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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Code:Atom.pm</title> | |
4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
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13 <pre> | |
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 <msud@san.rr.com></span> | |
21 8 <span class="c">#</span> | |
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
23 10 <span class="c">#</span> | |
24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
25 12 <span class="c">#</span> | |
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
29 16 <span class="c"># later version.</span> | |
30 17 <span class="c">#</span> | |
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
34 21 <span class="c"># details.</span> | |
35 22 <span class="c">#</span> | |
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
40 27 <span class="c">#</span> | |
41 28 | |
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
45 32 <span class="k">use</span> <span class="w">Storable</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
46 33 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
47 34 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span> | |
48 35 <span class="k">use</span> <span class="w">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">=></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">$ObjectID</span><span class="cm">,</span> <span class="i">%MDLValenceModelDataMap</span><span class="cm">,</span> <span class="i">%DaylightValenceModelDataMap</span><span class="s">)</span><span class="sc">;</span> | |
65 52 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
66 53 | |
67 54 <span class="c"># Overload Perl functions...</span> | |
68 55 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyAtom'</span><span class="sc">;</span> | |
69 56 | |
70 57 <span class="c"># Class constructor...</span> | |
71 <a name="new-"></a> 58 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
72 59 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->_InitializeAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
78 65 | |
79 66 <span class="i">$This</span><span class="i">->_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">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
88 75 | |
89 76 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> | |
90 77 <span class="c"># are implemented on-demand using ObjectProperty class.</span> | |
91 78 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span> | |
92 79 <span class="i">$This</span>->{<span class="w">Name</span>} = <span class="q">"Atom ${ObjectID}"</span><span class="sc">;</span> | |
93 80 <span class="i">$This</span>->{<span class="w">AtomSymbol</span>} = <span class="q">''</span><span class="sc">;</span> | |
94 81 <span class="i">$This</span>->{<span class="w">AtomicNumber</span>} = <span class="n">0</span><span class="sc">;</span> | |
95 82 <span class="i">$This</span>->{<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">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
105 92 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
106 93 <span class="s">}</span> | |
107 94 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'AtomSymbol'</span>}<span class="s">)</span> <span class="s">{</span> | |
108 95 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Atom object instantiated without setting atom symbol..."</span><span class="sc">;</span> | |
109 96 <span class="s">}</span> | |
110 97 | |
111 98 <span class="k">return</span> <span class="i">$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">"Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> | |
131 118 | |
132 119 <span class="k">return</span> <span class="i">$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">"Warning: ${ClassName}->SetMolecule: Molecule property can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> | |
140 127 | |
141 128 <span class="k">return</span> <span class="i">$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">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$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'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">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
155 142 | |
156 143 <span class="k">return</span> <span class="i">$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's explicity</span> | |
166 153 <span class="c"># set using "MassNumber" 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>->{<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>->{<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">"Warning: ${ClassName}->SetAtomicNumber: Didn't set atomic number: Invalid atomic number, $AtomicNumber, specified..."</span><span class="sc">;</span> | |
188 175 <span class="k">return</span><span class="sc">;</span> | |
189 176 <span class="s">}</span> | |
190 177 <span class="i">$This</span>->{<span class="w">AtomicNumber</span>} = <span class="i">$AtomicNumber</span><span class="sc">;</span> | |
191 178 <span class="i">$This</span>->{<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">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'StereoCenter'</span><span class="cm">,</span> <span class="i">$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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'StereoCenter'</span><span class="s">)</span><span class="sc">;</span> | |
213 200 | |
214 201 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$StereoCenter</span><span class="s">)</span> && <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">"Warning: ${ClassName}->SetStereochemistry: Assigning non-supported Stereochemistry value of $Stereochemistry. Supported values: R, S..."</span><span class="sc">;</span> | |
236 223 <span class="s">}</span> | |
237 224 | |
238 225 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'StereoCenter'</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
239 226 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'Stereochemistry'</span><span class="cm">,</span> <span class="i">$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">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
250 237 <span class="i">$AtomSymbol</span> = <span class="i">$This</span>->{<span class="w">AtomSymbol</span>}<span class="sc">;</span> | |
251 238 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span> | |
252 239 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMassNumber: Didn't set mass number: Non standard atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol..."</span><span class="sc">;</span> | |
253 240 <span class="k">return</span><span class="sc">;</span> | |
254 241 <span class="s">}</span> | |
255 242 <span class="k">if</span> <span class="s">(</span>!<span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$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">"Warning: ${ClassName}->SetMassNumber: Unknown mass number, $MassNumber, specified for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope..."</span><span class="sc">;</span> | |
257 244 <span class="s">}</span> | |
258 245 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'MassNumber'</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">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
270 257 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span> | |
271 258 <span class="s">}</span> | |
272 259 | |
273 260 <span class="c"># Is it an element symbol?</span> | |
274 261 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
275 262 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'AtomicWeight'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
292 279 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'AtomicWeight'</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>->{<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">->HasProperty</span><span class="s">(</span><span class="q">'ExactMass'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
315 302 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ExactMass'</span><span class="s">)</span><span class="sc">;</span> | |
316 303 <span class="s">}</span> | |
317 304 | |
318 305 <span class="c"># Is it an element symbol?</span> | |
319 306 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> = <span class="i">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
320 307 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
326 313 <span class="k">my</span><span class="s">(</span><span class="i">$MassNumber</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span> | |
327 314 <span class="k">if</span> <span class="s">(</span><span class="i">PeriodicTable::IsElementNaturalIsotopeMassNumber</span><span class="s">(</span><span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</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">->GetProperty</span><span class="s">(</span><span class="q">'FormalCharge'</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">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</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">->GetProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
368 355 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</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">"Warning: ${ClassName}->GetSpinMultiplicity: It's not possible to determine spin multiplicity from the specified free radical electrons value, $FreeRadicalElectrons. It has been set to 0..."</span><span class="sc">;</span> | |
375 362 <span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
403 390 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="sc">;</span> | |
404 391 <span class="k">return</span> <span class="k">defined</span><span class="s">(</span><span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span> | |
410 397 | |
411 398 <span class="j">SPINMULTIPLICITY:</span> <span class="s">{</span> | |
412 399 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Warning: ${ClassName}->GetFreeRadicalElectrons: It's not possible to determine free radical electrons from the specified spin multiplicity value, $FreeRadicalElectrons. It has been set to 0..."</span><span class="sc">;</span> | |
416 403 <span class="i">$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">"Warning: ${ClassName}->SetXYZ: No values specified..."</span><span class="sc">;</span> | |
433 420 <span class="k">return</span><span class="sc">;</span> | |
434 421 <span class="s">}</span> | |
435 422 | |
436 423 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->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">"Warning: ${ClassName}->SetX: Undefined X value..."</span><span class="sc">;</span> | |
446 433 <span class="k">return</span><span class="sc">;</span> | |
447 434 <span class="s">}</span> | |
448 435 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->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">"Warning: ${ClassName}->SetY: Undefined Y value..."</span><span class="sc">;</span> | |
458 445 <span class="k">return</span><span class="sc">;</span> | |
459 446 <span class="s">}</span> | |
460 447 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->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">"Warning: ${ClassName}->SetZ: Undefined Z value..."</span><span class="sc">;</span> | |
470 457 <span class="k">return</span><span class="sc">;</span> | |
471 458 <span class="s">}</span> | |
472 459 <span class="i">$This</span>->{<span class="w">XYZ</span>}<span class="i">->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>->{<span class="w">XYZ</span>}<span class="i">->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>->{<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>->{<span class="w">XYZ</span>}<span class="i">->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>->{<span class="w">XYZ</span>}<span class="i">->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>->{<span class="w">XYZ</span>}<span class="i">->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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
525 512 | |
526 513 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
535 522 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
536 523 <span class="s">}</span> | |
537 524 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
538 525 | |
539 526 <span class="k">if</span> <span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span> <span class="s">{</span> | |
540 527 <span class="k">return</span> <span class="i">$This</span><span class="i">->_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">$This</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
544 531 <span class="s">}</span> | |
545 532 <span class="s">}</span> | |
546 533 | |
547 534 <span class="c"># Get atom neighbor objects as array. In scalar conetxt, return number of neighbors...</span> | |
548 <a name="_GetAtomNeighbors-"></a> 535 <span class="k">sub </span><span class="m">_GetAtomNeighbors</span> <span class="s">{</span> | |
