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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Code:Bond.pm</title> | |
4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
6 </head> | |
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
8 <br/> | |
9 <center> | |
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
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13 <pre> | |
14 <a name="package-Bond-"></a> 1 <span class="k">package </span><span class="i">Bond</span><span class="sc">;</span> | |
15 2 <span class="c">#</span> | |
16 3 <span class="c"># $RCSfile: Bond.pm,v $</span> | |
17 4 <span class="c"># $Date: 2015/02/28 20:47:02 $</span> | |
18 5 <span class="c"># $Revision: 1.40 $</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 | |
49 36 <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> | |
50 37 | |
51 38 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> | |
52 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
53 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
54 41 | |
55 42 <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> | |
56 43 | |
57 44 <span class="c"># Setup class variables...</span> | |
58 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">$ObjectID</span><span class="s">)</span><span class="sc">;</span> | |
59 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
60 47 | |
61 48 <span class="c"># Overload Perl functions...</span> | |
62 49 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyBond'</span><span class="sc">;</span> | |
63 50 | |
64 51 <span class="c"># Class constructor...</span> | |
65 <a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
66 53 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
67 54 | |
68 55 <span class="c"># Initialize object...</span> | |
69 56 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> | |
70 57 <span class="k">bless</span> <span class="i">$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> | |
71 58 <span class="i">$This</span><span class="i">->_InitializeBond</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
72 59 | |
73 60 <span class="i">$This</span><span class="i">->_InitializeBondProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
74 61 | |
75 62 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
76 63 <span class="s">}</span> | |
77 64 | |
78 65 <span class="c"># Initialize object data...</span> | |
79 66 <span class="c">#</span> | |
80 <a name="_InitializeBond-"></a> 67 <span class="k">sub </span><span class="m">_InitializeBond</span> <span class="s">{</span> | |
81 68 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
82 69 <span class="k">my</span><span class="s">(</span><span class="i">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
83 70 | |
84 71 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> | |
85 72 <span class="c"># are implemented on-demand using ObjectProperty class.</span> | |
86 73 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span> | |
87 74 | |
88 75 <span class="c"># Bond from and to atoms indicate begining and ending bond atoms...</span> | |
89 76 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="k">undef</span><span class="sc">;</span> | |
90 77 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="k">undef</span><span class="sc">;</span> | |
91 78 | |
92 79 <span class="i">$This</span>->{<span class="w">BondOrder</span>} = <span class="q">''</span><span class="sc">;</span> | |
93 80 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="q">''</span><span class="sc">;</span> | |
94 81 <span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} = <span class="q">''</span><span class="sc">;</span> | |
95 82 <span class="s">}</span> | |
96 83 | |
97 84 <span class="c"># Initialize class ...</span> | |
98 <a name="_InitializeClass-"></a> 85 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
99 86 <span class="c">#Class name...</span> | |
100 87 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
101 88 | |
102 89 <span class="c"># ID to keep track of objects...</span> | |
103 90 <span class="i">$ObjectID</span> = <span class="n">0</span><span class="sc">;</span> | |
104 91 <span class="s">}</span> | |
105 92 | |
106 93 <span class="c"># Initialize bond properties...</span> | |
107 <a name="_InitializeBondProperties-"></a> 94 <span class="k">sub </span><span class="m">_InitializeBondProperties</span> <span class="s">{</span> | |
108 95 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
109 96 | |
110 97 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
111 98 <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> | |
112 99 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
113 100 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
114 101 <span class="s">}</span> | |
115 102 | |
116 103 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'Atoms'</span>}<span class="s">)</span> <span class="s">{</span> | |
117 104 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Bond object instantiated without specifying atoms list..."</span><span class="sc">;</span> | |
118 105 <span class="s">}</span> | |
119 106 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'BondOrder'</span>}<span class="s">)</span> <span class="s">{</span> | |
120 107 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Bond object instantiated without setting bond order..."</span><span class="sc">;</span> | |
121 108 <span class="s">}</span> | |
122 109 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
123 110 <span class="s">}</span> | |
124 111 | |
125 112 <span class="c"># Setup an explicit SetID method to block setting of ID by AUTOLOAD function...</span> | |
126 <a name="SetID-"></a> 113 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span> | |
127 114 <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> | |
128 115 | |
129 116 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> | |
130 117 | |
131 118 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
132 119 <span class="s">}</span> | |
133 120 | |
134 121 <span class="c"># Setup an explicit SetMolecule method to block setting of ID by AUTOLOAD function...</span> | |
135 <a name="SetMolecule-"></a> 122 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> | |
136 123 <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> | |
137 124 | |
138 125 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMolecule: Molecule property can't be changed: it's used for internal tracking..."</span><span class="sc">;</span> | |
139 126 | |
140 127 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
141 128 <span class="s">}</span> | |
142 129 | |
143 130 <span class="c"># Assign bond to molecule...</span> | |
144 <a name="_SetMolecule-"></a> 131 <span class="k">sub </span><span class="m">_SetMolecule</span> <span class="s">{</span> | |
145 132 <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> | |
146 133 | |
147 134 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> | |
148 135 | |
149 136 <span class="c"># Weaken the reference to disable increment of reference count; otherwise,</span> | |
150 137 <span class="c"># it it becomes a circular reference and destruction of Molecule object doesn't</span> | |
151 138 <span class="c"># get initiated which in turn disables destruction of bond object.</span> | |
152 139 <span class="c">#</span> | |
153 140 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
154 141 | |
155 142 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
156 143 <span class="s">}</span> | |
157 144 | |
158 145 <span class="c"># Set bond atoms...</span> | |
159 <a name="SetAtoms-"></a> 146 <span class="k">sub </span><span class="m">SetAtoms</span> <span class="s">{</span> | |
160 147 <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> | |
161 148 | |
162 149 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> | |
163 150 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtoms: No atoms specified..."</span><span class="sc">;</span> | |
164 151 <span class="s">}</span> | |
165 152 | |
166 153 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span> | |
167 154 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> | |
168 155 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> | |
169 156 | |
170 157 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> | |
171 158 <span class="c"># Initialize using array refernce...</span> | |
172 159 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FirstValue</span>} != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
