...</span>
3442 3429 <span class="i">$FirstMatch</span> = <span class="n">0</span><span class="sc">;</span>
3443 3430 <span class="i">$AtomicInvariantMatched</span> = <span class="i">$This</span><span class="i">-&gt;_MatchAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="sc">;</span>
3444 3431 <span class="s">}</span>
3445 3432 <span class="k">else</span> <span class="s">{</span>
3446 3433 <span class="c"># Match non atom symbol atomic invariant...</span>
3447 3434 <span class="i">$AtomicInvariantMatched</span> = <span class="i">$This</span><span class="i">-&gt;_MatchNonAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="sc">;</span>
3448 3435 <span class="s">}</span>
3449 3436
3450 3437 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicInvariantMatched</span><span class="s">)</span> <span class="s">{</span>
3451 3438 <span class="c"># No need to match other atomic invariants...</span>
3452 3439 <span class="i">$AtomSpecificationMatched</span> = <span class="n">0</span><span class="sc">;</span>
3453 3440 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span>
3454 3441 <span class="s">}</span>
3455 3442 <span class="s">}</span>
3456 3443
3457 3444 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomSpecificationMatched</span><span class="s">)</span> <span class="s">{</span>
3458 3445 <span class="c"># No need to match other atom specifications...</span>
3459 3446 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
3460 3447 <span class="s">}</span>
3461 3448 <span class="s">}</span>
3462 3449
3463 3450 <span class="c"># Nothing matched...</span>
3464 3451 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3465 3452 <span class="s">}</span>
3466 3453
3467 3454 <span class="c"># Check whether atom matches atom symbol atomic invariant...</span>
3468 3455 <span class="c">#</span>
3469 <a name="_MatchAtomSymbolAtomicInvariant-"></a>3456 <span class="k">sub </span><span class="m">_MatchAtomSymbolAtomicInvariant</span> <span class="s">{</span>
3470 3457 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3471 3458 <span class="k">my</span><span class="s">(</span><span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="s">)</span><span class="sc">;</span>
3472 3459
3473 3460 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
3474 3461 <span class="i">$NegateMatch</span> = <span class="n">0</span><span class="sc">;</span>
3475 3462
3476 3463 <span class="c"># Does match needs to be negated?</span>
3477 3464 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span>
3478 3465 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span>
3479 3466 <span class="i">$AtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span>
3480 3467 <span class="s">}</span>
3481 3468
3482 3469 <span class="j">ATOMICINVARIANT:</span> <span class="s">{</span>
3483 3470 <span class="c"># Any atom match...</span>
3484 3471 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;_IsWildCardAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3485 3472 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span>
3486 3473 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span>
3487 3474 <span class="s">}</span>
3488 3475
3489 3476 <span class="c"># Atomic number match...</span>
3490 3477 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
3491 3478 <span class="i">$AtomicNumber</span> = <span class="i">$AtomicInvariant</span><span class="sc">;</span> <span class="i">$AtomicNumber</span> =~ <span class="q">s/^#//</span><span class="sc">;</span>
3492 3479 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomicNumber</span>} == <span class="i">$AtomicNumber</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3493 3480 <span class="k">last</span> <span class="j">ATOMICINVARIANT</span><span class="sc">;</span>
3494 3481 <span class="s">}</span>
3495 3482
3496 3483 <span class="c"># Atom symbol match...</span>
3497 3484 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomSymbol</span>} =~ <span class="q">/^$AtomicInvariant$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3498 3485 <span class="s">}</span>
3499 3486
3500 3487 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span>
3501 3488 <span class="i">$Status</span> = <span class="i">$Status</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
3502 3489 <span class="s">}</span>
3503 3490
3504 3491 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
3505 3492 <span class="s">}</span>
3506 3493
3507 3494 <span class="c"># Is it a wild card atom symbol atomic invariant?</span>
3508 3495 <span class="c">#</span>
3509 <a name="_IsWildCardAtomSymbolAtomicInvariant-"></a>3496 <span class="k">sub </span><span class="m">_IsWildCardAtomSymbolAtomicInvariant</span> <span class="s">{</span>
3510 3497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3511 3498
3512 3499 <span class="k">return</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(A|\*)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3513 3500 <span class="s">}</span>
3514 3501
3515 3502 <span class="c"># Check whether atom matches non atom symbol atomic invariants...</span>
3516 3503 <span class="c">#</span>
3517 <a name="_MatchNonAtomSymbolAtomicInvariant-"></a>3504 <span class="k">sub </span><span class="m">_MatchNonAtomSymbolAtomicInvariant</span> <span class="s">{</span>
3518 3505 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3519 3506 <span class="k">my</span><span class="s">(</span><span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$UnknownName</span><span class="s">)</span><span class="sc">;</span>
3520 3507
3521 3508 <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$UnknownName</span><span class="s">)</span> = <span class="s">(</span><span class="q">&#39;0&#39;</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
3522 3509
3523 3510 <span class="c"># Does match needs to be negated?</span>
3524 3511 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span>
3525 3512 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span>
3526 3513 <span class="i">$AtomicInvariant</span> =~ <span class="q">s/^!//</span><span class="sc">;</span>
3527 3514 <span class="s">}</span>
3528 3515
3529 3516 <span class="c"># Extract atomic invariant name and any value...</span>
3530 3517 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/[0-9\*]+/</span><span class="s">)</span> <span class="s">{</span>
3531 3518 <span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">$AtomicInvariant</span> =~ <span class="q">/^([a-zA-Z]+)([0-9\-\+\*\&gt;\&lt;\=]+)$/</span><span class="sc">;</span>
3532 3519 <span class="s">}</span>
3533 3520 <span class="k">else</span> <span class="s">{</span>
3534 3521 <span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
3535 3522 <span class="s">}</span>
3536 3523
3537 3524 <span class="j">NAME:</span> <span class="s">{</span>
3538 3525 <span class="c"># Match number of non-hydrogen atom neighbors</span>
3539 3526 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^X$/i</span><span class="s">)</span> <span class="s">{</span>
3540 3527 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="i">$This</span><span class="i">-&gt;GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3541 3528 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3542 3529 <span class="s">}</span>
3543 3530
3544 3531 <span class="c"># Match total number of atom neighbors including missing hydrogens...</span>
3545 3532 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^T$/i</span><span class="s">)</span> <span class="s">{</span>
3546 3533 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">-&gt;GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3547 3534 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3548 3535 <span class="s">}</span>
3549 3536
3550 3537 <span class="c"># Match formal charge...</span>
3551 3538 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^FC$/i</span><span class="s">)</span> <span class="s">{</span>
3552 3539 <span class="k">my</span> <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">-&gt;GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
3553 3540 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">-&gt;_MatchNonAtomSymbolAtomicInvariantValue</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
3554 3541 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3555 3542 <span class="s">}</span>
3556 3543
3557 3544 <span class="c"># Match aromatic annotation indicating whether atom is aromatic...</span>
3558 3545 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^Ar$/i</span><span class="s">)</span> <span class="s">{</span>