549 536 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$Molecule</span><span class="i">->_GetAtomNeighbors</span><span class="s">(</span><span class="i">$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">$ExcludeNeighbor</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
562 549 <span class="i">$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">->_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">$Neighbor</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
570 557 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$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">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="i">@ExcludeNeighbors</span><span class="s">)</span><span class="sc">;</span> | |
592 579 | |
593 580 <span class="c"># Does atom has any neighbors and do they need to be filtered?</span> | |
594 581 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">@AtomNeighbors</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$AtomSpecification</span><span class="s">)</span> && <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">->_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">->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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->_GetFilteredAtomNeighbors</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
639 626 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
640 627 <span class="s">}</span> | |
641 628 <span class="k">my</span><span class="s">(</span><span class="i">$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">->_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">->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">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
658 645 | |
659 646 <span class="k">return</span> <span class="s">(</span><span class="i">@Neighbors</span> == <span class="n">1</span><span class="s">)</span> ? <span class="i">$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">->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">$NonHydrogenAtomsOnly</span> && <span class="i">$Neighbor</span><span class="i">->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">$HydrogenAtomsOnly</span> && <span class="s">(</span>!<span class="i">$Neighbor</span><span class="i">->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">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
696 683 | |
697 684 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$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">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
705 692 <span class="s">}</span> | |
706 693 | |
707 694 <span class="c"># Get number of neighbors which are non-hydrogen atoms...</span> | |
708 <a name="GetNumOfNonHydrogenAtomNeighbors-"></a> 695 <span class="k">sub </span><span class="m">GetNumOfNonHydrogenAtomNeighbors</span> <span class="s">{</span> | |
709 696 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->GetNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
713 700 | |
714 701 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$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">$This</span><span class="i">->GetHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
723 710 | |
724 711 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
733 720 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
734 721 <span class="s">}</span> | |
735 722 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
736 723 | |
737 724 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
749 736 | |
750 737 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondToAtom</span><span class="s">(</span><span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
762 749 | |
763 750 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondedToAtom</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
771 758 <span class="s">}</span> | |
772 759 | |
773 760 <span class="c"># Get bond objects to non-hydrogen atoms as array. In scalar context, return number of bonds...</span> | |
774 <a name="GetBondsToNonHydrogenAtoms-"></a> 761 <span class="k">sub </span><span class="m">GetBondsToNonHydrogenAtoms</span> <span class="s">{</span> | |
775 762 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
779 766 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
780 767 <span class="s">}</span> | |
781 768 <span class="k">my</span><span class="s">(</span><span class="i">$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">->_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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->_GetFilteredBonds</span><span class="s">(</span><span class="i">$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">->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">->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> && <span class="i">$BondedAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
817 804 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
818 805 <span class="s">}</span> | |
819 806 <span class="k">if</span> <span class="s">(</span><span class="i">$BondsToHydrogenAtomsOnly</span> && <span class="s">(</span>!<span class="i">$BondedAtom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
820 807 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span> | |
821 808 <span class="s">}</span> | |
822 809 <span class="k">push</span> <span class="i">@FilteredBonds</span><span class="cm">,</span> <span class="i">$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">->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">->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">->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">->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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
872 859 <span class="s">}</span> | |
873 860 | |
874 861 <span class="c"># Get number of double bonds to heavy atoms...</span> | |
875 <a name="GetNumOfDoubleBondsToHeavyAtoms-"></a> 862 <span class="k">sub </span><span class="m">GetNumOfDoubleBondsToHeavyAtoms</span> <span class="s">{</span> | |
876 863 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->GetNumOfDoubleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
879 866 <span class="s">}</span> | |
880 867 | |
881 868 <span class="c"># Get number of double bonds to non-hydrogen atoms...</span> | |
882 <a name="GetNumOfDoubleBondsToNonHydrogenAtoms-"></a> 869 <span class="k">sub </span><span class="m">GetNumOfDoubleBondsToNonHydrogenAtoms</span> <span class="s">{</span> | |
883 870 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
887 874 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
888 875 <span class="s">}</span> | |
889 876 <span class="k">return</span> <span class="i">$This</span><span class="i">->_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">->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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="n">3</span><span class="s">)</span><span class="sc">;</span> | |
908 895 <span class="s">}</span> | |
909 896 | |
910 897 <span class="c"># Get number of bonds of specified bond order to non-hydrogen atoms...</span> | |
911 <a name="_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms-"></a> 898 <span class="k">sub </span><span class="m">_GetNumOfBondsWithSpecifiedBondOrderToNonHydrogenAtoms</span> <span class="s">{</span> | |
912 899 <span class="k">my</span><span class="s">(</span><span class="i">$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">->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">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
919 906 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$This</span><span class="i">->GetNumOfAromaticBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
931 918 <span class="s">}</span> | |
932 919 | |
933 920 <span class="c"># Get number of aromatic bonds to non-hydrogen atoms...</span> | |
934 <a name="GetNumOfAromaticBondsToNonHydrogenAtoms-"></a> 921 <span class="k">sub </span><span class="m">GetNumOfAromaticBondsToNonHydrogenAtoms</span> <span class="s">{</span> | |
935 922 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
940 927 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
941 928 <span class="s">}</span> | |
942 929 | |
943 930 <span class="i">$NumOfBonds</span> = <span class="n">0</span><span class="sc">;</span> | |
944 931 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
945 932 <span class="k">for</span> <span class="i">$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">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$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">->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">$NumOfTripleBonds</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> | |
972 959 <span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
980 967 | |
981 968 <span class="k">for</span> <span class="i">$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">->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">->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">->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">->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">->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">->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">$This</span><span class="i">->GetNonHydrogenAtomNeighborsAtomInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1027 1014 <span class="s">}</span> | |
1028 1015 | |
1029 1016 <span class="c"># Get information related to atoms for all non-hydrogen atoms attached to an atom..</span> | |
1030 1017 <span class="c">#</span> | |
1031 1018 <span class="c"># The following values are returned:</span> | |
1032 1019 <span class="c"># . Number of non-hydrogen atom neighbors</span> | |
1033 1020 <span class="c"># . A reference to an array containing atom objects correpsonding to non-hydrogen</span> | |
1034 1021 <span class="c"># atom neighbors</span> | |
1035 1022 <span class="c"># . Number of different types of non-hydrogen atom neighbors</span> | |
1036 1023 <span class="c"># . A reference to a hash containing atom symbol as key with value corresponding</span> | |
1037 1024 <span class="c"># to its count for non-hydrogen atom neighbors</span> | |
1038 1025 <span class="c">#</span> | |
1039 <a name="GetNonHydrogenAtomNeighborsAtomInformation-"></a>1026 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighborsAtomInformation</span> <span class="s">{</span> | |
1040 1027 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1044 1031 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
1045 1032 <span class="s">}</span> | |
1046 1033 <span class="k">my</span><span class="s">(</span><span class="i">$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">->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>->{<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">$This</span><span class="i">->GetNonHydrogenAtomNeighborsBondInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1074 1061 <span class="s">}</span> | |
1075 1062 | |
1076 1063 <span class="c"># Get information related to bonds for all non-hydrogen atoms attached to an atom..</span> | |
1077 1064 <span class="c">#</span> | |
1078 1065 <span class="c"># The following values are returned:</span> | |
1079 1066 <span class="c"># . Number of bonds to non-hydrogen atom neighbors</span> | |
1080 1067 <span class="c"># . A reference to an array containing bond objects correpsonding to non-hydrogen</span> | |
1081 1068 <span class="c"># atom neighbors</span> | |
1082 1069 <span class="c"># . A reference to a hash containing bond type as key with value corresponding</span> | |
1083 1070 <span class="c"># to its count for non-hydrogen atom neighbors. Bond types are: Single, Double or Triple</span> | |
1084 1071 <span class="c"># . A reference to a hash containing atom symbol as key pointing to bond type as second</span> | |
1085 1072 <span class="c"># key with values correponding to count of bond types for atom symbol for non-hydrogen</span> | |
1086 1073 <span class="c"># atom neighbors</span> | |
1087 1074 <span class="c"># . A reference to a hash containing atom symbol as key pointing to bond type as second</span> | |
1088 1075 <span class="c"># key with values correponding to atom objects array involved in corresponding bond type for</span> | |
1089 1076 <span class="c"># atom symbol for non-hydrogen atom neighbors</span> | |
1090 1077 <span class="c">#</span> | |
1091 <a name="GetNonHydrogenAtomNeighborsBondInformation-"></a>1078 <span class="k">sub </span><span class="m">GetNonHydrogenAtomNeighborsBondInformation</span> <span class="s">{</span> | |
1092 1079 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1096 1083 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
1097 1084 <span class="s">}</span> | |
