comparison mayachemtools/docs/modules/html/code/Bond.html @ 0:73ae111cf86f draft

Uploaded
author deepakjadmin
date Wed, 20 Jan 2016 11:55:01 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:73ae111cf86f
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>
11 </center>
12 <br/>
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 &lt;msud@san.rr.com&gt;</span>
21 8 <span class="c">#</span>
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
23 10 <span class="c">#</span>
24 11 <span class="c"># This file is part of MayaChemTools.</span>
25 12 <span class="c">#</span>
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
29 16 <span class="c"># later version.</span>
30 17 <span class="c">#</span>
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
34 21 <span class="c"># details.</span>
35 22 <span class="c">#</span>
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
40 27 <span class="c">#</span>
41 28
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
45 32 <span class="k">use</span> <span class="w">Storable</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
46 33 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
47 34 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span>
48 35
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">=&gt;</span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
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">$ObjectID</span><span class="s">)</span><span class="sc">;</span>
59 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
60 47
61 48 <span class="c"># Overload Perl functions...</span>
62 49 <span class="k">use</span> <span class="w">overload</span> <span class="q">&#39;&quot;&quot;&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;StringifyBond&#39;</span><span class="sc">;</span>
63 50
64 51 <span class="c"># Class constructor...</span>
65 <a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
66 53 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">-&gt;_InitializeBond</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
72 59
73 60 <span class="i">$This</span><span class="i">-&gt;_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">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
83 70
84 71 <span class="c"># All other property names and values along with all Set/Get&lt;PropertyName&gt; methods</span>
85 72 <span class="c"># are implemented on-demand using ObjectProperty class.</span>
86 73 <span class="i">$This</span>-&gt;{<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>-&gt;{<span class="w">BondFromAtom</span>} = <span class="k">undef</span><span class="sc">;</span>
90 77 <span class="i">$This</span>-&gt;{<span class="w">BondToAtom</span>} = <span class="k">undef</span><span class="sc">;</span>
91 78
92 79 <span class="i">$This</span>-&gt;{<span class="w">BondOrder</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
93 80 <span class="i">$This</span>-&gt;{<span class="w">BondType</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
94 81 <span class="i">$This</span>-&gt;{<span class="w">BondStereochemistry</span>} = <span class="q">&#39;&#39;</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">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
113 100 <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
114 101 <span class="s">}</span>
115 102
116 103 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">&#39;Atoms&#39;</span>}<span class="s">)</span> <span class="s">{</span>
117 104 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;new: Bond object instantiated without specifying atoms list...&quot;</span><span class="sc">;</span>
118 105 <span class="s">}</span>
119 106 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">&#39;BondOrder&#39;</span>}<span class="s">)</span> <span class="s">{</span>
120 107 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;new: Bond object instantiated without setting bond order...&quot;</span><span class="sc">;</span>
121 108 <span class="s">}</span>
122 109 <span class="k">return</span> <span class="i">$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">&quot;Warning: ${ClassName}-&gt;SetID: Object ID can&#39;t be changed: it&#39;s used for internal tracking...&quot;</span><span class="sc">;</span>
130 117
131 118 <span class="k">return</span> <span class="i">$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">&quot;Warning: ${ClassName}-&gt;SetMolecule: Molecule property can&#39;t be changed: it&#39;s used for internal tracking...&quot;</span><span class="sc">;</span>
139 126
140 127 <span class="k">return</span> <span class="i">$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">$This</span>-&gt;{<span class="w">Molecule</span>} = <span class="i">$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&#39;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">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
154 141
155 142 <span class="k">return</span> <span class="i">$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">&quot;Error: ${ClassName}-&gt;SetAtoms: No atoms specified...&quot;</span><span class="sc">;</span>
164 151 <span class="s">}</span>
165 152
166 153 <span class="k">my</span><span class="s">(</span><span class="i">$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">&quot;Warning: ${ClassName}-&gt;SetAtoms: Number of atoms specified in bond object is not equal to 2...&quot;</span><span class="sc">;</span>
174 161 <span class="s">}</span>
175 162 <span class="s">(</span><span class="i">$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&#39;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">&quot;Warning: ${ClassName}-&gt;SetAtoms: Number of atoms specified in bond object is not equal to 2...&quot;</span><span class="sc">;</span>