3559 3546 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">-&gt;IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3560 3547 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3561 3548 <span class="s">}</span>
3562 3549
3563 3550 <span class="c"># Match number of implicit and explicit hydrogens...</span>
3564 3551 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^H$/i</span><span class="s">)</span> <span class="s">{</span>
3565 3552 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3566 3553 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3567 3554 <span class="s">}</span>
3568 3555
3569 3556 <span class="c"># Match ring atom annotation indicating whether atom is in ring...</span>
3570 3557 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^RA$/i</span><span class="s">)</span> <span class="s">{</span>
3571 3558 <span class="i">$Status</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> ? <span class="i">$This</span><span class="i">-&gt;IsInRingOfSize</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;IsInRing</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="s">)</span><span class="sc">;</span>
3572 3559 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3573 3560 <span class="s">}</span>
3574 3561
3575 3562 <span class="c"># Match number of rings for atom..</span>
3576 3563 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^TR$/i</span><span class="s">)</span> <span class="s">{</span>
3577 3564 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$Value</span> == <span class="i">$This</span><span class="i">-&gt;GetNumOfRings</span><span class="s">(</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>
3578 3565 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3579 3566 <span class="s">}</span>
3580 3567
3581 3568 <span class="c"># Match sum of bond orders to non-hydrogen atom neighbors...</span>
3582 3569 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^BO$/i</span><span class="s">)</span> <span class="s">{</span>
3583 3570 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="i">$This</span><span class="i">-&gt;GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3584 3571 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3585 3572 <span class="s">}</span>
3586 3573
3587 3574 <span class="c"># Match largest bond order of non-hydrogen atom neighbors...</span>
3588 3575 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^LBO$/i</span><span class="s">)</span> <span class="s">{</span>
3589 3576 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="i">$This</span><span class="i">-&gt;GetLargestBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3590 3577 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3591 3578 <span class="s">}</span>
3592 3579
3593 3580 <span class="c"># Match number of single bonds to non-hydrogen atom neighbors...</span>
3594 3581 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^SB$/i</span><span class="s">)</span> <span class="s">{</span>
3595 3582 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="i">$This</span><span class="i">-&gt;GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3596 3583 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3597 3584 <span class="s">}</span>
3598 3585
3599 3586 <span class="c"># Match total number of single bonds to atom neighbors including missing and explicit hydrogens...</span>
3600 3587 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^TSB$/i</span><span class="s">)</span> <span class="s">{</span>
3601 3588 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">-&gt;GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3602 3589 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3603 3590 <span class="s">}</span>
3604 3591
3605 3592 <span class="c"># Match number of double bonds to non-hydrogen atom neighbors...</span>
3606 3593 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^DB$/i</span><span class="s">)</span> <span class="s">{</span>
3607 3594 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="i">$This</span><span class="i">-&gt;GetNumOfDoubleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3608 3595 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3609 3596 <span class="s">}</span>
3610 3597
3611 3598 <span class="c"># Match number of triple bonds to non-hydrogen atom neighbors...</span>
3612 3599 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^TB$/i</span><span class="s">)</span> <span class="s">{</span>
3613 3600 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="i">$This</span><span class="i">-&gt;GetNumOfTripleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3614 3601 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3615 3602 <span class="s">}</span>
3616 3603
3617 3604 <span class="c"># Match number of aromatic bonds to non-hydrogen atom neighbors...</span>
3618 3605 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^AB$/i</span><span class="s">)</span> <span class="s">{</span>
3619 3606 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="i">$This</span><span class="i">-&gt;GetNumOfAromaticBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3620 3607 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3621 3608 <span class="s">}</span>
3622 3609
3623 3610
3624 3611 <span class="c"># Match mass number indicating isotope other than most abundant isotope...</span>
3625 3612 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^MN$/i</span><span class="s">)</span> <span class="s">{</span>
3626 3613 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="i">$This</span><span class="i">-&gt;GetMassNumber</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Value</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3627 3614 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3628 3615 <span class="s">}</span>
3629 3616
3630 3617 <span class="c"># Match spin multiplicity...</span>
3631 3618 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^SM$/i</span><span class="s">)</span> <span class="s">{</span>
3632 3619 <span class="k">my</span> <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">-&gt;GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
3633 3620 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SpinMultiplicity</span><span class="s">)</span> <span class="s">{</span> <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span> <span class="s">}</span>
3634 3621 <span class="i">$Status</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> &amp;&amp; <span class="k">defined</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span> &amp;&amp; <span class="i">$Value</span> == <span class="i">$SpinMultiplicity</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3635 3622 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span>
3636 3623 <span class="s">}</span>
3637 3624
3638 3625 <span class="i">$UnknownName</span> = <span class="n">1</span><span class="sc">;</span>
3639 3626 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;_MatchNonAtomSymbolAtomicInvariant: Unknown atomic invariant $AtomicInvariant...&quot;</span><span class="sc">;</span>
3640 3627 <span class="s">}</span>
3641 3628
3642 3629 <span class="k">if</span> <span class="s">(</span>!<span class="i">$UnknownName</span><span class="s">)</span> <span class="s">{</span>
3643 3630 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span>
3644 3631 <span class="i">$Status</span> = <span class="i">$Status</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
3645 3632 <span class="s">}</span>
3646 3633 <span class="s">}</span>
3647 3634
3648 3635 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
3649 3636 <span class="s">}</span>
3650 3637
3651 3638 <span class="c"># Match atomic invariant value...</span>
3652 3639 <span class="c">#</span>
3653 3640 <span class="c"># Specified value format:</span>
3654 3641 <span class="c"># . +* : Any positive value</span>
3655 3642 <span class="c"># . -* : Any negative value</span>
3656 3643 <span class="c"># . &gt;ValidNumber or &gt;=ValidNumber</span>
3657 3644 <span class="c"># . &lt;ValidNumber or &lt;=ValidNumber</span>
3658 3645 <span class="c"># . Any valid number</span>
3659 3646 <span class="c">#</span>
3660 <a name="_MatchNonAtomSymbolAtomicInvariantValue-"></a>3647 <span class="k">sub </span><span class="m">_MatchNonAtomSymbolAtomicInvariantValue</span> <span class="s">{</span>
3661 3648 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$TargetValue</span><span class="cm">,</span> <span class="i">$SpecifiedValue</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3662 3649 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