1098 1085 <span class="k">my</span><span class="s">(</span><span class="i">$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">->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">->IsSingle</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"Single"</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsDouble</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"Double"</span> <span class="co">:</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->IsTriple</span><span class="s">(</span><span class="s">)</span> ? <span class="q">"Triple"</span> <span class="co">:</span> <span class="q">""</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">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
1126 1113 <span class="i">$BondedAtomSymbol</span> = <span class="i">$BondedAtom</span>->{<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">->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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->_GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1173 1160 <span class="s">}</span> | |
1174 1161 | |
1175 1162 <span class="c"># Get sum of bond orders to non-hydrogen atoms only...</span> | |
1176 1163 <span class="c">#</span> | |
1177 <a name="GetSumOfBondOrdersToHeavyAtoms-"></a>1164 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToHeavyAtoms</span> <span class="s">{</span> | |
1178 1165 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1181 1168 <span class="s">}</span> | |
1182 1169 | |
1183 1170 <span class="c"># Get sum of bond orders to non-hydrogen atoms only...</span> | |
1184 1171 <span class="c">#</span> | |
1185 <a name="GetSumOfBondOrdersToNonHydrogenAtoms-"></a>1172 <span class="k">sub </span><span class="m">GetSumOfBondOrdersToNonHydrogenAtoms</span> <span class="s">{</span> | |
1186 1173 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1190 1177 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
1191 1178 <span class="s">}</span> | |
1192 1179 <span class="k">my</span><span class="s">(</span><span class="i">$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">->_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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->_GetSumOfBondOrders</span><span class="s">(</span><span class="i">$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">->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">->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">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1235 1222 <span class="s">}</span> | |
1236 1223 | |
1237 1224 <span class="i">$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">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1240 1227 <span class="s">}</span> | |
1241 1228 | |
1242 1229 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1263 1250 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
1264 1251 <span class="s">}</span> | |
1265 1252 | |
1266 1253 <span class="k">return</span> <span class="i">$This</span><span class="i">->_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">->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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">->_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">$This</span><span class="i">->GetBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1309 1296 <span class="s">}</span> | |
1310 1297 <span class="k">elsif</span> <span class="s">(</span><span class="i">$ToHydrogenAtomsOnly</span><span class="s">)</span> <span class="s">{</span> | |
1311 1298 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetBondsToHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1312 1299 <span class="s">}</span> | |
1313 1300 <span class="k">else</span> <span class="s">{</span> | |
1314 1301 <span class="c"># All bonds...</span> | |
1315 1302 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->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">->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">$BondOrder</span> > <span class="i">$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">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1335 1322 <span class="s">}</span> | |
1336 1323 | |
1337 1324 <span class="c"># Get number of implicit hydrogen for atom...</span> | |
1338 1325 <span class="c">#</span> | |
1339 <a name="GetNumOfImplicitHydrogens-"></a>1326 <span class="k">sub </span><span class="m">GetNumOfImplicitHydrogens</span> <span class="s">{</span> | |
1340 1327 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1344 1331 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
1345 1332 <span class="s">}</span> | |
1346 1333 | |
1347 1334 <span class="c"># Is ImplicitHydrogens property explicitly set?</span> | |
1348 1335 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1349 1336 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</span><span class="s">)</span><span class="sc">;</span> | |
1350 1337 <span class="s">}</span> | |
1351 1338 | |
1352 1339 <span class="c"># Is it an element symbol?</span> | |
1353 1340 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<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">->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">->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">$PotentialTotalValence</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$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> > <span class="n">0</span> ? <span class="i">$ImplicitHydrogens</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
1369 1356 <span class="s">}</span> | |
1370 1357 | |
1371 1358 <span class="c"># Get number of bonds available to form additional bonds with heavy atoms, excluding</span> | |
1372 1359 <span class="c"># any implicit bonds to hydrogens set using ImplicitHydrogens property.</span> | |
1373 1360 <span class="c">#</span> | |
1374 1361 <span class="c"># It's different from number of implicit or missing hydrogens, both of which are equivalent.</span> | |
1375 1362 <span class="c">#</span> | |
1376 1363 <span class="c"># For example, in a SMILES string, [nH] ring atom corresponds to an aromatic nitrogen.</span> | |
1377 1364 <span class="c"># Although the hydrogen specified for n is treated internally as implicit hydrogen and shows</span> | |
1378 1365 <span class="c"># up in missing hydrogen count, it's not available to participate in double bonds to additional</span> | |
1379 1366 <span class="c"># heavy atoms.</span> | |
1380 1367 <span class="c">#</span> | |
1381 <a name="GetNumOfBondsAvailableForHeavyAtoms-"></a>1368 <span class="k">sub </span><span class="m">GetNumOfBondsAvailableForHeavyAtoms</span> <span class="s">{</span> | |
1382 1369 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->GetNumOfBondsAvailableForNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1385 1372 <span class="s">}</span> | |
1386 1373 | |
1387 1374 <span class="c"># It's another name for GetNumOfBondsAvailableForHeavyAtoms</span> | |
1388 1375 <span class="c">#</span> | |
1389 <a name="GetNumOfBondsAvailableForNonHydrogenAtoms-"></a>1376 <span class="k">sub </span><span class="m">GetNumOfBondsAvailableForNonHydrogenAtoms</span> <span class="s">{</span> | |
1390 1377 <span class="k">my</span><span class="s">(</span><span class="i">$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">->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">->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">$PotentialTotalValence</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</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">->GetProperty</span><span class="s">(</span><span class="q">'ImplicitHydrogens'</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">$NumOfAvailableBonds</span> > <span class="n">0</span> ? <span class="i">$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">"Warning: ${ClassName}->SetExplicitHydrogens: Setting of explicit hydrogens is not supported..."</span><span class="sc">;</span> | |
1415 1402 | |
1416 1403 <span class="k">return</span> <span class="i">$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">->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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1435 1422 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
1436 1423 <span class="s">}</span> | |
1437 1424 | |
1438 1425 <span class="i">$HydrogenAtomNbrs</span> = <span class="i">$This</span><span class="i">->GetNumOfHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1439 1426 | |
1440 1427 <span class="k">return</span> <span class="k">defined</span> <span class="i">$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">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1449 1436 <span class="s">}</span> | |
1450 1437 | |
1451 1438 <span class="c"># Get num of missing hydrogens...</span> | |
1452 1439 <span class="c">#</span> | |
1453 <a name="GetNumOfMissingHydrogens-"></a>1440 <span class="k">sub </span><span class="m">GetNumOfMissingHydrogens</span> <span class="s">{</span> | |
1454 1441 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1458 1445 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
1459 1446 <span class="s">}</span> | |
1460 1447 | |
1461 1448 <span class="k">return</span> <span class="i">$This</span><span class="i">->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">->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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->GetNumOfImplicitHydrogens</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->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'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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Valence'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1525 1512 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Valence'</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">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1530 1517 | |
1531 1518 <span class="k">return</span> <span class="i">$Valence</span> > <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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ValenceFreeElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1580 1567 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ValenceFreeElectrons'</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">$This</span>->{<span class="w">AtomicNumber</span>}<span class="s">)</span> <span class="s">{</span> | |
1584 1571 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
1585 1572 <span class="s">}</span> | |
1586 1573 | |
1587 1574 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetValenceElectrons</span><span class="s">(</span><span class="s">)</span> - <span class="i">$This</span><span class="i">->GetValence</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1590 1577 <span class="k">if</span> <span class="s">(</span><span class="i">$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">->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">$ValenceFreeElectrons</span> > <span class="n">0</span> ? <span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="i">->GetValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1611 1598 | |
1612 1599 <span class="j">VALENCEMODEL:</span> <span class="s">{</span> | |
1613 1600 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingMDLValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1615 1602 <span class="k">last</span> <span class="j">VALENCEMODEL</span><span class="sc">;</span> | |
1616 1603 <span class="s">}</span> | |
1617 1604 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingDaylightValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1619 1606 <span class="k">last</span> <span class="j">VALENCEMODEL</span><span class="sc">;</span> | |
1620 1607 <span class="s">}</span> | |
1621 1608 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Warning: ${ClassName}->GetPotentialTotalCommonValence: The current release of MayaChemTools doesn't support the specified valence model $ValenceModel. Supported valence models: MDLValenceModel, DaylightValenceModel, InternalValenceModel. Using internal valence model..."</span><span class="sc">;</span> | |
1623 1610 <span class="s">}</span> | |
1624 1611 <span class="c"># Use internal valence model as the default valence model...</span> | |
1625 1612 <span class="i">$PotentialTotalValence</span> = <span class="i">$This</span><span class="i">->_GetPotentialTotalCommonValenceUsingInternalValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1626 1613 <span class="s">}</span> | |
1627 1614 | |
1628 1615 <span class="k">return</span> <span class="i">$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">->_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">->_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>->{<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">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1662 1649 | |
1663 1650 <span class="c"># Is any valence model data available for atomic number and formal charge?</span> | |
1664 1651 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ValenceModelDataRef</span>->{<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>->{<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">->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">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1678 1665 | |