173 160 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Number of atoms specified in bond object is not equal to 2..."</span><span class="sc">;</span> | |
174 161 <span class="s">}</span> | |
175 162 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span> | |
176 163 <span class="s">}</span> | |
177 164 <span class="k">else</span> <span class="s">{</span> | |
178 165 <span class="c"># It's a list of values...</span> | |
179 166 <span class="k">if</span> <span class="s">(</span><span class="i">@Values</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
180 167 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Number of atoms specified in bond object is not equal to 2..."</span><span class="sc">;</span> | |
181 168 <span class="s">}</span> | |
182 169 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@Values</span><span class="sc">;</span> | |
183 170 <span class="s">}</span> | |
184 171 | |
185 172 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
186 173 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID1</span> == <span class="i">$AtomID2</span><span class="s">)</span> <span class="s">{</span> | |
187 174 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Can't specify same atoms to create a bond..."</span><span class="sc">;</span> | |
188 175 <span class="s">}</span> | |
189 176 | |
190 177 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="i">$Atom1</span><span class="sc">;</span> | |
191 178 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="i">$Atom2</span><span class="sc">;</span> | |
192 179 | |
193 180 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
194 181 <span class="s">}</span> | |
195 182 | |
196 183 <span class="c"># Get bond atoms as array. In scalar context, return number of atoms involved in</span> | |
197 184 <span class="c"># bond...</span> | |
198 185 <span class="c">#</span> | |
199 <a name="GetAtoms-"></a> 186 <span class="k">sub </span><span class="m">GetAtoms</span> <span class="s">{</span> | |
200 187 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
201 188 | |
202 189 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondFromAtom</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">BondToAtom</span>}<span class="s">)</span> <span class="co">:</span> <span class="n">2</span><span class="sc">;</span> | |
203 190 <span class="s">}</span> | |
204 191 | |
205 192 <span class="c"># Get atom bonded to specified atom...</span> | |
206 <a name="GetBondedAtom-"></a> 193 <span class="k">sub </span><span class="m">GetBondedAtom</span> <span class="s">{</span> | |
207 194 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
208 195 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
209 196 | |
210 197 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
211 198 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
212 199 | |
213 200 <span class="k">return</span> <span class="s">(</span><span class="i">$AtomID1</span> == <span class="i">$AtomID</span><span class="s">)</span> ? <span class="i">$Atom2</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomID2</span> == <span class="i">$AtomID</span><span class="s">)</span> ? <span class="i">$Atom1</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span> <span class="sc">;</span> | |
214 201 <span class="s">}</span> | |
215 202 | |
216 203 <span class="c"># Get common atom between two bonds...</span> | |
217 <a name="GetCommonAtom-"></a> 204 <span class="k">sub </span><span class="m">GetCommonAtom</span> <span class="s">{</span> | |
218 205 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
219 206 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$OtherAtom1</span><span class="cm">,</span> <span class="i">$OtherAtom2</span><span class="cm">,</span> <span class="i">$OtherAtomID1</span><span class="cm">,</span> <span class="i">$OtherAtomID2</span><span class="s">)</span><span class="sc">;</span> | |
220 207 | |
221 208 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
222 209 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
223 210 | |
224 211 <span class="s">(</span><span class="i">$OtherAtom1</span><span class="cm">,</span> <span class="i">$OtherAtom2</span><span class="s">)</span> = <span class="i">$Other</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
225 212 <span class="i">$OtherAtomID1</span> = <span class="i">$OtherAtom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$OtherAtomID2</span> = <span class="i">$OtherAtom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
226 213 | |
227 214 <span class="k">return</span> <span class="s">(</span><span class="i">$AtomID1</span> == <span class="i">$OtherAtomID1</span> || <span class="i">$AtomID1</span> == <span class="i">$OtherAtomID2</span><span class="s">)</span> ? <span class="i">$Atom1</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomID2</span> == <span class="i">$OtherAtomID1</span> || <span class="i">$AtomID2</span> == <span class="i">$OtherAtomID2</span><span class="s">)</span> ? <span class="i">$Atom2</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span> <span class="sc">;</span> | |
228 215 <span class="s">}</span> | |
229 216 | |
230 217 <span class="c"># Get bond from atom indicating begining atom of a bond...</span> | |
231 <a name="GetBondFromAtom-"></a> 218 <span class="k">sub </span><span class="m">GetBondFromAtom</span> <span class="s">{</span> | |
232 219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
233 220 | |
234 221 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">BondFromAtom</span>}<span class="sc">;</span> | |
235 222 <span class="s">}</span> | |
236 223 | |
237 224 <span class="c"># Get begin bond atom...</span> | |
238 <a name="GetBondBeginAtom-"></a> 225 <span class="k">sub </span><span class="m">GetBondBeginAtom</span> <span class="s">{</span> | |
239 226 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
240 227 | |
241 228 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetBondFromAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
242 229 <span class="s">}</span> | |
243 230 | |
244 231 <span class="c"># Get bond to atom indicating ending atom of a bond...</span> | |
245 <a name="GetBondToAtom-"></a> 232 <span class="k">sub </span><span class="m">GetBondToAtom</span> <span class="s">{</span> | |
246 233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
247 234 | |
248 235 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">BondToAtom</span>}<span class="sc">;</span> | |
249 236 <span class="s">}</span> | |
250 237 | |
251 238 <span class="c"># Get begin bond atom...</span> | |
252 <a name="GetBondEndAtom-"></a> 239 <span class="k">sub </span><span class="m">GetBondEndAtom</span> <span class="s">{</span> | |
253 240 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
254 241 | |
255 242 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
256 243 <span class="s">}</span> | |
257 244 | |
258 245 <span class="c"># Switch bond from and to atoms...</span> | |
259 <a name="SwitchBondFromAndToAtoms-"></a> 246 <span class="k">sub </span><span class="m">SwitchBondFromAndToAtoms</span> <span class="s">{</span> | |
260 247 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
261 248 <span class="k">my</span><span class="s">(</span><span class="i">$FromAtom</span><span class="cm">,</span> <span class="i">$ToAtom</span><span class="s">)</span><span class="sc">;</span> | |
262 249 | |
263 250 <span class="s">(</span><span class="i">$FromAtom</span><span class="cm">,</span> <span class="i">$ToAtom</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
264 251 | |
265 252 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="i">$ToAtom</span><span class="sc">;</span> | |
266 253 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="i">$FromAtom</span><span class="sc">;</span> | |
267 254 | |
268 255 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
269 256 <span class="s">}</span> | |
270 257 | |
271 258 <span class="c"># Set bond order...</span> | |
272 259 <span class="c">#</span> | |
273 260 <span class="c"># Possible BondOrder are: 0 = None, 1 = Single, 1.5 = Aromatic, 2 = Double, 3 = Triple, 4 = Quadruple,</span> | |
274 261 <span class="c"># 5 = Quintuple, 6 = Sextuple, 7 = Septuple</span> | |
275 262 <span class="c">#</span> | |
276 263 <span class="c"># Possible BondType for different BondOrders are:</span> | |
277 264 <span class="c">#</span> | |
278 265 <span class="c"># 0 : None, Ionic, Unspecified</span> | |
279 266 <span class="c"># 1 : Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Tautomeric</span> | |