3663 3650
3664 3651 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
3665 3652
3666 3653 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$TargetValue</span><span class="s">)</span> &amp;&amp; <span class="k">defined</span><span class="s">(</span><span class="i">$SpecifiedValue</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3667 3654 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
3668 3655 <span class="s">}</span>
3669 3656
3670 3657 <span class="j">VALUE:</span> <span class="s">{</span>
3671 3658 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^\+\*/</span><span class="s">)</span> <span class="s">{</span>
3672 3659 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$TargetValue</span> &gt; <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3673 3660 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span>
3674 3661 <span class="s">}</span>
3675 3662 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^\-\*/</span><span class="s">)</span> <span class="s">{</span>
3676 3663 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$TargetValue</span> &lt; <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3677 3664 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span>
3678 3665 <span class="s">}</span>
3679 3666 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^&gt;/</span><span class="s">)</span> <span class="s">{</span>
3680 3667 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^&gt;=/</span><span class="s">)</span> <span class="s">{</span>
3681 3668 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^&gt;=//</span><span class="sc">;</span>
3682 3669 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> &gt;= <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3683 3670 <span class="s">}</span>
3684 3671 <span class="k">else</span> <span class="s">{</span>
3685 3672 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^&gt;//</span><span class="sc">;</span>
3686 3673 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> &gt; <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3687 3674 <span class="s">}</span>
3688 3675 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span>
3689 3676 <span class="s">}</span>
3690 3677 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^&lt;/</span><span class="s">)</span> <span class="s">{</span>
3691 3678 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^&lt;=/</span><span class="s">)</span> <span class="s">{</span>
3692 3679 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^&lt;=//</span><span class="sc">;</span>
3693 3680 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> &lt;= <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3694 3681 <span class="s">}</span>
3695 3682 <span class="k">else</span> <span class="s">{</span>
3696 3683 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^&lt;//</span><span class="sc">;</span>
3697 3684 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> &lt; <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3698 3685 <span class="s">}</span>
3699 3686 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span>
3700 3687 <span class="s">}</span>
3701 3688 <span class="c"># Default is do perform an equality match...</span>
3702 3689 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$SpecifiedValue</span> == <span class="i">$TargetValue</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3703 3690 <span class="s">}</span>
3704 3691
3705 3692 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
3706 3693 <span class="s">}</span>
3707 3694
3708 3695 <span class="c"># Check whether atoms match bond specifications...</span>
3709 3696 <span class="c">#</span>
3710 <a name="_DoesBondSpecificationMatch-"></a>3697 <span class="k">sub </span><span class="m">_DoesBondSpecificationMatch</span> <span class="s">{</span>
3711 3698 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondSpecificationToMatch</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3712 3699 <span class="k">my</span><span class="s">(</span><span class="i">$BondSpecification</span><span class="cm">,</span> <span class="i">$BondSymbolSpecification</span><span class="cm">,</span> <span class="i">$BondSpecificationMatched</span><span class="s">)</span><span class="sc">;</span>
3713 3700
3714 3701 <span class="c"># Anything to match...</span>
3715 3702 <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">$BondSpecificationToMatch</span><span class="s">)</span> &amp;&amp; <span class="i">$BondSpecificationToMatch</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3716 3703 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
3717 3704 <span class="s">}</span>
3718 3705
3719 3706 <span class="c"># Take out any spaces...</span>
3720 3707 <span class="i">$BondSpecificationToMatch</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
3721 3708
3722 3709 <span class="c"># Match specified bond specifications. For multiple bond specifications in a comma delimited string,</span>
3723 3710 <span class="c"># only one bond specification needs to match for a successful match...</span>
3724 3711 <span class="c">#</span>
3725 3712 <span class="k">for</span> <span class="i">$BondSpecification</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$BondSpecificationToMatch</span><span class="s">)</span> <span class="s">{</span>
3726 3713 <span class="i">$BondSpecificationMatched</span> = <span class="n">1</span><span class="sc">;</span>
3727 3714
3728 3715 <span class="c"># Match all specified bond symbol specifications...</span>
3729 3716 <span class="j">BONDSYMBOL:</span> <span class="k">for</span> <span class="i">$BondSymbolSpecification</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$BondSpecification</span><span class="s">)</span> <span class="s">{</span>
3730 3717 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_MatchBondSymbolSpecification</span><span class="s">(</span><span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondSymbolSpecification</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3731 3718 <span class="c"># No need to match other bond symbol specifications...</span>
3732 3719 <span class="i">$BondSpecificationMatched</span> = <span class="n">0</span><span class="sc">;</span>
3733 3720 <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span>
3734 3721 <span class="s">}</span>
3735 3722 <span class="s">}</span>
3736 3723 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSpecificationMatched</span><span class="s">)</span> <span class="s">{</span>
3737 3724 <span class="c"># No need to try matching other bond specifications...</span>
3738 3725 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
3739 3726 <span class="s">}</span>
3740 3727 <span class="s">}</span>
3741 3728
3742 3729 <span class="c"># Nothing matched...</span>
3743 3730 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
3744 3731 <span class="s">}</span>
3745 3732
3746 3733 <span class="c"># Check whether atoms match bond symbol specification...</span>
3747 3734 <span class="c">#</span>
3748 <a name="_MatchBondSymbolSpecification-"></a>3735 <span class="k">sub </span><span class="m">_MatchBondSymbolSpecification</span> <span class="s">{</span>
3749 3736 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondSymbolSpecification</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3750 3737 <span class="k">my</span><span class="s">(</span><span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondSymbol</span><span class="cm">,</span> <span class="i">$UnknownBondSymbol</span><span class="s">)</span><span class="sc">;</span>
3751 3738
3752 3739 <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$NegateMatch</span><span class="cm">,</span> <span class="i">$UnknownBondSymbol</span><span class="s">)</span> = <span class="s">(</span><span class="q">&#39;0&#39;</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
3753 3740
3754 3741 <span class="c"># Does match needs to be negated?</span>
3755 3742 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbolSpecification</span> =~ <span class="q">/^!/</span><span class="s">)</span> <span class="s">{</span>
3756 3743 <span class="i">$NegateMatch</span> = <span class="n">1</span><span class="sc">;</span>
3757 3744 <span class="i">$BondSymbolSpecification</span> =~ <span class="q">s/^!//</span><span class="sc">;</span>
3758 3745 <span class="s">}</span>