1679 1666 <span class="i">$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>->{<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">$CurrentEffectiveValence</span> <= <span class="i">$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 > 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>->{<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">$This</span><span class="i">->_GetFormalChargeAdjustedForInternalValenceModel</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1757 1744 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1758 1745 | |
1759 1746 <span class="i">$SumOfBondOrders</span> = <span class="i">$This</span><span class="i">->GetSumOfBondOrders</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1760 1747 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$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> < <span class="n">0</span> || <span class="i">$PotentialTotalValence</span> >= <span class="i">$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">$PotentialTotalValence</span> > <span class="n">0</span> ? <span class="i">$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">->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">$This</span><span class="i">->GetGroupNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1798 1785 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$GroupNumber</span><span class="s">)</span> <span class="s">{</span> | |
1799 1786 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span> | |
1800 1787 <span class="s">}</span> | |
1801 1788 | |
1802 1789 <span class="c"># Group numbers > 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He)</span> | |
1803 1790 <span class="c">#</span> | |
1804 1791 <span class="c"># Formal charge sign is not adjusted. Positive and negative values result in the</span> | |
1805 1792 <span class="c"># increase and decrease of valence.</span> | |
1806 1793 <span class="c">#</span> | |
1807 1794 <span class="c"># Group 14 containing C, Si, Ge, Sn, Pb...</span> | |
1808 1795 <span class="c">#</span> | |
1809 1796 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> | |
1810 1797 <span class="c"># values result in the decrease of valence.</span> | |
1811 1798 <span class="c">#</span> | |
1812 1799 <span class="c"># Group 13 containing B, Al, Ga, In, Tl...</span> | |
1813 1800 <span class="c">#</span> | |
1814 1801 <span class="c"># Formal charge sign is always reversed. Positive and negative values result in the</span> | |
1815 1802 <span class="c"># decrease and increase of valence.</span> | |
1816 1803 <span class="c">#</span> | |
1817 1804 <span class="c"># Groups 1 (H) through 12 (Zn)...</span> | |
1818 1805 <span class="c">#</span> | |
1819 1806 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> | |
1820 1807 <span class="c"># values result in the decrease of valence.</span> | |
1821 1808 <span class="c">#</span> | |
1822 1809 <span class="c"># Lanthanides and actinides...</span> | |
1823 1810 <span class="c">#</span> | |
1824 1811 <span class="c"># Formal charge sign is reversed for positive values. Both positive and negative</span> | |
1825 1812 <span class="c"># values result in the decrease of valence.</span> | |
1826 1813 <span class="c">#</span> | |
1827 1814 | |
1828 1815 <span class="i">$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> > <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> > <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">$GroupNumber</span> >=<span class="n">1</span> && <span class="i">$GroupNumber</span> <= <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> > <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> > <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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'LowestCommonValence'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1872 1859 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'LowestCommonValence'</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>->{<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">->HasProperty</span><span class="s">(</span><span class="q">'HighestCommonValence'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1897 1884 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'HighestCommonValence'</span><span class="s">)</span><span class="sc">;</span> | |
1898 1885 <span class="s">}</span> | |
1899 1886 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
1902 1889 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ValenceElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1923 1910 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ValenceElectrons'</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>->{<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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1948 1935 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
1949 1936 <span class="s">}</span> | |
1950 1937 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$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">"Warning: ${ClassName}->AddHydrogens: The current release of MayaChemTools doesn't assign any hydrogen positions..."</span><span class="sc">;</span> | |
1955 1942 <span class="s">}</span> | |
1956 1943 | |
1957 1944 <span class="c"># Is it an element symbol?</span> | |
1958 1945 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
1965 1952 <span class="i">$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">->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">$HydrogensToAdd</span> <= <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
1968 1955 <span class="k">return</span> <span class="i">$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">$Molecule</span><span class="i">->NewAtom</span><span class="s">(</span><span class="q">'AtomSymbol'</span> <span class="cm">=></span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'XYZ'</span> <span class="cm">=></span> <span class="s">[</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> | |
1977 1964 <span class="i">$Molecule</span><span class="i">->NewBond</span><span class="s">(</span><span class="q">'Atoms'</span> <span class="cm">=></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">'BondOrder'</span> <span class="cm">=></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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
1989 1976 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
1990 1977 <span class="s">}</span> | |
1991 1978 | |
1992 1979 <span class="c"># Is it an element symbol?</span> | |
1993 1980 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
2000 1987 <span class="i">$HydrogensDeleted</span> = <span class="n">0</span><span class="sc">;</span> | |
2001 1988 <span class="i">@Neighbors</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
2002 1989 | |
2003 1990 <span class="j">NEIGHBOR:</span> <span class="k">for</span> <span class="i">$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">$Neighbor</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2005 1992 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> | |
2006 1993 <span class="s">}</span> | |
2007 1994 <span class="i">$Molecule</span><span class="i">->_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">""</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">->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">->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">->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">->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">->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">->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">->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">->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">->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">->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">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->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">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->GetNumOfHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
2080 2067 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
2081 2068 <span class="s">}</span> | |
2082 2069 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$This</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
2084 2071 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
2085 2072 <span class="s">}</span> | |
2086 2073 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
2088 2075 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
2089 2076 <span class="s">}</span> | |
2090 2077 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$This</span><span class="i">->GetStereochemistry</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
2092 2079 <span class="i">$Value</span>= <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$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">''</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">->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">->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">->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">->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">$Value</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> | |
2110 2097 <span class="k">last</span> <span class="j">ATOMICVARIANT</span><span class="sc">;</span> | |
2111 2098 <span class="s">}</span> | |
2112 2099 <span class="i">$Value</span> = <span class="q">""</span><span class="sc">;</span> | |
2113 2100 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetAtomicInvariantValue: Unknown atomic invariant $AtomicInvariant..."</span><span class="sc">;</span> | |
2114 2101 <span class="s">}</span> | |
2115 2102 | |
2116 2103 <span class="k">return</span> <span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'PeriodNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2126 2113 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'PeriodNumber'</span><span class="s">)</span><span class="sc">;</span> | |
2127 2114 <span class="s">}</span> | |
2128 2115 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
2131 2118 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'GroupNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2147 2134 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'GroupNumber'</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>->{<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">$This</span><span class="i">->_IsFunctionalClassType</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->_IsFunctionalClassType</span><span class="s">(</span><span class="i">$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">->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">->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">->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">->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">->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">->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">->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">->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">->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">"Warning: ${ClassName}->_IsType: Unknown functional/pharmacohore type $Type..."</span><span class="sc">;</span> | |
2224 2211 <span class="s">}</span> | |
2225 2212 <span class="k">return</span> <span class="i">$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>->{<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>->{<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>->{<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>->{<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>->{<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>->{<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>->{<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">->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>->{<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>->{<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>->{<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>->{<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>->{<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>->{<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>->{<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>->{<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">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(9|17|35|53)$/</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>->{<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>->{<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">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(7|8|15|16)$/</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">$This</span>->{<span class="w">AtomicNumber</span>}<span class="sc">;</span> | |