280 267 <span class="c"># 1.5 : Aromatic, Resonance, SingleOrAromatic, DoubleOrAromatic</span> | |
281 268 <span class="c"># 2 : Double, Tautomeric, SingleOrDouble, DoubleOrAromatic</span> | |
282 269 <span class="c"># 3 : Triple</span> | |
283 270 <span class="c"># 4 : Quadruple</span> | |
284 271 <span class="c"># 5 : Quintuple</span> | |
285 272 <span class="c"># 6 : Sextuple</span> | |
286 273 <span class="c"># 7 : Septuple</span> | |
287 274 <span class="c">#</span> | |
288 275 <span class="c"># Note: BondType Any is valid for all BondOrders.</span> | |
289 276 <span class="c">#</span> | |
290 277 <span class="c"># Possible BondStereochemistry values for different BondOrders are:</span> | |
291 278 <span class="c">#</span> | |
292 279 <span class="c"># 0 : None, Unspecified</span> | |
293 280 <span class="c"># 1 : Wedge, Up, Hash, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward, None, Unspecified</span> | |
294 281 <span class="c"># 2 : Cis, Trans, Z, E, DoubleCross, CisOrTrans, None, Unspecified</span> | |
295 282 <span class="c">#</span> | |
296 283 <span class="c"># Notes:</span> | |
297 284 <span class="c"># . BondType property is automatically assigned using default BondType values for</span> | |
298 285 <span class="c"># specified BondOrder.</span> | |
299 286 <span class="c"># . BondType values can also be explicit set.</span> | |
300 287 <span class="c"># . To make bonds aromatic in a ring, explicitly set "Aromatic" property for bond/atoms and make sure</span> | |
301 288 <span class="c"># appropriate BondOrder values are assigned.</span> | |
302 289 <span class="c"># . Dative or coordinate bond types are treated as single bond types with explicit formal charge</span> | |
303 290 <span class="c"># of + and - on first and second bond atoms.</span> | |
304 291 <span class="c">#</span> | |
305 <a name="SetBondOrder-"></a> 292 <span class="k">sub </span><span class="m">SetBondOrder</span> <span class="s">{</span> | |
306 293 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
307 294 | |
308 295 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> !~ <span class="q">/^(0|1|1.5|2|3|4|5|6|7)$/</span><span class="s">)</span> <span class="s">{</span> | |
309 296 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondOrder: BondOrder value $BondOrder is not valid. Supported values: 0, 1, 1.5, 2, 3, 4, 5, 6, 7"</span><span class="sc">;</span> | |
310 297 <span class="s">}</span> | |
311 298 | |
312 299 <span class="c"># Set bond order and type...</span> | |
313 300 <span class="k">my</span><span class="s">(</span><span class="i">$BondType</span><span class="s">)</span><span class="sc">;</span> | |
314 301 | |
315 302 <span class="j">BONDORDER:</span> <span class="s">{</span> | |
316 303 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Single'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
317 304 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1.5</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Aromatic'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
318 305 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Double'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
319 306 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Triple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
320 307 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">4</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Quadruple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
321 308 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">5</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Quintuple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
322 309 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">6</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Sextuple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
323 310 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">7</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Septuple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
324 311 <span class="i">$BondType</span> = <span class="q">''</span><span class="sc">;</span> | |
325 312 <span class="i">$BondOrder</span> = <span class="n">0</span><span class="sc">;</span> | |
326 313 <span class="s">}</span> | |
327 314 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="i">$BondType</span><span class="sc">;</span> | |
328 315 <span class="i">$This</span>->{<span class="w">BondOrder</span>} = <span class="i">$BondOrder</span><span class="sc">;</span> | |
329 316 | |
330 317 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
331 318 | |
332 319 <span class="s">}</span> | |
333 320 | |
334 321 <span class="c"># Set bond type for a specific bond...</span> | |
335 322 <span class="c">#</span> | |
336 <a name="SetBondType-"></a> 323 <span class="k">sub </span><span class="m">SetBondType</span> <span class="s">{</span> | |
337 324 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
338 325 | |
339 326 <span class="k">if</span> <span class="s">(</span><span class="i">$BondType</span> !~ <span class="q">/^(None|Ionic|Unspecified|Single|Dative|Coordinate|SingleOrDouble|SingleOrAromatic|Aromatic|Tautomeric|Resonance|DoubleOrAromatic|Double|Triple|Quadruple|Any)$/i</span><span class="s">)</span> <span class="s">{</span> | |
340 327 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondType: BondType value $BondType is not valid. Supported values: None, Ionic, Unspecified, Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Aromatic, Tautomeric, Resonance, DoubleOrAromatic, Double, Triple, Quadruple, Any..."</span><span class="sc">;</span> | |
341 328 <span class="s">}</span> | |
342 329 | |
343 330 <span class="c"># Make sure its a valid BondType value for BondOrder...</span> | |
344 331 <span class="k">my</span><span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$ValidBondType</span><span class="s">)</span><span class="sc">;</span> | |
345 332 | |
346 333 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> | |
347 334 <span class="i">$BondOrder</span> = <span class="i">$This</span>->{<span class="w">BondOrder</span>}<span class="sc">;</span> | |
348 335 | |
349 336 <span class="j">BONDORDER:</span> <span class="s">{</span> | |
350 337 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">0</span> && <span class="i">$BondType</span> =~ <span class="q">/^(None|Ionic|Unspecified|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
351 338 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Single|Dative|Coordinate|SingleOrDouble|SingleOrAromatic|Tautomeric|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
352 339 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1.5</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Aromatic|Resonance|SingleOrAromatic|DoubleOrAromatic|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
353 340 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Double|SingleOrDouble|DoubleOrAromatic|Tautomeric|Any)$/i</span> <span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
354 341 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">3</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Triple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
355 342 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">4</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Quadruple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
356 343 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">5</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Quintuple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
357 344 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">6</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Sextuple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
358 345 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">7</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Septuple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
359 346 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> | |
360 347 <span class="s">}</span> | |
361 348 | |
362 349 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ValidBondType</span><span class="s">)</span> <span class="s">{</span> | |
363 350 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetBondType: Assigning invalid BondType value, $BondType, for BondOrder $BondOrder..."</span><span class="sc">;</span> | |
364 351 <span class="s">}</span> | |
365 352 | |
366 353 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="i">$BondType</span><span class="sc">;</span> | |