181 168 <span class="s">}</span>
182 169 <span class="s">(</span><span class="i">$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">$Atom1</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
186 173 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Warning: ${ClassName}-&gt;SetAtoms: Can&#39;t specify same atoms to create a bond...&quot;</span><span class="sc">;</span>
188 175 <span class="s">}</span>
189 176
190 177 <span class="i">$This</span>-&gt;{<span class="w">BondFromAtom</span>} = <span class="i">$Atom1</span><span class="sc">;</span>
191 178 <span class="i">$This</span>-&gt;{<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>-&gt;{<span class="w">BondFromAtom</span>}<span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">BondToAtom</span>}<span class="s">)</span> <span class="co">:</span> <span class="n">2</span><span class="sc">;</span>
203 190 <span class="s">}</span>
204 191
205 192 <span class="c"># Get atom bonded to specified atom...</span>
206 <a name="GetBondedAtom-"></a> 193 <span class="k">sub </span><span class="m">GetBondedAtom</span> <span class="s">{</span>
207 194 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
211 198 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
212 199
213 200 <span class="k">return</span> <span class="s">(</span><span class="i">$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">-&gt;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">-&gt;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">-&gt;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">$Other</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
225 212 <span class="i">$OtherAtomID1</span> = <span class="i">$OtherAtom1</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$OtherAtomID2</span> = <span class="i">$OtherAtom2</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
226 213
227 214 <span class="k">return</span> <span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">BondFromAtom</span>}<span class="sc">;</span>
235 222 <span class="s">}</span>
236 223
237 224 <span class="c"># Get begin bond atom...</span>
238 <a name="GetBondBeginAtom-"></a> 225 <span class="k">sub </span><span class="m">GetBondBeginAtom</span> <span class="s">{</span>
239 226 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">-&gt;GetBondFromAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
242 229 <span class="s">}</span>
243 230
244 231 <span class="c"># Get bond to atom indicating ending atom of a bond...</span>
245 <a name="GetBondToAtom-"></a> 232 <span class="k">sub </span><span class="m">GetBondToAtom</span> <span class="s">{</span>
246 233 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">BondToAtom</span>}<span class="sc">;</span>
249 236 <span class="s">}</span>
250 237
251 238 <span class="c"># Get begin bond atom...</span>
252 <a name="GetBondEndAtom-"></a> 239 <span class="k">sub </span><span class="m">GetBondEndAtom</span> <span class="s">{</span>
253 240 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">-&gt;GetBondToAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
256 243 <span class="s">}</span>
257 244
258 245 <span class="c"># Switch bond from and to atoms...</span>
259 <a name="SwitchBondFromAndToAtoms-"></a> 246 <span class="k">sub </span><span class="m">SwitchBondFromAndToAtoms</span> <span class="s">{</span>
260 247 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
264 251
265 252 <span class="i">$This</span>-&gt;{<span class="w">BondFromAtom</span>} = <span class="i">$ToAtom</span><span class="sc">;</span>
266 253 <span class="i">$This</span>-&gt;{<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 &quot;Aromatic&quot; 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">&quot;Error: ${ClassName}-&gt;SetBondOrder: BondOrder value $BondOrder is not valid. Supported values: 0, 1, 1.5, 2, 3, 4, 5, 6, 7&quot;</span><span class="sc">;</span>
310 297 <span class="s">}</span>
311 298
312 299 <span class="c"># Set bond order and type...</span>
313 300 <span class="k">my</span><span class="s">(</span><span class="i">$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">&#39;Single&#39;</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">&#39;Aromatic&#39;</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">&#39;Double&#39;</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">&#39;Triple&#39;</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">&#39;Quadruple&#39;</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">&#39;Quintuple&#39;</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">&#39;Sextuple&#39;</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">&#39;Septuple&#39;</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">$BondType</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
325 312 <span class="i">$BondOrder</span> = <span class="n">0</span><span class="sc">;</span>
326 313 <span class="s">}</span>
327 314 <span class="i">$This</span>-&gt;{<span class="w">BondType</span>} = <span class="i">$BondType</span><span class="sc">;</span>
328 315 <span class="i">$This</span>-&gt;{<span class="w">BondOrder</span>} = <span class="i">$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">&quot;Error: ${ClassName}-&gt;SetBondType: BondType value $BondType is not valid. Supported values: None, Ionic, Unspecified, Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Aromatic, Tautomeric, Resonance, DoubleOrAromatic, Double, Triple, Quadruple, Any...&quot;</span><span class="sc">;</span>