2376 2363 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2381 2368 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2382 2369 <span class="s">}</span> | |
2383 2370 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'MassNumber'</span><span class="s">)</span><span class="sc">;</span> | |
2386 2373 <span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2397 2384 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
2398 2385 <span class="s">}</span> | |
2399 2386 | |
2400 2387 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> <= <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">->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">$Aromatic</span><span class="s">)</span> && <span class="i">$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">->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">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
2424 2411 <span class="k">if</span> <span class="s">(</span><span class="i">@Bonds</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
2425 2412 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2426 2413 <span class="s">}</span> | |
2427 2414 | |
2428 2415 <span class="k">my</span><span class="s">(</span><span class="i">$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">->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">->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">$This</span><span class="i">->IsHydrogenBondDonor</span><span class="s">(</span><span class="i">$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">'HBondsType1'</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">$This</span><span class="i">->_IsHydrogenBondDonorOfType1</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
2478 2465 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> | |
2479 2466 <span class="s">}</span> | |
2480 2467 | |
2481 2468 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$This</span><span class="i">->_IsHydrogenBondDonorOfType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
2483 2470 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> | |
2484 2471 <span class="s">}</span> | |
2485 2472 | |
2486 2473 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
2487 2474 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->IsHydrogenBondDonor: The current release of MayaChemTools doesn't support specified value, $HydrogenBondsType, for HydrogenBondsType. Valid values: HBondsType1, HydrogenBondsType1, HBondsType2 HydrogenBondsType2 ..."</span><span class="sc">;</span> | |
2488 2475 <span class="s">}</span> | |
2489 2476 | |
2490 2477 <span class="k">return</span> <span class="i">$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">->_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">->_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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(7|8)$/</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">$This</span><span class="i">->GetExplicitHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2532 2519 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
2533 2520 <span class="s">}</span> | |
2534 2521 | |
2535 2522 <span class="c"># Any missing hydrogens?</span> | |
2536 2523 <span class="k">return</span> <span class="i">$This</span><span class="i">->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">$This</span><span class="i">->IsHydrogenBondAcceptor</span><span class="s">(</span><span class="i">$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">'HBondsType1'</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">$This</span><span class="i">->_IsHydrogenBondAcceptorOfType1</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
2560 2547 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> | |
2561 2548 <span class="s">}</span> | |
2562 2549 | |
2563 2550 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$This</span><span class="i">->_IsHydrogenBondAcceptorOfType2</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
2565 2552 <span class="k">last</span> <span class="j">HYDROGENBONDSTYPE</span><span class="sc">;</span> | |
2566 2553 <span class="s">}</span> | |
2567 2554 | |
2568 2555 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
2569 2556 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->IsHydrogenBondAcceptor: The current release of MayaChemTools doesn't support specified value, $HydrogenBondsType, for HydrogenBondsType. Valid values: HBondsType1, HydrogenBondsType1, HBondsType2 HydrogenBondsType2 ..."</span><span class="sc">;</span> | |
2570 2557 <span class="s">}</span> | |
2571 2558 | |
2572 2559 <span class="k">return</span> <span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(7|8)$/</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">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">8</span> <span class="s">)</span> <span class="s">{</span> | |
2598 2585 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
2599 2586 <span class="s">}</span> | |
2600 2587 | |
2601 2588 <span class="c"># Any explicitly attached hydrogens?</span> | |
2602 2589 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->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">$This</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> | |
2608 2595 <span class="s">}</span> | |
2609 2596 | |
2610 2597 <span class="c"># Is it a MayaChemTools HBondType2 hydrogen bond acceptor atom?</span> | |
2611 2598 <span class="c">#</span> | |
2612 2599 <span class="c"># HydrogenBondAcceptor definition [ Ref 91 ]: N, O</span> | |
2613 2600 <span class="c">#</span> | |
2614 2601 <span class="c"># In other words:</span> | |
2615 2602 <span class="c"># . Any Nitrogen or Oxygen atom</span> | |
2616 2603 <span class="c">#</span> | |
2617 2604 <span class="c"># Note:</span> | |
2618 2605 <span class="c"># . HydrogenBondsType2 definition corresponds to Rule of 5.</span> | |
2619 2606 <span class="c">#</span> | |
2620 <a name="_IsHydrogenBondAcceptorOfType2-"></a>2607 <span class="k">sub </span><span class="m">_IsHydrogenBondAcceptorOfType2</span> <span class="s">{</span> | |
2621 2608 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2625 2612 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2626 2613 <span class="s">}</span> | |
2627 2614 | |
2628 2615 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">->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">$FormalCharge</span><span class="s">)</span> && <span class="i">$FormalCharge</span> > <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">$This</span>->{<span class="w">AtomicNumber</span>} != <span class="n">7</span> <span class="s">)</span> <span class="s">{</span> | |
2656 2643 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2657 2644 <span class="s">}</span> | |
2658 2645 | |
2659 2646 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">->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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2678 2665 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2679 2666 <span class="s">}</span> | |
2680 2667 | |
2681 2668 <span class="c"># Any explicit negative formal charge?</span> | |
2682 2669 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
2683 2670 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> && <span class="i">$FormalCharge</span> < <span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
2684 2671 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
2685 2672 <span class="s">}</span> | |
2686 2673 | |
2687 2674 <span class="c"># Is it C, P or S?</span> | |
2688 2675 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<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">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2699 2686 <span class="c"># Is it an oxygen?</span> | |
2700 2687 <span class="k">if</span> <span class="s">(</span><span class="i">$Neighbor</span>->{<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">$Neighbor</span><span class="i">->GetNumOfHeavyAtomNeighbors</span><span class="s">(</span><span class="s">)</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
2705 2692 <span class="k">next</span> <span class="j">NEIGHBOR</span><span class="sc">;</span> | |
2706 2693 <span class="s">}</span> | |
2707 2694 <span class="i">$NeighborOxygenBondOrder</span> = <span class="i">$This</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="i">$Neighbor</span><span class="s">)</span><span class="i">->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">$NumOfNeighborOxygensWithDoubleBonds</span> >= <span class="n">1</span> && <span class="i">$NumOfNeighborOxygensWithSingleBonds</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> | |
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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span>->{<span class="w">AtomicNumber</span>} =~ <span class="q">/^(17|35|53)$/</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">$This</span>->{<span class="w">AtomicNumber</span>} !~ <span class="q">/^(6|16)$/</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">->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>->{<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">$This</span>->{<span class="w">AtomicNumber</span>} == <span class="n">16</span><span class="s">)</span> <span class="s">{</span> | |
2759 2746 <span class="k">if</span> <span class="s">(</span><span class="i">@HeavyAtomNeighbors</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
2760 2747 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2761 2748 <span class="s">}</span> | |
2762 2749 <span class="s">}</span> | |
2763 2750 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
2764 2751 <span class="s">}</span> | |
2765 2752 | |
2766 2753 <span class="c"># Is it hydrophobic?</span> | |
2767 2754 <span class="c">#</span> | |
2768 <a name="IsHydrophobic-"></a>2755 <span class="k">sub </span><span class="m">IsHydrophobic</span> <span class="s">{</span> | |
2769 2756 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->IsLipophilic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
2772 2759 <span class="s">}</span> | |
2773 2760 | |
2774 2761 <span class="c"># Is it a Nitrogen atom in Guadinium group?</span> | |
2775 2762 <span class="c">#</span> | |
2776 <a name="IsGuadiniumNitrogen-"></a>2763 <span class="k">sub </span><span class="m">IsGuadiniumNitrogen</span> <span class="s">{</span> | |
2777 2764 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2781 2768 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2782 2769 <span class="s">}</span> | |
2783 2770 | |
2784 2771 <span class="c"># Is it connected to a Guadinium Carbon?</span> | |
2785 2772 <span class="k">my</span><span class="s">(</span><span class="i">$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">->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">$AtomNeighbor</span><span class="i">->IsGuadiniumCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2789 2776 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
2790 2777 <span class="s">}</span> | |
2791 2778 <span class="s">}</span> | |
2792 2779 | |
2793 2780 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2794 2781 <span class="s">}</span> | |
2795 2782 | |
2796 2783 <span class="c"># Is it a Carbon atom in Guadinium group?</span> | |
2797 2784 <span class="c">#</span> | |
2798 2785 <span class="c"># Guadinium group definition:</span> | |
2799 2786 <span class="c">#</span> | |
2800 2787 <span class="c"># R2N-C(=NR)-(NR2) or R2N-C(=NR2+)-(NR2)</span> | |
2801 2788 <span class="c">#</span> | |
2802 2789 <span class="c"># where:</span> | |
2803 2790 <span class="c"># . R = Hydrogens or group of atoms attached through Carbon</span> | |
2804 2791 <span class="c"># . Only one of the three Nitrogens has a double bond to Carbon and has optional</span> | |
2805 2792 <span class="c"># formal charge allowing it to be neutral or charged state</span> | |
2806 2793 <span class="c">#</span> | |
2807 <a name="IsGuadiniumCarbon-"></a>2794 <span class="k">sub </span><span class="m">IsGuadiniumCarbon</span> <span class="s">{</span> | |
2808 2795 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2812 2799 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2813 2800 <span class="s">}</span> | |
2814 2801 | |
2815 2802 <span class="c"># Match atom neighborhood...</span> | |
2816 2803 <span class="k">my</span><span class="s">(</span><span class="i">$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">$CentralAtomSpec</span> = <span class="q">'C.X3.BO4'</span><span class="sc">;</span> | |
2819 2806 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'N.FC0'</span><span class="cm">,</span> <span class="q">'N.FC0'</span><span class="cm">,</span> <span class="q">'N.FC0,N.FC+1'</span><span class="s">)</span><span class="sc">;</span> | |
2820 2807 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="s">)</span><span class="sc">;</span> | |
2821 2808 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="s">)</span><span class="sc">;</span> | |
2822 2809 | |