3759 3746 <span class="i">$BondSymbol</span> = <span class="i">$BondSymbolSpecification</span><span class="sc">;</span>
3760 3747 <span class="i">$Bond</span> = <span class="i">$This</span><span class="i">-&gt;GetBondToAtom</span><span class="s">(</span><span class="i">$BondedAtom</span><span class="s">)</span><span class="sc">;</span>
3761 3748
3762 3749 <span class="j">BONDSYMBOL:</span> <span class="s">{</span>
3763 3750 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(-|1|s|Single)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">-&gt;IsSingle</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> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
3764 3751 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(=|2|d|Double)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">-&gt;IsDouble</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> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
3765 3752 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(#|3|t|Triple)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">-&gt;IsTriple</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> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
3766 3753 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(:|a|Ar|Aromatic)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">-&gt;IsAromatic</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> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
3767 3754
3768 3755 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(\@|RB|Ring)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="i">$Bond</span><span class="i">-&gt;IsInRing</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> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
3769 3756
3770 3757 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> =~ <span class="q">/^(\~|\*|Any)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDSYMBOL</span><span class="sc">;</span> <span class="s">}</span>
3771 3758
3772 3759 <span class="i">$UnknownBondSymbol</span> = <span class="n">1</span><span class="sc">;</span>
3773 3760 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;_MatchBondSpecification: Unknown bond specification $BondSymbolSpecification...&quot;</span><span class="sc">;</span>
3774 3761 <span class="s">}</span>
3775 3762
3776 3763 <span class="k">if</span> <span class="s">(</span>!<span class="i">$UnknownBondSymbol</span><span class="s">)</span> <span class="s">{</span>
3777 3764 <span class="k">if</span> <span class="s">(</span><span class="i">$NegateMatch</span><span class="s">)</span> <span class="s">{</span>
3778 3765 <span class="i">$Status</span> = <span class="i">$Status</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
3779 3766 <span class="s">}</span>
3780 3767 <span class="s">}</span>
3781 3768
3782 3769 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
3783 3770 <span class="s">}</span>
3784 3771
3785 3772 <span class="c"># Is it a saturated atom?</span>
3786 3773 <span class="c">#</span>
3787 <a name="IsSaturated-"></a>3774 <span class="k">sub </span><span class="m">IsSaturated</span> <span class="s">{</span>
3788 3775 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3789 3776
3790 3777 <span class="k">return</span> !<span class="i">$This</span><span class="i">-&gt;IsUnsaturated</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
3791 3778 <span class="s">}</span>
3792 3779
3793 3780 <span class="c"># Is it an unsaturated atom containing at least one non-single bond?</span>
3794 3781 <span class="c">#</span>
3795 <a name="IsUnsaturated-"></a>3782 <span class="k">sub </span><span class="m">IsUnsaturated</span> <span class="s">{</span>
3796 3783 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3797 3784 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span><span class="sc">;</span>
3798 3785
3799 3786 <span class="s">(</span><span class="i">$NumOfSingleBonds</span><span class="cm">,</span> <span class="i">$NumOfDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfTripleBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticBonds</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfBondTypesToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
3800 3787
3801 3788 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfDoubleBonds</span> || <span class="i">$NumOfTripleBonds</span> || <span class="i">$NumOfAromaticBonds</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
3802 3789 <span class="s">}</span>
3803 3790
3804 3791 <span class="c"># Is atom in a ring?</span>
3805 3792 <span class="c">#</span>
3806 <a name="IsInRing-"></a>3793 <span class="k">sub </span><span class="m">IsInRing</span> <span class="s">{</span>
3807 3794 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3808 3795
3809 3796 <span class="c"># Is this atom in a molecule?</span>
3810 3797 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3811 3798 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3812 3799 <span class="s">}</span>
3813 3800 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3814 3801 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3815 3802
3816 3803 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_IsAtomInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
3817 3804 <span class="s">}</span>
3818 3805
3819 3806 <span class="c"># Is atom not in a ring?</span>
3820 3807 <span class="c">#</span>
3821 <a name="IsNotInRing-"></a>3808 <span class="k">sub </span><span class="m">IsNotInRing</span> <span class="s">{</span>
3822 3809 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3823 3810
3824 3811 <span class="c"># Is this atom in a molecule?</span>
3825 3812 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3826 3813 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3827 3814 <span class="s">}</span>
3828 3815 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3829 3816 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3830 3817
3831 3818 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_IsAtomNotInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
3832 3819 <span class="s">}</span>
3833 3820
3834 3821 <span class="c"># Is atom only in one ring?</span>
3835 3822 <span class="c">#</span>
3836 <a name="IsOnlyInOneRing-"></a>3823 <span class="k">sub </span><span class="m">IsOnlyInOneRing</span> <span class="s">{</span>
3837 3824 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3838 3825
3839 3826 <span class="c"># Is this atom in a molecule?</span>
3840 3827 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3841 3828 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3842 3829 <span class="s">}</span>
3843 3830 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3844 3831 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3845 3832
3846 3833 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_IsAtomInOnlyOneRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
3847 3834 <span class="s">}</span>
3848 3835
3849 3836 <span class="c"># Is atom in a ring of specific size?</span>
3850 3837 <span class="c">#</span>
3851 <a name="IsInRingOfSize-"></a>3838 <span class="k">sub </span><span class="m">IsInRingOfSize</span> <span class="s">{</span>
3852 3839 <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>
3853 3840
3854 3841 <span class="c"># Is this atom in a molecule?</span>
3855 3842 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3856 3843 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3857 3844 <span class="s">}</span>
3858 3845 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3859 3846 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3860 3847
3861 3848 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_IsAtomInRingOfSize</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
3862 3849 <span class="s">}</span>
3863 3850
3864 3851 <span class="c"># Get size of smallest ring containing the atom...</span>
3865 3852 <span class="c">#</span>
3866 <a name="GetSizeOfSmallestRing-"></a>3853 <span class="k">sub </span><span class="m">GetSizeOfSmallestRing</span> <span class="s">{</span>
3867 3854 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3868 3855
3869 3856 <span class="c"># Is this atom in a molecule?</span>
3870 3857 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3871 3858 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3872 3859 <span class="s">}</span>
3873 3860 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3874 3861 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3875 3862
3876 3863 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetSizeOfSmallestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