341 328 <span class="s">}</span>
342 329
343 330 <span class="c"># Make sure its a valid BondType value for BondOrder...</span>
344 331 <span class="k">my</span><span class="s">(</span><span class="i">$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>-&gt;{<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">$BondOrder</span> == <span class="n">0</span> &amp;&amp; <span class="i">$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">$BondOrder</span> == <span class="n">1</span> &amp;&amp; <span class="i">$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">$BondOrder</span> == <span class="n">1.5</span> &amp;&amp; <span class="i">$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">$BondOrder</span> == <span class="n">2</span> &amp;&amp; <span class="i">$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">$BondOrder</span> == <span class="n">3</span> &amp;&amp; <span class="i">$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">$BondOrder</span> == <span class="n">4</span> &amp;&amp; <span class="i">$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">$BondOrder</span> == <span class="n">5</span> &amp;&amp; <span class="i">$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">$BondOrder</span> == <span class="n">6</span> &amp;&amp; <span class="i">$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">$BondOrder</span> == <span class="n">7</span> &amp;&amp; <span class="i">$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">&quot;Warning: ${ClassName}-&gt;SetBondType: Assigning invalid BondType value, $BondType, for BondOrder $BondOrder...&quot;</span><span class="sc">;</span>
364 351 <span class="s">}</span>
365 352
366 353 <span class="i">$This</span>-&gt;{<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">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
371 358 <span class="i">$Atom1</span><span class="i">-&gt;SetFormalCharge</span><span class="s">(</span><span class="q">&#39;1&#39;</span><span class="s">)</span><span class="sc">;</span>
372 359 <span class="i">$Atom2</span><span class="i">-&gt;SetFormalCharge</span><span class="s">(</span><span class="q">&#39;-1&#39;</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">&quot;Error: ${ClassName}-&gt;SetBondStereochemistry: BondStereochemistry value $BondStereochemistry is not valid. Supported values: None, Unspecified, Wedge, Hash, Up, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward, Cis, Trans, Z, E, DoubleCross, CisOrTrans...&quot;</span><span class="sc">;</span>
410 397 <span class="s">}</span>
411 398
412 399 <span class="c"># Make sure its a valid BondStereochemistry value for BondOrder...</span>
413 400 <span class="k">my</span><span class="s">(</span><span class="i">$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>-&gt;{<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">$BondOrder</span> == <span class="n">0</span> &amp;&amp; <span class="i">$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">$BondOrder</span> == <span class="n">1</span> &amp;&amp; <span class="i">$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">$BondOrder</span> == <span class="n">2</span> &amp;&amp; <span class="i">$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">&quot;Warning: ${ClassName}-&gt;SetBondStereochemistry: Assigning invalid BondStereochemistry value, $BondStereochemistry, for BondOrder $BondOrder...&quot;</span><span class="sc">;</span>
427 414 <span class="s">}</span>
428 415
429 416 <span class="i">$This</span>-&gt;{<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>-&gt;{<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>-&gt;{<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>-&gt;{<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>-&gt;{<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">-&gt;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">$Aromatic</span><span class="s">)</span> &amp;&amp; <span class="i">$Aromatic</span><span class="s">)</span> || <span class="i">$This</span>-&gt;{<span class="w">BondOrder</span>} == <span class="n">1.5</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
470 457 <span class="s">}</span>
471 458
472 459 <span class="c"># Is it a quintuple bond?</span>
473 <a name="IsQuintuple-"></a> 460 <span class="k">sub </span><span class="m">IsQuintuple</span> <span class="s">{</span>
474 461 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">BondOrder</span>} == <span class="n">5</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
477 464 <span class="s">}</span>
478 465
479 466 <span class="c"># Is it a sextuple bond?</span>
480 <a name="IsSextuple-"></a> 467 <span class="k">sub </span><span class="m">IsSextuple</span> <span class="s">{</span>
481 468 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">BondOrder</span>} == <span class="n">6</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
484 471 <span class="s">}</span>
485 472
486 473 <span class="c"># Is bond type specified?</span>
487 <a name="IsBondTypeSpecified-"></a> 474 <span class="k">sub </span><span class="m">IsBondTypeSpecified</span> <span class="s">{</span>