2823 2810 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->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">$This</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2837 2824 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2838 2825 <span class="s">}</span> | |
2839 2826 | |
2840 2827 <span class="c"># Is it connected to a Amide Carbon?</span> | |
2841 2828 <span class="k">my</span><span class="s">(</span><span class="i">$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">->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">$AtomNeighbor</span><span class="i">->IsAmideCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2845 2832 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
2846 2833 <span class="s">}</span> | |
2847 2834 <span class="s">}</span> | |
2848 2835 | |
2849 2836 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2850 2837 <span class="s">}</span> | |
2851 2838 | |
2852 2839 <span class="c"># Is it a Carbon atom in Amide group?</span> | |
2853 2840 <span class="c">#</span> | |
2854 2841 <span class="c"># Amide group definition: R-C(=O)-N(-R')-R''</span> | |
2855 2842 <span class="c">#</span> | |
2856 2843 <span class="c"># where:</span> | |
2857 2844 <span class="c"># . R = Hydrogen or groups of atoms attached through Carbon</span> | |
2858 2845 <span class="c"># . R' = Hydrogens or groups of atoms attached through Carbon or hetro atoms</span> | |
2859 2846 <span class="c"># . R'' = Hydrogens or groups of atoms attached through Carbon or hetro atoms</span> | |
2860 2847 <span class="c">#</span> | |
2861 <a name="IsAmideCarbon-"></a>2848 <span class="k">sub </span><span class="m">IsAmideCarbon</span> <span class="s">{</span> | |
2862 2849 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2866 2853 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2867 2854 <span class="s">}</span> | |
2868 2855 | |
2869 2856 <span class="c"># Is it Carbon?</span> | |
2870 2857 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->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">'C.X3.BO4,C.X2.BO3'</span><span class="sc">;</span> | |
2878 2865 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'N'</span><span class="s">)</span><span class="sc">;</span> | |
2879 2866 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">)</span><span class="sc">;</span> | |
2880 2867 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C'</span><span class="cm">,</span> <span class="q">'C,H,N,O,S,P,F,Cl,Br,I'</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">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$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">->_MatchCarboxylateAndOrCarboxylOxygen</span><span class="s">(</span><span class="q">'Carboxylate'</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">->_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="q">'Carboxylate'</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">->_MatchCarboxylateAndOrCarboxylOxygen</span><span class="s">(</span><span class="q">'Carboxyl'</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">->_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="q">'Carboxyl'</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">$This</span><span class="i">->IsOxygen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2932 2919 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2933 2920 <span class="s">}</span> | |
2934 2921 | |
2935 2922 <span class="c"># Is it connected to a Carboxylate Carbon?</span> | |
2936 2923 <span class="k">my</span><span class="s">(</span><span class="i">$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">->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">$AtomNeighbor</span><span class="i">->_MatchCarboxylateAndOrCarboxylCarbon</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
2960 2947 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2961 2948 <span class="s">}</span> | |
2962 2949 | |
2963 2950 <span class="c"># Is it Carbon?</span> | |
2964 2951 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->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">'C.X3.BO4,C.X2.BO3'</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">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O.X1.FC-1'</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">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O.X1.FC0'</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">'C,H'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O.X1.FC-1,O.X1.FC0'</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">"Warning: ${ClassName}->_MatchCarboxylateAndCarboxylCarbon.: Unknown mode $Mode..."</span><span class="sc">;</span> | |
2986 2973 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
2987 2974 <span class="s">}</span> | |
2988 2975 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">)</span><span class="sc">;</span> | |
2989 2976 <span class="i">@NbrOfNbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'C,H'</span><span class="cm">,</span> <span class="q">'C'</span><span class="cm">,</span> <span class="q">'C'</span><span class="s">)</span><span class="sc">;</span> | |
2990 2977 | |
2991 2978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->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">$This</span><span class="i">->IsOxygen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3005 2992 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
3006 2993 <span class="s">}</span> | |
3007 2994 | |
3008 2995 <span class="c"># Is it connected to a Phosphate Phosphorus?</span> | |
3009 2996 <span class="k">my</span><span class="s">(</span><span class="i">$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">->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">$AtomNeighbor</span><span class="i">->IsPhosphatePhosphorus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3013 3000 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
3014 3001 <span class="s">}</span> | |
3015 3002 <span class="s">}</span> | |
3016 3003 | |
3017 3004 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
3018 3005 <span class="s">}</span> | |
3019 3006 | |
3020 3007 <span class="c"># Is it a Phosphorus atom in Phosphate group?</span> | |
3021 3008 <span class="c">#</span> | |
3022 3009 <span class="c"># Phosphate group definition: AO-(O=)P(-OA)-OA</span> | |
3023 3010 <span class="c">#</span> | |
3024 3011 <span class="c"># where:</span> | |
3025 3012 <span class="c"># . A = Any Groups of atoms including hydrogens</span> | |
3026 3013 <span class="c">#</span> | |
3027 <a name="IsPhosphatePhosphorus-"></a>3014 <span class="k">sub </span><span class="m">IsPhosphatePhosphorus</span> <span class="s">{</span> | |
3028 3015 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3032 3019 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
3033 3020 <span class="s">}</span> | |
3034 3021 | |
3035 3022 <span class="c"># Is it Phosphorus?</span> | |
3036 3023 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->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">'P.X4.BO5'</span><span class="sc">;</span> | |
3044 3031 <span class="i">@NbrAtomSpecsRef</span> = <span class="s">(</span><span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="s">)</span><span class="sc">;</span> | |
3045 3032 <span class="i">@NbrBondSpecsRef</span> = <span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</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">$This</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$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<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
3063 3050 <span class="c"># T<n> = Total number of atom neighbors including implcit and explicit hydrogens</span> | |
3064 3051 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
3065 3052 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
3066 3053 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
3067 3054 <span class="c"># TSB<n> = Total number of single bonds to atom neighbors including implcit and explicit hydrogens</span> | |
3068 3055 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
3069 3056 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
3070 3057 <span class="c"># H<n> = 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<n> = Ring atom annotation indicating whether atom is a ring</span> | |
3073 3060 <span class="c"># TR<n> = Total number of rings containing atom</span> | |
3074 3061 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span> | |
3075 3062 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span> | |
3076 3063 <span class="c"># SM<n> = 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<n>.T<n>.BO<n>.LBO<n>.<SB><n>.TSB<n>.<DB><n>.<TB><n>.H<n>.Ar.RA<n>.TR<n>FC<+n/-n>.MN<n>.SM<n></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"># . ('N', 'N', 'N')</span> | |
3098 3085 <span class="c"># . ('N.FC0', 'N.FC0', 'N,N.FC+1.H1')</span> | |
3099 3086 <span class="c"># . ('N.H2', 'N.H2', 'N.H1')</span> | |
3100 3087 <span class="c"># . ('C,N', '!N', '!H')</span> | |
3101 3088 <span class="c"># . ('C,N', 'N.Ar', 'N.R5')</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">$CentralAtom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3131 3118 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
3132 3119 <span class="s">}</span> | |
3133 3120 | |
3134 3121 <span class="i">$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">$NumOfNbrBondSpecs</span> && <span class="s">(</span><span class="i">$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">"Warning: ${ClassName}->DoesAtomNeighborhoodMatch: Number of specified central atom, $NumOfNbrAtomSpecs, and bond, $NumOfNbrBondSpecs, specifications must be same; No neighborhood match performed ..."</span><span class="sc">;</span> | |
3141 3128 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
3142 3129 <span class="s">}</span> | |
3143 3130 | |
3144 3131 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNbrOfNbrAtomSpecs</span> && <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">"Warning: ${ClassName}->DoesAtomNeighborhoodMatch: Number of specified central atom, $NumOfNbrAtomSpecs, and neighbor of neighbor atoms specifications, $NumOfNbrOfNbrAtomSpecs, must be same; No neighborhood match performed ..."</span><span class="sc">;</span> | |
3146 3133 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
3147 3134 <span class="s">}</span> | |
3148 3135 | |
3149 3136 <span class="c"># Sort atom and bond specifications in terms of being most specific to least specific..</span> | |
3150 3137 <span class="s">(</span><span class="i">$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">$CentralAtom</span><span class="i">->_SortSpecificationsForAtomNeighborhoodMatch</span><span class="s">(</span><span class="i">$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">$CentralAtom</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$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">->_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'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'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">$CentralAtom</span><span class="i">->_MatchAtomNeighborhoodUsingMissingHydrogens</span><span class="s">(</span><span class="i">$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">$NbrSpecsMatched</span><span class="s">)</span> <span class="s">{</span> | |
3182 3169 <span class="c"># It's match...</span> | |
3183 3170 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
3184 3171 <span class="s">}</span> | |
3185 3172 | |
3186 3173 <span class="c"># No match...</span> | |
3187 3174 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
3188 3175 <span class="s">}</span> | |
3189 3176 | |
3190 3177 <span class="c"># Match central atom neighborhood atom and bond specifications...</span> | |
3191 3178 <span class="c">#</span> | |
3192 <a name="_MatchAtomNeighborhoodUsingAtomBondSpecs-"></a>3179 <span class="k">sub </span><span class="m">_MatchAtomNeighborhoodUsingAtomBondSpecs</span> <span class="s">{</span> | |
3193 3180 <span class="k">my</span><span class="s">(</span><span class="i">$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> && <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'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">->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">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$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>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
3207 3194 <span class="i">$NbrBondSpec</span> = <span class="i">$NbrBondSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
3208 3195 | |