367 354 | |
368 355 <span class="c"># Set explicit formal charge for atoms involved in Dative or coordinate bonds...</span> | |
369 356 <span class="k">if</span> <span class="s">(</span><span class="i">$BondType</span> =~ <span class="q">/^(Dative|Coordinate)$/i</span><span class="s">)</span> <span class="s">{</span> | |
370 357 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
371 358 <span class="i">$Atom1</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="q">'1'</span><span class="s">)</span><span class="sc">;</span> | |
372 359 <span class="i">$Atom2</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="q">'-1'</span><span class="s">)</span><span class="sc">;</span> | |
373 360 <span class="s">}</span> | |
374 361 | |
375 362 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
376 363 <span class="s">}</span> | |
377 364 | |
378 365 <span class="c"># Set bond stereochemistry...</span> | |
379 366 <span class="c">#</span> | |
380 367 <span class="c"># Single bond stereochemistry:</span> | |
381 368 <span class="c">#</span> | |
382 369 <span class="c"># None, Unspecified: Not a stereo bond or unspecified</span> | |
383 370 <span class="c">#</span> | |
384 371 <span class="c"># Wedge, Up : Wedge end pointing up</span> | |
385 372 <span class="c"># Hash, Down: Wedge end pointing down</span> | |
386 373 <span class="c"># Wavy, WedgeOrHash, UpOrDown: Wedge end up or down</span> | |
387 374 <span class="c">#</span> | |
388 375 <span class="c"># Note: Wedge starts at begin atom of bond making wedge pointed end always at this</span> | |
389 376 <span class="c"># atom.</span> | |
390 377 <span class="c">#</span> | |
391 378 <span class="c"># Upward: Single bond around cis/trans double bonds pointing upward</span> | |
392 379 <span class="c"># Downward: Single bond around cis/trans double bonds pointing upward</span> | |
393 380 <span class="c">#</span> | |
394 381 <span class="c"># Note: Upward/downward bonds start at atoms involved in cis/trans double bond.</span> | |
395 382 <span class="c">#</span> | |
396 383 <span class="c"># Double bond stereochemistry:</span> | |
397 384 <span class="c">#</span> | |
398 385 <span class="c"># None, Unspecified: Not a stereo bond or unspecified</span> | |
399 386 <span class="c">#</span> | |
400 387 <span class="c"># Z, cis: Similar groups on same side of double bond</span> | |
401 388 <span class="c"># E, trans: Similar groups on different side of double bond</span> | |
402 389 <span class="c">#</span> | |
403 390 <span class="c"># CisOrTrans, DoubleCross: cis or trans</span> | |
404 391 <span class="c">#</span> | |
405 <a name="SetBondStereochemistry-"></a> 392 <span class="k">sub </span><span class="m">SetBondStereochemistry</span> <span class="s">{</span> | |
406 393 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondStereochemistry</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
407 394 | |
408 395 <span class="k">if</span> <span class="s">(</span><span class="i">$BondStereochemistry</span> !~ <span class="q">/^(None|Unspecified|Wedge|Hash|Up|Down|Wavy|WedgeOrHash|UpOrDown|Upward|Downward|Cis|Trans|Z|E|DoubleCross|CisOrTrans)$/i</span><span class="s">)</span> <span class="s">{</span> | |
409 396 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondStereochemistry: BondStereochemistry value $BondStereochemistry is not valid. Supported values: None, Unspecified, Wedge, Hash, Up, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward, Cis, Trans, Z, E, DoubleCross, CisOrTrans..."</span><span class="sc">;</span> | |
410 397 <span class="s">}</span> | |
411 398 | |
412 399 <span class="c"># Make sure its a valid BondStereochemistry value for BondOrder...</span> | |
413 400 <span class="k">my</span><span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$ValidBondType</span><span class="s">)</span><span class="sc">;</span> | |
414 401 | |
415 402 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> | |
416 403 <span class="i">$BondOrder</span> = <span class="i">$This</span>->{<span class="w">BondOrder</span>}<span class="sc">;</span> | |
417 404 | |
418 405 <span class="j">BONDORDER:</span> <span class="s">{</span> | |
419 406 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">0</span> && <span class="i">$BondStereochemistry</span> =~ <span class="q">/^(None|Unspecified)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
420 407 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span> && <span class="i">$BondStereochemistry</span> =~ <span class="q">/^(Wedge|Hash|Up|Down|Wavy|WedgeOrHash|UpOrDown|Upward|Downward|None|Unspecified)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
421 408 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span> && <span class="i">$BondStereochemistry</span> =~ <span class="q">/^(Cis|Trans|Z|E|DoubleCross|CisOrTrans|None|Unspecified)$/i</span> <span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span> | |
422 409 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span> | |
423 410 <span class="s">}</span> | |
424 411 | |
425 412 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ValidBondType</span><span class="s">)</span> <span class="s">{</span> | |
426 413 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetBondStereochemistry: Assigning invalid BondStereochemistry value, $BondStereochemistry, for BondOrder $BondOrder..."</span><span class="sc">;</span> | |
427 414 <span class="s">}</span> | |
428 415 | |
429 416 <span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} = <span class="i">$BondStereochemistry</span><span class="sc">;</span> | |
430 417 | |
431 418 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
432 419 <span class="s">}</span> | |
433 420 | |
434 421 <span class="c"># Is it a single bond?</span> | |
435 <a name="IsSingle-"></a> 422 <span class="k">sub </span><span class="m">IsSingle</span> <span class="s">{</span> | |
436 423 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
437 424 | |
438 425 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</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> | |
439 426 <span class="s">}</span> | |
440 427 | |
441 428 <span class="c"># Is it a double bond?</span> | |
442 <a name="IsDouble-"></a> 429 <span class="k">sub </span><span class="m">IsDouble</span> <span class="s">{</span> | |
443 430 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
444 431 | |
445 432 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</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> | |
446 433 <span class="s">}</span> | |
447 434 | |
448 435 <span class="c"># Is it a triple bond?</span> | |
449 <a name="IsTriple-"></a> 436 <span class="k">sub </span><span class="m">IsTriple</span> <span class="s">{</span> | |
450 437 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
451 438 | |
452 439 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">3</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
453 440 <span class="s">}</span> | |
454 441 | |
455 442 <span class="c"># Is it a quadruple bond?</span> | |
456 <a name="IsQuadruple-"></a> 443 <span class="k">sub </span><span class="m">IsQuadruple</span> <span class="s">{</span> | |
457 444 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
458 445 | |
459 446 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">4</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
460 447 <span class="s">}</span> | |
461 448 | |
462 449 <span class="c"># Is aromatic property set for the bond?</span> | |
463 <a name="IsAromatic-"></a> 450 <span class="k">sub </span><span class="m">IsAromatic</span> <span class="s">{</span> | |
464 451 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
465 452 <span class="k">my</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span><span class="sc">;</span> | |
466 453 | |
467 454 <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> | |
468 455 | |
469 456 <span class="k">return</span> <span class="s">(</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="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">1.5</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
470 457 <span class="s">}</span> | |
471 458 | |
472 459 <span class="c"># Is it a quintuple bond?</span> | |
473 <a name="IsQuintuple-"></a> 460 <span class="k">sub </span><span class="m">IsQuintuple</span> <span class="s">{</span> | |
474 461 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
475 462 | |
476 463 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">5</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