488 475 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">BondType</span>} &amp;&amp; <span class="i">$This</span>-&gt;{<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">$This</span>-&gt;{<span class="w">BondType</span>} =~ <span class="q">/^(Dative|Coordinate)$/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">-&gt;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>-&gt;{<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">$This</span>-&gt;{<span class="w">BondType</span>} =~ <span class="q">/^Tautomeric$/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>-&gt;{<span class="w">BondStereochemistry</span>} &amp;&amp; <span class="i">$This</span>-&gt;{<span class="w">BondStereochemistry</span>} !~ <span class="q">/^(None|Unspecified)$/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">-&gt;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>-&gt;{<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">$This</span><span class="i">-&gt;IsDown</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
547 534 <span class="s">}</span>
548 535
549 536 <span class="c"># Is it a Hash or Down single bond?</span>
550 <a name="IsDown-"></a> 537 <span class="k">sub </span><span class="m">IsDown</span> <span class="s">{</span>
551 538 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Hash|Down)$/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">-&gt;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>-&gt;{<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">$This</span>-&gt;{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^Upward$/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>-&gt;{<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">$This</span>-&gt;{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Cis|Z)$/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>-&gt;{<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">$This</span>-&gt;{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(CisOrTrans|DoubleCross)$/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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
615 602 <span class="i">$Molecule</span><span class="i">-&gt;DeleteBond</span><span class="s">(</span><span class="i">$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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
641 628
642 629 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
652 639 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
653 640 <span class="s">}</span>
654 641 <span class="k">my</span><span class="s">(</span><span class="i">$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">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
656 643
657 644 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_IsBondNotInRing</span><span class="s">(</span><span class="i">$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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
671 658
672 659 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
686 673
687 674 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
701 688
702 689 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
712 699 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
713 700 <span class="s">}</span>
714 701 <span class="k">my</span><span class="s">(</span><span class="i">$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">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
716 703
717 704 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetSizeOfLargestBondRing</span><span class="s">(</span><span class="i">$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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
731 718
732 719 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
742 729 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
743 730 <span class="s">}</span>
744 731 <span class="k">my</span><span class="s">(</span><span class="i">$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">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
746 733
747 734 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetNumOfBondRingsWithOddSize</span><span class="s">(</span><span class="i">$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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
761 748
762 749 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
776 763
777 764 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
787 774 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
788 775 <span class="s">}</span>
789 776 <span class="k">my</span><span class="s">(</span><span class="i">$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">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
791 778
792 779 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetNumOfBondRingsWithSizeLessThan</span><span class="s">(</span><span class="i">$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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
806 793
807 794 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
821 808
822 809 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
832 819 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
833 820 <span class="s">}</span>
834 821 <span class="k">my</span><span class="s">(</span><span class="i">$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">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
836 823
837 824 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetSmallestBondRing</span><span class="s">(</span><span class="i">$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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
851 838
852 839 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
862 849 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
863 850 <span class="s">}</span>
864 851 <span class="k">my</span><span class="s">(</span><span class="i">$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">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
866 853
867 854 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetBondRingsWithOddSize</span><span class="s">(</span><span class="i">$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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