3209 3196 <span class="i">$NbrOfNbrAtomSpec</span> = <span class="i">$MatchNbrOfNbrAtomSpecs</span> ? <span class="i">$NbrOfNbrAtomSpecsRef</span>->[<span class="i">$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">$NbrAtom</span><span class="i">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$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">$CentralAtom</span><span class="i">->_DoesBondSpecificationMatch</span><span class="s">(</span><span class="i">$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">->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">->_DoesAtomSpecificationMatch</span><span class="s">(</span><span class="i">$NbrOfNbrAtomSpec</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3226 3213 <span class="k">next</span> <span class="j">NBRATOMSPEC</span><span class="sc">;</span> | |
3227 3214 <span class="s">}</span> | |
3228 3215 <span class="s">}</span> | |
3229 3216 <span class="s">}</span> | |
3230 3217 | |
3231 3218 <span class="c"># It's a match for a neighbor atom specification...</span> | |
3232 3219 <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<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">$NbrSpecCount</span><span class="s">)</span> <span class="s">{</span> | |
3236 3223 <span class="c"># It's match...</span> | |
3237 3224 <span class="i">$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'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">->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> > <span class="i">$NumOfMissingHydrogens</span><span class="s">)</span> <span class="s">{</span> | |
3258 3245 <span class="c"># It won't match...</span> | |
3259 3246 <span class="k">return</span> <span class="s">(</span><span class="i">$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>->{<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">$NbrAtomSpecsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
3268 3255 <span class="i">$NbrBondSpec</span> = <span class="i">$NbrBondSpecsRef</span>->[<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's a match for a neighbor atom specification...</span> | |
3294 3281 <span class="i">$NbrSpecAlreadyMatchedRef</span>->{<span class="i">$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'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">$NbrSpecMatchCount</span><span class="s">)</span><span class="sc">;</span> | |
3308 3295 <span class="s">}</span> | |
3309 3296 | |
3310 3297 <span class="c"># Sort atom and bond specifications base on neighbor atom specifications going</span> | |
3311 3298 <span class="c"># from most to least specific atom specifications.</span> | |
3312 3299 <span class="c">#</span> | |
3313 3300 <span class="c"># Atom specifications are sorted at the following two levels:</span> | |
3314 3301 <span class="c">#</span> | |
3315 3302 <span class="c"># o By atom specification count with in each specification going from most specific</span> | |
3316 3303 <span class="c"># to least specific, where count is determined by the number of "," in each</span> | |
3317 3304 <span class="c"># specification. Wild card containing specifications are considered least specific</span> | |
3318 3305 <span class="c"># and end up at the end of the sorted list.</span> | |
3319 3306 <span class="c"># o By atomic invariant count with in each sorted list going from most specific to</span> | |
3320 3307 <span class="c"># least specific, where count is determined by the number of "." in each atom</span> | |
3321 3308 <span class="c"># specification.</span> | |
3322 3309 <span class="c">#</span> | |
3323 3310 <span class="c">#A single atom specification,</span> | |
3324 3311 <span class="c"># without any commas in atom specification, is is considered most specific...</span> | |
3325 3312 <span class="c">#</span> | |
3326 <a name="_SortSpecificationsForAtomNeighborhoodMatch-"></a>3313 <span class="k">sub </span><span class="m">_SortSpecificationsForAtomNeighborhoodMatch</span> <span class="s">{</span> | |
3327 3314 <span class="k">my</span><span class="s">(</span><span class="i">$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">$NumOfNbrAtomSpecs</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
3335 3322 <span class="j">ATOMSPEC:</span> <span class="k">for</span> <span class="i">$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">$NbrAtomSpecsRef</span>->[<span class="i">$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">->_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> <=> <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">$b</span> <=> <span class="i">$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">$NbrAtomSpecsRef</span>->[<span class="i">$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>->[<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">$NbrOfNbrAtomSpecsRef</span>->[<span class="i">$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> && <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'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">->_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">$This</span><span class="i">->_MatchNonAtomSymbolAtomicInvariant</span><span class="s">(</span><span class="i">$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">->_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>->{<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">$This</span>->{<span class="w">AtomSymbol</span>} =~ <span class="q">/^$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">$UnknownName</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> | |
3522 3509 | |
3523 3510 <span class="c"># Does match needs to be negated?</span> | |
3524 3511 <span class="k">if</span> <span class="s">(</span><span class="i">$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\-\+\*\>\<\=]+)$/</span><span class="sc">;</span> | |
3532 3519 <span class="s">}</span> | |
3533 3520 <span class="k">else</span> <span class="s">{</span> | |
3534 3521 <span class="s">(</span><span class="i">$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> && <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> == <span class="i">$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> && <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtomNeighbors</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->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">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
3553 3540 <span class="i">$Status</span> = <span class="i">$This</span><span class="i">->_MatchNonAtomSymbolAtomicInvariantValue</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
3560 3547 <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> | |
3561 3548 <span class="s">}</span> | |
3562 3549 | |
3563 3550 <span class="c"># Match number of implicit and explicit hydrogens...</span> | |
3564 3551 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$Value</span><span class="s">)</span> && <span class="s">(</span><span class="i">$This</span><span class="i">->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">->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">->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> && <span class="s">(</span><span class="i">$Value</span> == <span class="i">$This</span><span class="i">->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> && <span class="i">$This</span><span class="i">->GetSumOfBondOrdersToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$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> && <span class="i">$This</span><span class="i">->GetLargestBondOrderToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$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> && <span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> == <span class="i">$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> && <span class="s">(</span><span class="i">$This</span><span class="i">->GetNumOfSingleBondsToNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> + <span class="i">$This</span><span class="i">->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">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->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">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->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">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->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">$Value</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->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">$This</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
3633 3620 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$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">$Value</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$SpinMultiplicity</span><span class="s">)</span> && <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">"Warning: ${ClassName}->_MatchNonAtomSymbolAtomicInvariant: Unknown atomic invariant $AtomicInvariant..."</span><span class="sc">;</span> | |
3640 3627 <span class="s">}</span> | |
3641 3628 | |
3642 3629 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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"># . >ValidNumber or >=ValidNumber</span> | |
3657 3644 <span class="c"># . <ValidNumber or <=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> && <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">$TargetValue</span> > <span class="n">0</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
3673 3660 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span> | |
3674 3661 <span class="s">}</span> | |
3675 3662 <span class="k">if</span> <span class="s">(</span><span class="i">$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> < <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">$SpecifiedValue</span> =~ <span class="q">/^>/</span><span class="s">)</span> <span class="s">{</span> | |
3680 3667 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^>=/</span><span class="s">)</span> <span class="s">{</span> | |
3681 3668 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^>=//</span><span class="sc">;</span> | |
3682 3669 <span class="i">$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> | |
3683 3670 <span class="s">}</span> | |
3684 3671 <span class="k">else</span> <span class="s">{</span> | |
3685 3672 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^>//</span><span class="sc">;</span> | |
3686 3673 <span class="i">$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> | |
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">$SpecifiedValue</span> =~ <span class="q">/^</</span><span class="s">)</span> <span class="s">{</span> | |
3691 3678 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedValue</span> =~ <span class="q">/^<=/</span><span class="s">)</span> <span class="s">{</span> | |
3692 3679 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^<=//</span><span class="sc">;</span> | |
3693 3680 <span class="i">$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> | |
3694 3681 <span class="s">}</span> | |
3695 3682 <span class="k">else</span> <span class="s">{</span> | |
3696 3683 <span class="i">$SpecifiedValue</span> =~ <span class="q">s/^<//</span><span class="sc">;</span> | |
3697 3684 <span class="i">$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> | |
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">$BondSpecificationToMatch</span><span class="s">)</span> && <span class="i">$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">$This</span><span class="i">->_MatchBondSymbolSpecification</span><span class="s">(</span><span class="i">$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">'0'</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">$This</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="i">$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">->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">->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">->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">->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">->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">"Warning: ${ClassName}->_MatchBondSpecification: Unknown bond specification $BondSymbolSpecification..."</span><span class="sc">;</span> | |
3774 3761 <span class="s">}</span> | |
3775 3762 | |
3776 3763 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">->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">->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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3811 3798 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
3812 3799 <span class="s">}</span> | |
3813 3800 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3815 3802 | |
3816 3803 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomInRing</span><span class="s">(</span><span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3830 3817 | |
3831 3818 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3841 3828 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
3842 3829 <span class="s">}</span> | |
3843 3830 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3845 3832 | |
3846 3833 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomInOnlyOneRing</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3856 3843 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