477 464 <span class="s">}</span> | |
478 465 | |
479 466 <span class="c"># Is it a sextuple bond?</span> | |
480 <a name="IsSextuple-"></a> 467 <span class="k">sub </span><span class="m">IsSextuple</span> <span class="s">{</span> | |
481 468 <span class="k">my</span><span class="s">(</span><span class="i">$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="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">6</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
484 471 <span class="s">}</span> | |
485 472 | |
486 473 <span class="c"># Is bond type specified?</span> | |
487 <a name="IsBondTypeSpecified-"></a> 474 <span class="k">sub </span><span class="m">IsBondTypeSpecified</span> <span class="s">{</span> | |
488 475 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
489 476 | |
490 477 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} && <span class="i">$This</span>->{<span class="w">BondType</span>} !~ <span class="q">/^(None|Unspecified)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
491 478 <span class="s">}</span> | |
492 479 | |
493 480 <span class="c"># Is it a dative or coordinate bond?</span> | |
494 <a name="IsDative-"></a> 481 <span class="k">sub </span><span class="m">IsDative</span> <span class="s">{</span> | |
495 482 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
496 483 | |
497 484 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} =~ <span class="q">/^(Dative|Coordinate)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
498 485 <span class="s">}</span> | |
499 486 | |
500 487 <span class="c"># Is it a dative or coordinate bond?</span> | |
501 <a name="IsCoordinate-"></a> 488 <span class="k">sub </span><span class="m">IsCoordinate</span> <span class="s">{</span> | |
502 489 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
503 490 | |
504 491 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsDative</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
505 492 <span class="s">}</span> | |
506 493 | |
507 494 <span class="c"># Is it a ionic bond?</span> | |
508 <a name="IsIonic-"></a> 495 <span class="k">sub </span><span class="m">IsIonic</span> <span class="s">{</span> | |
509 496 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
510 497 | |
511 498 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} =~ <span class="q">/^Ionic$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
512 499 <span class="s">}</span> | |
513 500 | |
514 501 <span class="c"># Is it a tautomeric bond?</span> | |
515 <a name="IsTautomeric-"></a> 502 <span class="k">sub </span><span class="m">IsTautomeric</span> <span class="s">{</span> | |
516 503 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
517 504 | |
518 505 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} =~ <span class="q">/^Tautomeric$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
519 506 <span class="s">}</span> | |
520 507 | |
521 508 <span class="c"># Is bond stereochemistry specified?</span> | |
522 <a name="IsBondStereochemistrySpecified-"></a> 509 <span class="k">sub </span><span class="m">IsBondStereochemistrySpecified</span> <span class="s">{</span> | |
523 510 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
524 511 | |
525 512 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} && <span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} !~ <span class="q">/^(None|Unspecified)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
526 513 <span class="s">}</span> | |
527 514 | |
528 515 <span class="c"># Is it a Wedge or Up single bond?</span> | |
529 <a name="IsWedge-"></a> 516 <span class="k">sub </span><span class="m">IsWedge</span> <span class="s">{</span> | |
530 517 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
531 518 | |
532 519 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUp</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
533 520 <span class="s">}</span> | |
534 521 | |
535 522 <span class="c"># Is it a Wedge or Up single bond?</span> | |
536 <a name="IsUp-"></a> 523 <span class="k">sub </span><span class="m">IsUp</span> <span class="s">{</span> | |
537 524 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
538 525 | |
539 526 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Wedge|Up)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
540 527 <span class="s">}</span> | |
541 528 | |
542 529 <span class="c"># Is it a Hash or Down single bond?</span> | |
543 <a name="IsHash-"></a> 530 <span class="k">sub </span><span class="m">IsHash</span> <span class="s">{</span> | |
544 531 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
545 532 | |
546 533 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsDown</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
547 534 <span class="s">}</span> | |
548 535 | |
549 536 <span class="c"># Is it a Hash or Down single bond?</span> | |
550 <a name="IsDown-"></a> 537 <span class="k">sub </span><span class="m">IsDown</span> <span class="s">{</span> | |
551 538 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
552 539 | |
553 540 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Hash|Down)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
554 541 <span class="s">}</span> | |
555 542 | |
556 543 <span class="c"># Is it a Wavy, WedgeOrHash or UpOrDown single bond?</span> | |
557 <a name="IsWedgeOrHash-"></a> 544 <span class="k">sub </span><span class="m">IsWedgeOrHash</span> <span class="s">{</span> | |
558 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
559 546 | |
560 547 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUpOrDown</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
561 548 <span class="s">}</span> | |
562 549 | |
563 550 <span class="c"># Is it a Wavy, WedgeOrHash or UpOrDown single bond?</span> | |
564 <a name="IsUpOrDown-"></a> 551 <span class="k">sub </span><span class="m">IsUpOrDown</span> <span class="s">{</span> | |
565 552 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
566 553 | |
567 554 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Wavy|WedgeOrHash|UpOrDown)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
568 555 <span class="s">}</span> | |
569 556 | |
570 557 <span class="c"># Is it a upward single bond?</span> | |
571 <a name="IsUpward-"></a> 558 <span class="k">sub </span><span class="m">IsUpward</span> <span class="s">{</span> | |
572 559 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
573 560 | |
574 561 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^Upward$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
575 562 <span class="s">}</span> | |
576 563 | |
577 564 <span class="c"># Is it a Downward single bond?</span> | |
578 <a name="IsDownward-"></a> 565 <span class="k">sub </span><span class="m">IsDownward</span> <span class="s">{</span> | |
579 566 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
580 567 | |
581 568 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^Downward$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
582 569 <span class="s">}</span> | |
583 570 <span class="c"># Is it a cis or Z double bond?</span> | |
584 <a name="IsCis-"></a> 571 <span class="k">sub </span><span class="m">IsCis</span> <span class="s">{</span> | |
585 572 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
586 573 | |
587 574 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Cis|Z)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
588 575 <span class="s">}</span> | |
589 576 | |
590 577 <span class="c"># Is it a trans or E double bond?</span> | |
591 <a name="IsTrans-"></a> 578 <span class="k">sub </span><span class="m">IsTrans</span> <span class="s">{</span> | |
592 579 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
593 580 | |
594 581 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Trans|E)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
595 582 <span class="s">}</span> | |
596 583 | |
597 584 <span class="c"># Is it a cis or trans double bond?</span> | |
598 <a name="IsCisOrTrans-"></a> 585 <span class="k">sub </span><span class="m">IsCisOrTrans</span> <span class="s">{</span> | |
599 586 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
600 587 | |
601 588 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(CisOrTrans|DoubleCross)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
602 589 <span class="s">}</span> | |
603 590 | |
604 591 <span class="c"># Delete bond...</span> | |
605 <a name="DeleteBond-"></a> 592 <span class="k">sub </span><span class="m">DeleteBond</span> <span class="s">{</span> | |