3877 3864 <span class="s">}</span>
3878 3865
3879 3866 <span class="c"># Get size of largest ring containing the atom...</span>
3880 3867 <span class="c">#</span>
3881 <a name="GetSizeOfLargestRing-"></a>3868 <span class="k">sub </span><span class="m">GetSizeOfLargestRing</span> <span class="s">{</span>
3882 3869 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3883 3870
3884 3871 <span class="c"># Is this atom in a molecule?</span>
3885 3872 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3886 3873 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3887 3874 <span class="s">}</span>
3888 3875 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3889 3876 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3890 3877
3891 3878 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetSizeOfLargestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
3892 3879 <span class="s">}</span>
3893 3880
3894 3881 <span class="c"># Get number of rings containing the atom...</span>
3895 3882 <span class="c">#</span>
3896 <a name="GetNumOfRings-"></a>3883 <span class="k">sub </span><span class="m">GetNumOfRings</span> <span class="s">{</span>
3897 3884 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3898 3885
3899 3886 <span class="c"># Is this atom in a molecule?</span>
3900 3887 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3901 3888 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3902 3889 <span class="s">}</span>
3903 3890 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3904 3891 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3905 3892
3906 3893 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetNumOfAtomRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
3907 3894 <span class="s">}</span>
3908 3895
3909 3896 <span class="c"># Get number of rings with odd size containing the atom...</span>
3910 3897 <span class="c">#</span>
3911 <a name="GetNumOfRingsWithOddSize-"></a>3898 <span class="k">sub </span><span class="m">GetNumOfRingsWithOddSize</span> <span class="s">{</span>
3912 3899 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3913 3900
3914 3901 <span class="c"># Is this atom in a molecule?</span>
3915 3902 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3916 3903 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3917 3904 <span class="s">}</span>
3918 3905 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3919 3906 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3920 3907
3921 3908 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetNumOfAtomRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
3922 3909 <span class="s">}</span>
3923 3910
3924 3911 <span class="c"># Get number of rings with even size containing the atom...</span>
3925 3912 <span class="c">#</span>
3926 <a name="GetNumOfRingsWithEvenSize-"></a>3913 <span class="k">sub </span><span class="m">GetNumOfRingsWithEvenSize</span> <span class="s">{</span>
3927 3914 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3928 3915
3929 3916 <span class="c"># Is this atom in a molecule?</span>
3930 3917 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3931 3918 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3932 3919 <span class="s">}</span>
3933 3920 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3934 3921 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3935 3922
3936 3923 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetNumOfAtomRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
3937 3924 <span class="s">}</span>
3938 3925
3939 3926 <span class="c"># Get number of rings with specified size containing the atom...</span>
3940 3927 <span class="c">#</span>
3941 <a name="GetNumOfRingsWithSize-"></a>3928 <span class="k">sub </span><span class="m">GetNumOfRingsWithSize</span> <span class="s">{</span>
3942 3929 <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>
3943 3930
3944 3931 <span class="c"># Is this atom in a molecule?</span>
3945 3932 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3946 3933 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3947 3934 <span class="s">}</span>
3948 3935 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3949 3936 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3950 3937
3951 3938 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetNumOfAtomRingsWithSize</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
3952 3939
3953 3940 <span class="s">}</span>
3954 3941
3955 3942 <span class="c"># Get number of rings with size less than specified containing the atom...</span>
3956 3943 <span class="c">#</span>
3957 <a name="GetNumOfRingsWithSizeLessThan-"></a>3944 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeLessThan</span> <span class="s">{</span>
3958 3945 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3959 3946
3960 3947 <span class="c"># Is this atom in a molecule?</span>
3961 3948 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3962 3949 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3963 3950 <span class="s">}</span>
3964 3951 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3965 3952 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3966 3953
3967 3954 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetNumOfAtomRingsWithSizeLessThan</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="sc">;</span>
3968 3955 <span class="s">}</span>
3969 3956
3970 3957 <span class="c"># Get number of rings with size greater than specified size containing the atom...</span>
3971 3958 <span class="c">#</span>
3972 <a name="GetNumOfRingsWithSizeGreaterThan-"></a>3959 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeGreaterThan</span> <span class="s">{</span>
3973 3960 <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>
3974 3961
3975 3962 <span class="c"># Is this atom in a molecule?</span>
3976 3963 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3977 3964 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3978 3965 <span class="s">}</span>
3979 3966 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3980 3967 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3981 3968
3982 3969 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetNumOfAtomRingsWithSizeGreaterThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
3983 3970 <span class="s">}</span>
3984 3971
3985 3972 <span class="c"># Get all rings an array of references to arrays containing ring atoms...</span>
3986 3973 <span class="c">#</span>
3987 <a name="GetRings-"></a>3974 <span class="k">sub </span><span class="m">GetRings</span> <span class="s">{</span>
3988 3975 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
3989 3976
3990 3977 <span class="c"># Is this atom in a molecule?</span>
3991 3978 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
3992 3979 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
3993 3980 <span class="s">}</span>
3994 3981 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
3995 3982 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
3996 3983
3997 3984 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetAtomRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
3998 3985 <span class="s">}</span>
3999 3986
4000 3987 <span class="c"># Get smallest ring as an array containing ring atoms...</span>
4001 3988 <span class="c">#</span>
4002 <a name="GetSmallestRing-"></a>3989 <span class="k">sub </span><span class="m">GetSmallestRing</span> <span class="s">{</span>
4003 3990 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4004 3991
4005 3992 <span class="c"># Is this atom in a molecule?</span>
4006 3993 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4007 3994 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4008 3995 <span class="s">}</span>
4009 3996 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
4010 3997 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
4011 3998
4012 3999 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetSmallestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
4013 4000 <span class="s">}</span>
4014 4001
4015 4002 <span class="c"># Get largest ring as an array containing ring atoms...</span>
4016 4003 <span class="c">#</span>
4017 <a name="GetLargestRing-"></a>4004 <span class="k">sub </span><span class="m">GetLargestRing</span> <span class="s">{</span>
4018 4005 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4019 4006
4020 4007 <span class="c"># Is this atom in a molecule?</span>