881 868
882 869 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
896 883
897 884 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">$This</span><span class="i">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
907 894 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
908 895 <span class="s">}</span>
909 896 <span class="k">my</span><span class="s">(</span><span class="i">$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">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
911 898
912 899 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_GetBondRingsWithSizeLessThan</span><span class="s">(</span><span class="i">$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">-&gt;HasProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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">$This</span><span class="i">-&gt;GetProperty</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span><span class="s">)</span><span class="sc">;</span>
926 913
927 914 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">-&gt;_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">-&gt;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">-&gt;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">&quot;undefined&quot;</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">-&gt;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">&quot;undefined&quot;</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">$BondOrder</span><span class="s">)</span> &amp;&amp; <span class="i">$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">-&gt;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">&quot;undefined&quot;</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">-&gt;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">$RingBond</span> ? <span class="q">&#39;Yes&#39;</span> <span class="co">:</span> <span class="q">&#39;No&#39;</span><span class="sc">;</span>
959 946 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
960 947 <span class="s">}</span>
961 948 <span class="k">else</span> <span class="s">{</span>
962 949 <span class="i">$RingBond</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
963 950 <span class="i">$NumOfRings</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
964 951 <span class="s">}</span>
965 952
966 953 <span class="i">$AromaticBond</span> = <span class="i">$This</span><span class="i">-&gt;GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
967 954 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$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">&#39;Yes&#39;</span> <span class="co">:</span> <span class="q">&#39;No&#39;</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">$AromaticBond</span> = <span class="q">&#39;undefined&#39;</span><span class="sc">;</span>
972 959 <span class="s">}</span>
973 960
974 961 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
975 962 <span class="i">$AtomsString</span> = <span class="q">&quot;Atoms: undefined&quot;</span><span class="sc">;</span>
976 963 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span> &amp;&amp; <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">$AtomsString</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
982 969 <span class="k">for</span> <span class="i">$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">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
985 972 <span class="i">$AtomName</span> = <span class="i">$Atom</span><span class="i">-&gt;GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
986 973 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">-&gt;GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
987 974 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">-&gt;GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
988 975 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomCount</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
989 976 <span class="i">$AtomsString</span> .= <span class="q">&quot;FirstAtom:&quot;</span><span class="sc">;</span>
990 977 <span class="s">}</span>
991 978 <span class="k">else</span> <span class="s">{</span>
992 979 <span class="i">$AtomsString</span> .= <span class="q">&quot;; SecondAtom:&quot;</span><span class="sc">;</span>
993 980 <span class="s">}</span>
994 981 <span class="i">$AtomsString</span> .= <span class="q">&quot; [ ID: $AtomID; Name: \&quot;$AtomName\&quot;; AtomSymbol: \&quot;$AtomSymbol\&quot;; AtomicNumber: $AtomicNumber ]&quot;</span><span class="sc">;</span>
995 982 <span class="s">}</span>
996 983 <span class="s">}</span>
997 984 <span class="i">$BondString</span> = <span class="q">&quot;Bond: ID: $ID; BondOrder: $BondOrder; BondType: $BondType; RingBond: $RingBond; NumOfBondRings: $NumOfRings; AromaticBond: $AromaticBond;&quot;</span><span class="sc">;</span>
998 985 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$BondOrder</span><span class="s">)</span> &amp;&amp; <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">&quot; Stereochemistry: $Stereochemistry;&quot;</span><span class="sc">;</span>
1000 987 <span class="s">}</span>
1001 988 <span class="i">$BondString</span> .= <span class="q">&quot; $AtomsString&quot;</span><span class="sc">;</span>
1002 989
1003 990 <span class="k">return</span> <span class="i">$BondString</span><span class="sc">;</span>
1004 991 <span class="s">}</span>
1005 992
1006 <a name="EOF-"></a></pre>
1007 <p>&nbsp;</p>
1008 <br />
1009 <center>
1010 <img src="../../../images/h2o2.png">
1011 </center>
1012 </body>
1013 </html>