606 593 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
607 594 | |
608 595 <span class="c"># Is this atom in a molecule?</span> | |
609 596 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
610 597 <span class="c"># Nothing to do...</span> | |
611 598 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
612 599 <span class="s">}</span> | |
613 600 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
614 601 <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> | |
615 602 <span class="i">$Molecule</span><span class="i">->DeleteBond</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
616 603 | |
617 604 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
618 605 <span class="s">}</span> | |
619 606 | |
620 607 <span class="c"># Copy bond and all its associated data...</span> | |
621 <a name="Copy-"></a> 608 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span> | |
622 609 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
623 610 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span> | |
624 611 | |
625 612 <span class="i">$Bond</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
626 613 | |
627 614 <span class="k">return</span> <span class="i">$Bond</span><span class="sc">;</span> | |
628 615 <span class="s">}</span> | |
629 616 | |
630 617 <span class="c"># Is bond in a ring?</span> | |
631 618 <span class="c">#</span> | |
632 <a name="IsInRing-"></a> 619 <span class="k">sub </span><span class="m">IsInRing</span> <span class="s">{</span> | |
633 620 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
634 621 | |
635 622 <span class="c"># Is this bond in a molecule?</span> | |
636 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
637 624 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
638 625 <span class="s">}</span> | |
639 626 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
640 627 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
641 628 | |
642 629 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
643 630 <span class="s">}</span> | |
644 631 | |
645 632 <span class="c"># Is bond not in a ring?</span> | |
646 633 <span class="c">#</span> | |
647 <a name="IsNotInRing-"></a> 634 <span class="k">sub </span><span class="m">IsNotInRing</span> <span class="s">{</span> | |
648 635 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
649 636 | |
650 637 <span class="c"># Is this bond in a molecule?</span> | |
651 638 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
652 639 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
653 640 <span class="s">}</span> | |
654 641 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
655 642 <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> | |
656 643 | |
657 644 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondNotInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
658 645 <span class="s">}</span> | |
659 646 | |
660 647 <span class="c"># Is bond only in one ring?</span> | |
661 648 <span class="c">#</span> | |
662 <a name="IsOnlyInOneRing-"></a> 649 <span class="k">sub </span><span class="m">IsOnlyInOneRing</span> <span class="s">{</span> | |
663 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
664 651 | |
665 652 <span class="c"># Is this bond in a molecule?</span> | |
666 653 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
667 654 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
668 655 <span class="s">}</span> | |
669 656 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
670 657 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
671 658 | |
672 659 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondInOnlyOneRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
673 660 <span class="s">}</span> | |
674 661 | |
675 662 <span class="c"># Is bond in a ring of specific size?</span> | |
676 663 <span class="c">#</span> | |
677 <a name="IsInRingOfSize-"></a> 664 <span class="k">sub </span><span class="m">IsInRingOfSize</span> <span class="s">{</span> | |
678 665 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
679 666 | |
680 667 <span class="c"># Is this bond in a molecule?</span> | |
681 668 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
682 669 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
683 670 <span class="s">}</span> | |
684 671 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
685 672 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
686 673 | |
687 674 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondInRingOfSize</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> | |
688 675 <span class="s">}</span> | |
689 676 | |
690 677 <span class="c"># Get size of smallest ring containing the bond...</span> | |
691 678 <span class="c">#</span> | |
692 <a name="GetSizeOfSmallestRing-"></a> 679 <span class="k">sub </span><span class="m">GetSizeOfSmallestRing</span> <span class="s">{</span> | |
693 680 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
694 681 | |
695 682 <span class="c"># Is this bond in a molecule?</span> | |
696 683 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
697 684 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
698 685 <span class="s">}</span> | |
699 686 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
700 687 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
701 688 | |
702 689 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfSmallestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
703 690 <span class="s">}</span> | |
704 691 | |
705 692 <span class="c"># Get size of largest ring containing the bond...</span> | |
706 693 <span class="c">#</span> | |
707 <a name="GetSizeOfLargestRing-"></a> 694 <span class="k">sub </span><span class="m">GetSizeOfLargestRing</span> <span class="s">{</span> | |
708 695 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
709 696 | |
710 697 <span class="c"># Is this bond in a molecule?</span> | |
711 698 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
712 699 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
713 700 <span class="s">}</span> | |
714 701 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
715 702 <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> | |
716 703 | |
717 704 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfLargestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
718 705 <span class="s">}</span> | |
719 706 | |
720 707 <span class="c"># Get number of rings containing the bond...</span> | |
721 708 <span class="c">#</span> | |
722 <a name="GetNumOfRings-"></a> 709 <span class="k">sub </span><span class="m">GetNumOfRings</span> <span class="s">{</span> | |
723 710 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
724 711 | |
725 712 <span class="c"># Is this bond in a molecule?</span> | |
726 713 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
727 714 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
728 715 <span class="s">}</span> | |
729 716 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
730 717 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
731 718 | |
732 719 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
733 720 <span class="s">}</span> | |
734 721 | |
735 722 <span class="c"># Get number of rings with odd size containing the bond...</span> | |
736 723 <span class="c">#</span> | |
737 <a name="GetNumOfRingsWithOddSize-"></a> 724 <span class="k">sub </span><span class="m">GetNumOfRingsWithOddSize</span> <span class="s">{</span> | |
738 725 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
739 726 | |
740 727 <span class="c"># Is this bond in a molecule?</span> | |
741 728 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
742 729 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
743 730 <span class="s">}</span> | |
744 731 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
745 732 <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> | |
746 733 | |
747 734 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
748 735 <span class="s">}</span> | |
749 736 | |
750 737 <span class="c"># Get number of rings with even size containing the bond...</span> | |
751 738 <span class="c">#</span> | |
752 <a name="GetNumOfRingsWithEvenSize-"></a> 739 <span class="k">sub </span><span class="m">GetNumOfRingsWithEvenSize</span> <span class="s">{</span> | |
753 740 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
754 741 | |
755 742 <span class="c"># Is this bond in a molecule?</span> | |
756 743 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
757 744 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