4021 4008 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4022 4009 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4023 4010 <span class="s">}</span>
4024 4011 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
4025 4012 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
4026 4013
4027 4014 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetLargestAtomRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
4028 4015 <span class="s">}</span>
4029 4016
4030 4017 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span>
4031 4018 <span class="c">#</span>
4032 <a name="GetRingsWithOddSize-"></a>4019 <span class="k">sub </span><span class="m">GetRingsWithOddSize</span> <span class="s">{</span>
4033 4020 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4034 4021
4035 4022 <span class="c"># Is this atom in a molecule?</span>
4036 4023 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4037 4024 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4038 4025 <span class="s">}</span>
4039 4026 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
4040 4027 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
4041 4028
4042 4029 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetAtomRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
4043 4030 <span class="s">}</span>
4044 4031
4045 4032 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span>
4046 4033 <span class="c">#</span>
4047 <a name="GetRingsWithEvenSize-"></a>4034 <span class="k">sub </span><span class="m">GetRingsWithEvenSize</span> <span class="s">{</span>
4048 4035 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4049 4036
4050 4037 <span class="c"># Is this atom in a molecule?</span>
4051 4038 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4052 4039 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4053 4040 <span class="s">}</span>
4054 4041 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
4055 4042 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
4056 4043
4057 4044 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetAtomRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
4058 4045 <span class="s">}</span>
4059 4046
4060 4047 <span class="c"># Get rings with specified size as an array of references to arrays containing ring atoms...</span>
4061 4048 <span class="c">#</span>
4062 <a name="GetRingsWithSize-"></a>4049 <span class="k">sub </span><span class="m">GetRingsWithSize</span> <span class="s">{</span>
4063 4050 <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>
4064 4051
4065 4052 <span class="c"># Is this atom in a molecule?</span>
4066 4053 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4067 4054 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4068 4055 <span class="s">}</span>
4069 4056 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
4070 4057 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
4071 4058
4072 4059 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetAtomRingsWithSize</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
4073 4060 <span class="s">}</span>
4074 4061
4075 4062 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span>
4076 4063 <span class="c">#</span>
4077 <a name="GetRingsWithSizeLessThan-"></a>4064 <span class="k">sub </span><span class="m">GetRingsWithSizeLessThan</span> <span class="s">{</span>
4078 4065 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4079 4066
4080 4067 <span class="c"># Is this atom in a molecule?</span>
4081 4068 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4082 4069 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4083 4070 <span class="s">}</span>
4084 4071 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
4085 4072 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
4086 4073
4087 4074 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetAtomRingsWithSizeLessThan</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="sc">;</span>
4088 4075 <span class="s">}</span>
4089 4076
4090 4077 <span class="c"># Get rings with size greater than specfied size as an array of references to arrays containing ring atoms...</span>
4091 4078 <span class="c">#</span>
4092 <a name="GetRingsWithSizeGreaterThan-"></a>4079 <span class="k">sub </span><span class="m">GetRingsWithSizeGreaterThan</span> <span class="s">{</span>
4093 4080 <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>
4094 4081
4095 4082 <span class="c"># Is this atom in a molecule?</span>
4096 4083 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4097 4084 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
4098 4085 <span class="s">}</span>
4099 4086 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
4100 4087 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
4101 4088
4102 4089 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetAtomRingsWithSizeGreaterThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
4103 4090 <span class="s">}</span>
4104 4091
4105 4092 <span class="c"># Get next object ID...</span>
4106 <a name="_GetNewObjectID-"></a>4093 <span class="k">sub </span><span class="m">_GetNewObjectID</span> <span class="s">{</span>
4107 4094 <span class="i">$ObjectID</span>++<span class="sc">;</span>
4108 4095 <span class="k">return</span> <span class="i">$ObjectID</span><span class="sc">;</span>
4109 4096 <span class="s">}</span>
4110 4097
4111 4098 <span class="c"># Return a string containing vertices, edges and other properties...</span>
4112 <a name="StringifyAtom-"></a>4099 <span class="k">sub </span><span class="m">StringifyAtom</span> <span class="s">{</span>
4113 4100 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4114 4101 <span class="k">my</span><span class="s">(</span><span class="i">$AtomString</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$XYZVector</span><span class="cm">,</span> <span class="i">$AtomicWeight</span><span class="cm">,</span> <span class="i">$ExactMass</span><span class="cm">,</span> <span class="i">$NumOfNeighbors</span><span class="cm">,</span> <span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$Valence</span><span class="cm">,</span> <span class="i">$MissingHydrogens</span><span class="cm">,</span> <span class="i">$TotalHydrogens</span><span class="cm">,</span> <span class="i">$ImplicitHydrogens</span><span class="cm">,</span> <span class="i">$ExplicitHydrogens</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$SpinMultiplicity</span><span class="cm">,</span> <span class="i">$FreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$StereoCenter</span><span class="cm">,</span> <span class="i">$StereoCenterStatus</span><span class="cm">,</span> <span class="i">$StereoChemistry</span><span class="cm">,</span> <span class="i">$StereochemistryString</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$NumOfRings</span><span class="cm">,</span> <span class="i">$AromaticAtom</span><span class="s">)</span><span class="sc">;</span>
4115 4102
4116 4103 <span class="i">$ID</span> = <span class="i">$This</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4117 4104 <span class="i">$Name</span> = <span class="i">$This</span><span class="i">-&gt;GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4118 4105 <span class="i">$AtomSymbol</span> = <span class="i">$This</span><span class="i">-&gt;GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4119 4106 <span class="i">$AtomicNumber</span> = <span class="i">$This</span><span class="i">-&gt;GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4120 4107 <span class="i">$XYZVector</span> = <span class="i">$This</span><span class="i">-&gt;GetXYZVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4121 4108
4122 4109 <span class="i">$AtomicWeight</span> = <span class="i">$This</span><span class="i">-&gt;GetAtomicWeight</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4123 4110 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$AtomicWeight</span><span class="s">)</span> <span class="s">{</span>
4124 4111 <span class="i">$AtomicWeight</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4125 4112 <span class="s">}</span>
4126 4113 <span class="i">$ExactMass</span> = <span class="i">$This</span><span class="i">-&gt;GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4127 4114 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ExactMass</span><span class="s">)</span> <span class="s">{</span>
4128 4115 <span class="i">$ExactMass</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4129 4116 <span class="s">}</span>
4130 4117 <span class="i">$NumOfNeighbors</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4131 4118 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NumOfNeighbors</span><span class="s">)</span> <span class="s">{</span>