3857 3844 <span class="s">}</span> | |
3858 3845 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3860 3847 | |
3861 3848 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsAtomInRingOfSize</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3871 3858 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
3872 3859 <span class="s">}</span> | |
3873 3860 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3875 3862 | |
3876 3863 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfSmallestAtomRing</span><span class="s">(</span><span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3890 3877 | |
3891 3878 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3901 3888 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
3902 3889 <span class="s">}</span> | |
3903 3890 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3905 3892 | |
3906 3893 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRings</span><span class="s">(</span><span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3920 3907 | |
3921 3908 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3931 3918 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
3932 3919 <span class="s">}</span> | |
3933 3920 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3935 3922 | |
3936 3923 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithEvenSize</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3946 3933 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
3947 3934 <span class="s">}</span> | |
3948 3935 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3950 3937 | |
3951 3938 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithSize</span><span class="s">(</span><span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3966 3953 | |
3967 3954 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3977 3964 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
3978 3965 <span class="s">}</span> | |
3979 3966 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3981 3968 | |
3982 3969 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfAtomRingsWithSizeGreaterThan</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
3992 3979 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
3993 3980 <span class="s">}</span> | |
3994 3981 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
3996 3983 | |
3997 3984 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRings</span><span class="s">(</span><span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
4011 3998 | |
4012 3999 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
4022 4009 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
4023 4010 <span class="s">}</span> | |
4024 4011 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
4026 4013 | |
4027 4014 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetLargestAtomRing</span><span class="s">(</span><span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
4041 4028 | |
4042 4029 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
4052 4039 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
4053 4040 <span class="s">}</span> | |
4054 4041 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
4056 4043 | |
4057 4044 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithEvenSize</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
4067 4054 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
4068 4055 <span class="s">}</span> | |
4069 4056 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
4071 4058 | |
4072 4059 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithSize</span><span class="s">(</span><span class="i">$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">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</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">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
4086 4073 | |
4087 4074 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_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">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
4097 4084 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
4098 4085 <span class="s">}</span> | |
4099 4086 <span class="k">my</span><span class="s">(</span><span class="i">$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">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
4101 4088 | |
4102 4089 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetAtomRingsWithSizeGreaterThan</span><span class="s">(</span><span class="i">$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">->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">->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">->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">->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">->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">->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">'undefined'</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">->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">'undefined'</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">->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">'undefined'</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">->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">'undefined'</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">->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">'undefined'</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">->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">'undefined'</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">->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">'undefined'</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">->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">'undefined'</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">->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">'undefined'</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">->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">'undefined'</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">->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">'undefined'</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">->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">'undefined'</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">->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">'undefined'</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">->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">$RingAtom</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> | |
4181 4168 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
4182 4169 <span class="s">}</span> | |
4183 4170 <span class="k">else</span> <span class="s">{</span> | |
4184 4171 <span class="i">$RingAtom</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
4185 4172 <span class="i">$NumOfRings</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
4186 4173 <span class="s">}</span> | |
4187 4174 | |
4188 4175 <span class="i">$AromaticAtom</span> = <span class="i">$This</span><span class="i">->GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
4189 4176 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$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">'Yes'</span> <span class="co">:</span> <span class="q">'No'</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">$AromaticAtom</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
4194 4181 <span class="s">}</span> | |
4195 4182 | |
4196 4183 <span class="i">$StereochemistryString</span> = <span class="q">''</span><span class="sc">;</span> | |
4197 4184 <span class="i">$StereoCenter</span> = <span class="i">$This</span><span class="i">->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">$This</span><span class="i">->IsStereoCenter</span><span class="s">(</span><span class="s">)</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> | |
4200 4187 <span class="i">$StereoChemistry</span> = <span class="i">$This</span><span class="i">->GetStereochemistry</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
4201 4188 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$StereoChemistry</span><span class="s">)</span> <span class="s">{</span> | |
4202 4189 <span class="i">$StereoChemistry</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
4203 4190 <span class="s">}</span> | |
4204 4191 <span class="i">$StereochemistryString</span> = <span class="q">"StereoCenter: $StereoCenterStatus; Stereochemistry: $StereoChemistry"</span><span class="sc">;</span> | |
4205 4192 <span class="s">}</span> | |
4206 4193 | |
4207 4194 <span class="i">$AtomString</span> = <span class="q">"Atom: ID: $ID; Name: \"$Name\"; AtomSymbol: \"$AtomSymbol\"; 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: $AromaticAtom"</span><span class="sc">;</span> | |
4208 4195 | |
4209 4196 <span class="k">if</span> <span class="s">(</span><span class="i">$StereochemistryString</span><span class="s">)</span> <span class="s">{</span> | |
4210 4197 <span class="i">$AtomString</span> .= <span class="q">"; $StereochemistryString"</span><span class="sc">;</span> | |
4211 4198 <span class="s">}</span> | |
4212 4199 | |
4213 4200 <span class="k">return</span> <span class="i">$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 <MayaChemTools>/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">"/data/MDLValenceModelData.csv"</span><span class="sc">;</span> | |
4239 4226 <span class="i">$DaylightValenceModelDataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">"/data/DaylightValenceModelData.csv"</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">"$MDLValenceModelDataFile"</span><span class="s">)</span> <span class="s">{</span> | |
4242 4229 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAtomValenceModelData: MayaChemTools package file, $MDLValenceModelDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> | |
4243 4230 <span class="s">}</span> | |
4244 4231 | |
4245 4232 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$DaylightValenceModelDataFile"</span><span class="s">)</span> <span class="s">{</span> | |
4246 4233 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAtomValenceModelData: MayaChemTools package file, $DaylightValenceModelDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> | |
4247 4234 <span class="s">}</span> | |
4248 4235 | |
4249 4236 <span class="i">_LoadValenceModelDataFile</span><span class="s">(</span><span class="i">$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">$DataMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
4259 4246 | |
4260 4247 <span class="c"># File format:</span> | |
4261 4248 <span class="c">#</span> | |
4262 4249 <span class="c"># "AtomicNumber","ElementSymbol","FormalCharge","CommomValences"</span> | |
4263 4250 <span class="c">#</span> | |
4264 4251 <span class="k">my</span><span class="s">(</span><span class="i">$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">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span> | |
4267 4254 <span class="k">open</span> <span class="w">DATAFILE</span><span class="cm">,</span> <span class="q">"$DataFile"</span> <span class="k">or</span> <span class="w">croak</span> <span class="q">"Couldn't open $DataFile: $! ..."</span><span class="sc">;</span> | |
4268 4255 | |
4269 4256 <span class="c"># Skip lines up to column labels...</span> | |
4270 4257 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$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">"Error: ${ClassName}::_LoadValenceModelDataFile: The number of data fields, @LineWords, in $DataFile must be $NumOfCols.\nLine: $Line..."</span><span class="sc">;</span> | |
4289 4276 <span class="s">}</span> | |
4290 4277 | |
4291 4278 <span class="s">(</span><span class="i">$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>->{<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>->{<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">"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: $Line..."</span><span class="sc">;</span> | |
4298 4285 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
4299 4286 <span class="s">}</span> | |
4300 4287 <span class="s">}</span> | |
4301 4288 <span class="k">else</span> <span class="s">{</span> | |
4302 4289 <span class="c"># Data for a new element...</span> | |
4303 4290 <span class="i">%</span>{<span class="i">$DataMapRef</span>->{<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>->{<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">$DataMapRef</span>->{<span class="i">$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">$DataMapRef</span>->{<span class="i">$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>->{<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">$a</span> <=> <span class="i">$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> </p> | |
4317 <br /> | |
4318 <center> | |
4319 <img src="../../../images/h2o2.png"> | |
4320 </center> | |
4321 </body> | |
4322 </html> |