758 745 <span class="s">}</span> | |
759 746 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
760 747 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
761 748 | |
762 749 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
763 750 <span class="s">}</span> | |
764 751 | |
765 752 <span class="c"># Get number of rings with specified size containing the bond...</span> | |
766 753 <span class="c">#</span> | |
767 <a name="GetNumOfRingsWithSize-"></a> 754 <span class="k">sub </span><span class="m">GetNumOfRingsWithSize</span> <span class="s">{</span> | |
768 755 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
769 756 | |
770 757 <span class="c"># Is this bond in a molecule?</span> | |
771 758 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
772 759 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
773 760 <span class="s">}</span> | |
774 761 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
775 762 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
776 763 | |
777 764 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithSize</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> | |
778 765 <span class="s">}</span> | |
779 766 | |
780 767 <span class="c"># Get number of rings with size less than specified containing the bond...</span> | |
781 768 <span class="c">#</span> | |
782 <a name="GetNumOfRingsWithSizeLessThan-"></a> 769 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeLessThan</span> <span class="s">{</span> | |
783 770 <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> | |
784 771 | |
785 772 <span class="c"># Is this bond in a molecule?</span> | |
786 773 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
787 774 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
788 775 <span class="s">}</span> | |
789 776 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
790 777 <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> | |
791 778 | |
792 779 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithSizeLessThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
793 780 <span class="s">}</span> | |
794 781 | |
795 782 <span class="c"># Get number of rings with size greater than specified size containing the bond...</span> | |
796 783 <span class="c">#</span> | |
797 <a name="GetNumOfRingsWithSizeGreaterThan-"></a> 784 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
798 785 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
799 786 | |
800 787 <span class="c"># Is this bond in a molecule?</span> | |
801 788 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
802 789 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
803 790 <span class="s">}</span> | |
804 791 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
805 792 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
806 793 | |
807 794 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithSizeGreaterThan</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> | |
808 795 <span class="s">}</span> | |
809 796 | |
810 797 <span class="c"># Get all rings as an array of references to arrays containing ring atoms...</span> | |
811 798 <span class="c">#</span> | |
812 <a name="GetRings-"></a> 799 <span class="k">sub </span><span class="m">GetRings</span> <span class="s">{</span> | |
813 800 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
814 801 | |
815 802 <span class="c"># Is this bond in a molecule?</span> | |
816 803 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
817 804 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
818 805 <span class="s">}</span> | |
819 806 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
820 807 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
821 808 | |
822 809 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
823 810 <span class="s">}</span> | |
824 811 | |
825 812 <span class="c"># Get smallest ring as an array containing ring atoms...</span> | |
826 813 <span class="c">#</span> | |
827 <a name="GetSmallestRing-"></a> 814 <span class="k">sub </span><span class="m">GetSmallestRing</span> <span class="s">{</span> | |
828 815 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
829 816 | |
830 817 <span class="c"># Is this bond in a molecule?</span> | |
831 818 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
832 819 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
833 820 <span class="s">}</span> | |
834 821 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
835 822 <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> | |
836 823 | |
837 824 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSmallestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
838 825 <span class="s">}</span> | |
839 826 | |
840 827 <span class="c"># Get largest ring as an array containing ring atoms...</span> | |
841 828 <span class="c">#</span> | |
842 <a name="GetLargestRing-"></a> 829 <span class="k">sub </span><span class="m">GetLargestRing</span> <span class="s">{</span> | |
843 830 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
844 831 | |
845 832 <span class="c"># Is this bond in a molecule?</span> | |
846 833 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
847 834 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
848 835 <span class="s">}</span> | |
849 836 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
850 837 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
851 838 | |
852 839 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetLargestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
853 840 <span class="s">}</span> | |
854 841 | |
855 842 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span> | |
856 843 <span class="c">#</span> | |
857 <a name="GetRingsWithOddSize-"></a> 844 <span class="k">sub </span><span class="m">GetRingsWithOddSize</span> <span class="s">{</span> | |
858 845 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
859 846 | |
860 847 <span class="c"># Is this bond in a molecule?</span> | |
861 848 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
862 849 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
863 850 <span class="s">}</span> | |
864 851 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
865 852 <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> | |
866 853 | |
867 854 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
868 855 <span class="s">}</span> | |
869 856 | |
870 857 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span> | |
871 858 <span class="c">#</span> | |
872 <a name="GetRingsWithEvenSize-"></a> 859 <span class="k">sub </span><span class="m">GetRingsWithEvenSize</span> <span class="s">{</span> | |
873 860 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
874 861 | |
875 862 <span class="c"># Is this bond in a molecule?</span> | |
876 863 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
877 864 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
878 865 <span class="s">}</span> | |
879 866 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
880 867 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
881 868 | |
882 869 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
883 870 <span class="s">}</span> | |
884 871 | |
885 872 <span class="c"># Get rings with specified size an array of references to arrays containing ring atoms...</span> | |
886 873 <span class="c">#</span> | |
887 <a name="GetRingsWithSize-"></a> 874 <span class="k">sub </span><span class="m">GetRingsWithSize</span> <span class="s">{</span> | |
888 875 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
889 876 | |
890 877 <span class="c"># Is this bond in a molecule?</span> | |
891 878 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
892 879 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
893 880 <span class="s">}</span> | |
894 881 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
895 882 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
896 883 | |
897 884 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithSize</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> | |
898 885 <span class="s">}</span> | |
899 886 | |
900 887 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span> | |
901 888 <span class="c">#</span> | |
902 <a name="GetRingsWithSizeLessThan-"></a> 889 <span class="k">sub </span><span class="m">GetRingsWithSizeLessThan</span> <span class="s">{</span> | |
903 890 <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> | |
904 891 | |
905 892 <span class="c"># Is this bond in a molecule?</span> | |
906 893 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