4132 4119 <span class="i">$NumOfNeighbors</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4133 4120 <span class="s">}</span>
4134 4121 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4135 4122 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NumOfBonds</span><span class="s">)</span> <span class="s">{</span>
4136 4123 <span class="i">$NumOfBonds</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4137 4124 <span class="s">}</span>
4138 4125 <span class="i">$Valence</span> = <span class="i">$This</span><span class="i">-&gt;GetValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4139 4126 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Valence</span><span class="s">)</span> <span class="s">{</span>
4140 4127 <span class="i">$Valence</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4141 4128 <span class="s">}</span>
4142 4129
4143 4130 <span class="i">$MissingHydrogens</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4144 4131 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$MissingHydrogens</span><span class="s">)</span> <span class="s">{</span>
4145 4132 <span class="i">$MissingHydrogens</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4146 4133 <span class="s">}</span>
4147 4134 <span class="i">$TotalHydrogens</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4148 4135 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$TotalHydrogens</span><span class="s">)</span> <span class="s">{</span>
4149 4136 <span class="i">$TotalHydrogens</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4150 4137 <span class="s">}</span>
4151 4138 <span class="i">$ImplicitHydrogens</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4152 4139 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ImplicitHydrogens</span><span class="s">)</span> <span class="s">{</span>
4153 4140 <span class="i">$ImplicitHydrogens</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4154 4141 <span class="s">}</span>
4155 4142 <span class="i">$ExplicitHydrogens</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4156 4143 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ExplicitHydrogens</span><span class="s">)</span> <span class="s">{</span>
4157 4144 <span class="i">$ExplicitHydrogens</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4158 4145 <span class="s">}</span>
4159 4146
4160 4147 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">-&gt;GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4161 4148 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$FormalCharge</span><span class="s">)</span> <span class="s">{</span>
4162 4149 <span class="i">$FormalCharge</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4163 4150 <span class="s">}</span>
4164 4151 <span class="i">$Charge</span> = <span class="i">$This</span><span class="i">-&gt;GetCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4165 4152 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Charge</span><span class="s">)</span> <span class="s">{</span>
4166 4153 <span class="i">$Charge</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4167 4154 <span class="s">}</span>
4168 4155
4169 4156 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">-&gt;GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4170 4157 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$SpinMultiplicity</span><span class="s">)</span> <span class="s">{</span>
4171 4158 <span class="i">$SpinMultiplicity</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4172 4159 <span class="s">}</span>
4173 4160 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">-&gt;GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4174 4161 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$FreeRadicalElectrons</span><span class="s">)</span> <span class="s">{</span>
4175 4162 <span class="i">$FreeRadicalElectrons</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4176 4163 <span class="s">}</span>
4177 4164
4178 4165 <span class="i">$RingAtom</span> = <span class="i">$This</span><span class="i">-&gt;IsInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4179 4166 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$RingAtom</span><span class="s">)</span> <span class="s">{</span>
4180 4167 <span class="i">$RingAtom</span> = <span class="i">$RingAtom</span> ? <span class="q">&#39;Yes&#39;</span> <span class="co">:</span> <span class="q">&#39;No&#39;</span><span class="sc">;</span>
4181 4168 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4182 4169 <span class="s">}</span>
4183 4170 <span class="k">else</span> <span class="s">{</span>
4184 4171 <span class="i">$RingAtom</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4185 4172 <span class="i">$NumOfRings</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4186 4173 <span class="s">}</span>
4187 4174
4188 4175 <span class="i">$AromaticAtom</span> = <span class="i">$This</span><span class="i">-&gt;GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4189 4176 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticAtom</span><span class="s">)</span> <span class="s">{</span>
4190 4177 <span class="i">$AromaticAtom</span> = <span class="i">$AromaticAtom</span> ? <span class="q">&#39;Yes&#39;</span> <span class="co">:</span> <span class="q">&#39;No&#39;</span><span class="sc">;</span>
4191 4178 <span class="s">}</span>
4192 4179 <span class="k">else</span> <span class="s">{</span>
4193 4180 <span class="i">$AromaticAtom</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4194 4181 <span class="s">}</span>
4195 4182
4196 4183 <span class="i">$StereochemistryString</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
4197 4184 <span class="i">$StereoCenter</span> = <span class="i">$This</span><span class="i">-&gt;GetStereoCenter</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4198 4185 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$StereoCenter</span><span class="s">)</span> <span class="s">{</span>
4199 4186 <span class="i">$StereoCenterStatus</span> = <span class="i">$This</span><span class="i">-&gt;IsStereoCenter</span><span class="s">(</span><span class="s">)</span> ? <span class="q">&#39;Yes&#39;</span> <span class="co">:</span> <span class="q">&#39;No&#39;</span><span class="sc">;</span>
4200 4187 <span class="i">$StereoChemistry</span> = <span class="i">$This</span><span class="i">-&gt;GetStereochemistry</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4201 4188 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$StereoChemistry</span><span class="s">)</span> <span class="s">{</span>
4202 4189 <span class="i">$StereoChemistry</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
4203 4190 <span class="s">}</span>
4204 4191 <span class="i">$StereochemistryString</span> = <span class="q">&quot;StereoCenter: $StereoCenterStatus; Stereochemistry: $StereoChemistry&quot;</span><span class="sc">;</span>
4205 4192 <span class="s">}</span>
4206 4193
4207 4194 <span class="i">$AtomString</span> = <span class="q">&quot;Atom: ID: $ID; Name: \&quot;$Name\&quot;; AtomSymbol: \&quot;$AtomSymbol\&quot;; AtomicNumber: $AtomicNumber; XYZ: $XYZVector; AtomicWeight: $AtomicWeight; ExactMass: $ExactMass; NumOfNeighbors: $NumOfNeighbors; NumOfBonds: $NumOfBonds; Valence: $Valence; MissingHydrogens: $MissingHydrogens; TotalHydrogens: $TotalHydrogens; ImplicitHydrogens: $ImplicitHydrogens; ExplicitHydrogens: $ExplicitHydrogens; FormalCharge: $FormalCharge; Charge: $Charge; SpinMultiplicity: $SpinMultiplicity; FreeRadicalElectrons: $FreeRadicalElectrons; RingAtom: $RingAtom; NumOfAtomRings: $NumOfRings; AromaticAtom: $AromaticAtom&quot;</span><span class="sc">;</span>
4208 4195
4209 4196 <span class="k">if</span> <span class="s">(</span><span class="i">$StereochemistryString</span><span class="s">)</span> <span class="s">{</span>
4210 4197 <span class="i">$AtomString</span> .= <span class="q">&quot;; $StereochemistryString&quot;</span><span class="sc">;</span>
4211 4198 <span class="s">}</span>
4212 4199
4213 4200 <span class="k">return</span> <span class="i">$AtomString</span><span class="sc">;</span>
4214 4201 <span class="s">}</span>
4215 4202
4216 4203 <span class="c"># Load appropriate atom data files from &lt;MayaChemTools&gt;/lib directory used by various</span>
4217 4204 <span class="c"># object methods in the current class...</span>
4218 4205 <span class="c">#</span>
4219 <a name="_LoadAtomClassData-"></a>4206 <span class="k">sub </span><span class="m">_LoadAtomClassData</span> <span class="s">{</span>