907 894 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
908 895 <span class="s">}</span> | |
909 896 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
910 897 <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> | |
911 898 | |
912 899 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithSizeLessThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span> | |
913 900 <span class="s">}</span> | |
914 901 | |
915 902 <span class="c"># Get rings with size greater than specfied size as an array of references to arrays containing ring atoms...</span> | |
916 903 <span class="c">#</span> | |
917 <a name="GetRingsWithSizeGreaterThan-"></a> 904 <span class="k">sub </span><span class="m">GetRingsWithSizeGreaterThan</span> <span class="s">{</span> | |
918 905 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
919 906 | |
920 907 <span class="c"># Is this bond in a molecule?</span> | |
921 908 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> | |
922 909 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
923 910 <span class="s">}</span> | |
924 911 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span> | |
925 912 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span> | |
926 913 | |
927 914 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithSizeGreaterThan</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> | |
928 915 <span class="s">}</span> | |
929 916 | |
930 917 <span class="c"># Get next object ID...</span> | |
931 <a name="_GetNewObjectID-"></a> 918 <span class="k">sub </span><span class="m">_GetNewObjectID</span> <span class="s">{</span> | |
932 919 <span class="i">$ObjectID</span>++<span class="sc">;</span> | |
933 920 <span class="k">return</span> <span class="i">$ObjectID</span><span class="sc">;</span> | |
934 921 <span class="s">}</span> | |
935 922 | |
936 923 <span class="c"># Return a string containing bond and other properties...</span> | |
937 <a name="StringifyBond-"></a> 924 <span class="k">sub </span><span class="m">StringifyBond</span> <span class="s">{</span> | |
938 925 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
939 926 <span class="k">my</span><span class="s">(</span><span class="i">$BondString</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$Stereochemistry</span><span class="cm">,</span> <span class="i">$AtomsString</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$AromaticBond</span><span class="cm">,</span> <span class="i">$NumOfRings</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
940 927 | |
941 928 <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> | |
942 929 <span class="i">$BondOrder</span> = <span class="i">$This</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
943 930 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span> | |
944 931 <span class="i">$BondOrder</span> = <span class="q">"undefined"</span><span class="sc">;</span> | |
945 932 <span class="s">}</span> | |
946 933 <span class="i">$BondType</span> = <span class="i">$This</span><span class="i">->GetBondType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
947 934 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span> | |
948 935 <span class="i">$BondType</span> = <span class="q">"undefined"</span><span class="sc">;</span> | |
949 936 <span class="s">}</span> | |
950 937 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$BondOrder</span><span class="s">)</span> && <span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
951 938 <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> | |
952 939 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Stereochemistry</span><span class="s">)</span> <span class="s">{</span> | |
953 940 <span class="i">$Stereochemistry</span> = <span class="q">"undefined"</span><span class="sc">;</span> | |
954 941 <span class="s">}</span> | |
955 942 <span class="s">}</span> | |
956 943 <span class="i">$RingBond</span> = <span class="i">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
957 944 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$RingBond</span><span class="s">)</span> <span class="s">{</span> | |
958 945 <span class="i">$RingBond</span> = <span class="i">$RingBond</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> | |
959 946 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
960 947 <span class="s">}</span> | |
961 948 <span class="k">else</span> <span class="s">{</span> | |
962 949 <span class="i">$RingBond</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
963 950 <span class="i">$NumOfRings</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
964 951 <span class="s">}</span> | |
965 952 | |
966 953 <span class="i">$AromaticBond</span> = <span class="i">$This</span><span class="i">->GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
967 954 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticBond</span><span class="s">)</span> <span class="s">{</span> | |
968 955 <span class="i">$AromaticBond</span> = <span class="i">$AromaticBond</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span> | |
969 956 <span class="s">}</span> | |
970 957 <span class="k">else</span> <span class="s">{</span> | |
971 958 <span class="i">$AromaticBond</span> = <span class="q">'undefined'</span><span class="sc">;</span> | |
972 959 <span class="s">}</span> | |
973 960 | |
974 961 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
975 962 <span class="i">$AtomsString</span> = <span class="q">"Atoms: undefined"</span><span class="sc">;</span> | |
976 963 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
977 964 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomCount</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">@BondAtoms</span><span class="s">)</span><span class="sc">;</span> | |
978 965 <span class="i">@BondAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
979 966 <span class="k">push</span> <span class="i">@BondAtoms</span><span class="cm">,</span> <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span> | |
980 967 <span class="i">$AtomCount</span> = <span class="n">0</span><span class="sc">;</span> | |
981 968 <span class="i">$AtomsString</span> = <span class="q">""</span><span class="sc">;</span> | |
982 969 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@BondAtoms</span><span class="s">)</span> <span class="s">{</span> | |
983 970 <span class="i">$AtomCount</span>++<span class="sc">;</span> | |
984 971 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
985 972 <span class="i">$AtomName</span> = <span class="i">$Atom</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
986 973 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
987 974 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
988 975 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomCount</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
989 976 <span class="i">$AtomsString</span> .= <span class="q">"FirstAtom:"</span><span class="sc">;</span> | |
990 977 <span class="s">}</span> | |
991 978 <span class="k">else</span> <span class="s">{</span> | |
992 979 <span class="i">$AtomsString</span> .= <span class="q">"; SecondAtom:"</span><span class="sc">;</span> | |
993 980 <span class="s">}</span> | |
994 981 <span class="i">$AtomsString</span> .= <span class="q">" [ ID: $AtomID; Name: \"$AtomName\"; AtomSymbol: \"$AtomSymbol\"; AtomicNumber: $AtomicNumber ]"</span><span class="sc">;</span> | |
995 982 <span class="s">}</span> | |
996 983 <span class="s">}</span> | |
997 984 <span class="i">$BondString</span> = <span class="q">"Bond: ID: $ID; BondOrder: $BondOrder; BondType: $BondType; RingBond: $RingBond; NumOfBondRings: $NumOfRings; AromaticBond: $AromaticBond;"</span><span class="sc">;</span> | |
998 985 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$BondOrder</span><span class="s">)</span> && <span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
999 986 <span class="i">$BondString</span> .= <span class="q">" Stereochemistry: $Stereochemistry;"</span><span class="sc">;</span> | |
1000 987 <span class="s">}</span> | |
1001 988 <span class="i">$BondString</span> .= <span class="q">" $AtomsString"</span><span class="sc">;</span> | |
1002 989 | |
1003 990 <span class="k">return</span> <span class="i">$BondString</span><span class="sc">;</span> | |
1004 991 <span class="s">}</span> | |
1005 992 | |
1006 <a name="EOF-"></a></pre> | |
1007 <p> </p> | |
1008 <br /> | |
1009 <center> | |
1010 <img src="../../../images/h2o2.png"> | |
1011 </center> | |
1012 </body> | |
1013 </html> |