4220 4207 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span>
4221 4208
4222 4209 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4223 4210
4224 4211 <span class="i">_LoadAtomValenceModelData</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span>
4225 4212
4226 4213 <span class="s">}</span>
4227 4214
4228 4215 <span class="c">#</span>
4229 4216 <span class="c"># Load data for supported valence models...</span>
4230 4217 <span class="c">#</span>
4231 <a name="_LoadAtomValenceModelData-"></a>4218 <span class="k">sub </span><span class="m">_LoadAtomValenceModelData</span> <span class="s">{</span>
4232 4219 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4233 4220 <span class="k">my</span><span class="s">(</span><span class="i">$MDLValenceModelDataFile</span><span class="cm">,</span> <span class="i">$DaylightValenceModelDataFile</span><span class="s">)</span><span class="sc">;</span>
4234 4221
4235 4222 <span class="i">%MDLValenceModelDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4236 4223 <span class="i">%DaylightValenceModelDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4237 4224
4238 4225 <span class="i">$MDLValenceModelDataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">&quot;/data/MDLValenceModelData.csv&quot;</span><span class="sc">;</span>
4239 4226 <span class="i">$DaylightValenceModelDataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">&quot;/data/DaylightValenceModelData.csv&quot;</span><span class="sc">;</span>
4240 4227
4241 4228 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">&quot;$MDLValenceModelDataFile&quot;</span><span class="s">)</span> <span class="s">{</span>
4242 4229 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}::_LoadAtomValenceModelData: MayaChemTools package file, $MDLValenceModelDataFile, is missing: Possible installation problems...&quot;</span><span class="sc">;</span>
4243 4230 <span class="s">}</span>
4244 4231
4245 4232 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">&quot;$DaylightValenceModelDataFile&quot;</span><span class="s">)</span> <span class="s">{</span>
4246 4233 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}::_LoadAtomValenceModelData: MayaChemTools package file, $DaylightValenceModelDataFile, is missing: Possible installation problems...&quot;</span><span class="sc">;</span>
4247 4234 <span class="s">}</span>
4248 4235
4249 4236 <span class="i">_LoadValenceModelDataFile</span><span class="s">(</span><span class="i">$MDLValenceModelDataFile</span><span class="cm">,</span> \<span class="i">%MDLValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span>
4250 4237 <span class="i">_LoadValenceModelDataFile</span><span class="s">(</span><span class="i">$DaylightValenceModelDataFile</span><span class="cm">,</span> \<span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span>
4251 4238
4252 4239 <span class="s">}</span>
4253 4240
4254 4241 <span class="c">#</span>
4255 4242 <span class="c"># Load valence model data file...</span>
4256 4243 <span class="c">#</span>
4257 <a name="_LoadValenceModelDataFile-"></a>4244 <span class="k">sub </span><span class="m">_LoadValenceModelDataFile</span> <span class="s">{</span>
4258 4245 <span class="k">my</span><span class="s">(</span><span class="i">$DataFile</span><span class="cm">,</span> <span class="i">$DataMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4259 4246
4260 4247 <span class="c"># File format:</span>
4261 4248 <span class="c">#</span>
4262 4249 <span class="c"># &quot;AtomicNumber&quot;,&quot;ElementSymbol&quot;,&quot;FormalCharge&quot;,&quot;CommomValences&quot;</span>
4263 4250 <span class="c">#</span>
4264 4251 <span class="k">my</span><span class="s">(</span><span class="i">$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">@ColLabels</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
4265 4252
4266 4253 <span class="i">$InDelim</span> = <span class="q">&quot;\,&quot;</span><span class="sc">;</span>
4267 4254 <span class="k">open</span> <span class="w">DATAFILE</span><span class="cm">,</span> <span class="q">&quot;$DataFile&quot;</span> <span class="k">or</span> <span class="w">croak</span> <span class="q">&quot;Couldn&#39;t open $DataFile: $! ...&quot;</span><span class="sc">;</span>
4268 4255
4269 4256 <span class="c"># Skip lines up to column labels...</span>
4270 4257 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$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>
4271 4258 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
4272 4259 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span>
4273 4260 <span class="s">}</span>
4274 4261 <span class="s">}</span>
4275 4262 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
4276 4263 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span>
4277 4264
4278 4265 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="s">)</span><span class="sc">;</span>
4279 4266
4280 4267 <span class="c"># Process element data...</span>
4281 4268 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*DATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4282 4269 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
4283 4270 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
4284 4271 <span class="s">}</span>
4285 4272 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4286 4273 <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>
4287 4274 <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>
4288 4275 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}::_LoadValenceModelDataFile: The number of data fields, @LineWords, in $DataFile must be $NumOfCols.\nLine: $Line...&quot;</span><span class="sc">;</span>
4289 4276 <span class="s">}</span>
4290 4277
4291 4278 <span class="s">(</span><span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$ElementSymbol</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="s">)</span> = <span class="i">@LineWords</span><span class="sc">;</span>
4292 4279
4293 4280 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataMapRef</span>-&gt;{<span class="i">$AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span>
4294 4281 <span class="c"># Additional data for an element...</span>
4295 4282 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataMapRef</span>-&gt;{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}<span class="s">)</span> <span class="s">{</span>
4296 4283 <span class="c"># Duplicate data entries for an element...</span>
4297 4284 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}::_LoadValenceModelDataFile: Ignoring valence data for element with atomic number $AtomicNumber and formal charge $FormalCharge in data file $DataFile: It has already been loaded.\nLine: $Line...&quot;</span><span class="sc">;</span>
4298 4285 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
4299 4286 <span class="s">}</span>
4300 4287 <span class="s">}</span>
4301 4288 <span class="k">else</span> <span class="s">{</span>
4302 4289 <span class="c"># Data for a new element...</span>
4303 4290 <span class="i">%</span>{<span class="i">$DataMapRef</span>-&gt;{<span class="i">$AtomicNumber</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4304 4291 <span class="s">}</span>
4305 4292
4306 4293 <span class="i">%</span>{<span class="i">$DataMapRef</span>-&gt;{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4307 4294 <span class="i">$DataMapRef</span>-&gt;{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">ElementSymbol</span>} = <span class="i">$ElementSymbol</span><span class="sc">;</span>
4308 4295
4309 4296 <span class="i">@</span>{<span class="i">$DataMapRef</span>-&gt;{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">CommonValences</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4310 4297 <span class="i">@</span>{<span class="i">$DataMapRef</span>-&gt;{<span class="i">$AtomicNumber</span>}{<span class="i">$FormalCharge</span>}{<span class="w">CommonValences</span>}} = <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> &lt;=&gt; <span class="i">$b</span> <span class="s">}</span> <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$CommonValences</span><span class="sc">;</span>
4311 4298 <span class="s">}</span>
4312 4299 <span class="k">close</span> <span class="w">DATAFILE</span><span class="sc">;</span>
4313 4300 <span class="s">}</span>
4314 4301
4315 <a name="EOF-"></a></pre>
4316 <p>&nbsp;</p>
4317 <br />
4318 <center>
4319 <img src="../../../images/h2o2.png">
4320 </center>
4321 </body>
4322 </html>