1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head><meta http-equiv="Content-Type" content="text/html;charset=utf-8">
<title>stereo.h Source File</title>
<link href="/site.css" rel="stylesheet" type="text/css">
<link href="doxygen.css" rel="stylesheet" type="text/css">
<link href="tabs.css" rel="stylesheet" type="text/css">
<script type="text/javascript" src="search/search.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
</head>
<body>
<!--#include file="header.html" -->
<!-- Generated by Doxygen 1.7.5.1 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<div id="navrow1" class="tabs">
<ul class="tablist">
<li><a href="index.shtml"><span>Main Page</span></a></li>
<li><a href="pages.shtml"><span>Related Pages</span></a></li>
<li><a href="modules.shtml"><span>Modules</span></a></li>
<li><a href="namespaces.shtml"><span>Namespaces</span></a></li>
<li><a href="annotated.shtml"><span>Classes</span></a></li>
<li class="current"><a href="files.shtml"><span>Files</span></a></li>
<li><a href="examples.shtml"><span>Examples</span></a></li>
<li>
<div id="MSearchBox" class="MSearchBoxInactive">
<span class="left">
<img id="MSearchSelect" src="search/mag_sel.png"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
alt=""/>
<input type="text" id="MSearchField" value="Search" accesskey="S"
onfocus="searchBox.OnSearchFieldFocus(true)"
onblur="searchBox.OnSearchFieldFocus(false)"
onkeyup="searchBox.OnSearchFieldChange(event)"/>
</span><span class="right">
<a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
</span>
</div>
</li>
</ul>
</div>
<div id="navrow2" class="tabs2">
<ul class="tablist">
<li><a href="files.shtml"><span>File List</span></a></li>
<li><a href="globals.shtml"><span>File Members</span></a></li>
</ul>
</div>
<div class="header">
<div class="headertitle">
<div class="title">stereo.h</div> </div>
</div>
<div class="contents">
<a href="stereo_8h.shtml">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/**********************************************************************</span>
<a name="l00002"></a>00002 <span class="comment"> stereo.h - OBStereo & OBStereoBase</span>
<a name="l00003"></a>00003 <span class="comment"></span>
<a name="l00004"></a>00004 <span class="comment"> Copyright (C) 2009-2010 by Tim Vandermeersch</span>
<a name="l00005"></a>00005 <span class="comment"></span>
<a name="l00006"></a>00006 <span class="comment"> This file is part of the Open Babel project.</span>
<a name="l00007"></a>00007 <span class="comment"> For more information, see <http://openbabel.org/></span>
<a name="l00008"></a>00008 <span class="comment"></span>
<a name="l00009"></a>00009 <span class="comment"> This program is free software; you can redistribute it and/or modify</span>
<a name="l00010"></a>00010 <span class="comment"> it under the terms of the GNU General Public License as published by</span>
<a name="l00011"></a>00011 <span class="comment"> the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00012"></a>00012 <span class="comment"> (at your option) any later version.</span>
<a name="l00013"></a>00013 <span class="comment"></span>
<a name="l00014"></a>00014 <span class="comment"> This program is distributed in the hope that it will be useful,</span>
<a name="l00015"></a>00015 <span class="comment"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00016"></a>00016 <span class="comment"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<a name="l00017"></a>00017 <span class="comment"> GNU General Public License for more details.</span>
<a name="l00018"></a>00018 <span class="comment"></span>
<a name="l00019"></a>00019 <span class="comment"> You should have received a copy of the GNU General Public License</span>
<a name="l00020"></a>00020 <span class="comment"> along with this program; if not, write to the Free Software</span>
<a name="l00021"></a>00021 <span class="comment"> Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA</span>
<a name="l00022"></a>00022 <span class="comment"> 02110-1301, USA.</span>
<a name="l00023"></a>00023 <span class="comment"> **********************************************************************/</span>
<a name="l00024"></a>00024 <span class="preprocessor">#ifndef OB_STEREO_H</span>
<a name="l00025"></a>00025 <span class="preprocessor"></span><span class="preprocessor">#define OB_STEREO_H</span>
<a name="l00026"></a>00026 <span class="preprocessor"></span>
<a name="l00027"></a>00027 <span class="preprocessor">#include <<a class="code" href="base_8h.shtml" title="Base classes to build a graph.">openbabel/base.h</a>></span> <span class="comment">// OBGenericData</span>
<a name="l00028"></a>00028 <span class="preprocessor">#include <<a class="code" href="isomorphism_8h.shtml" title="OBIsomorphismMapper class for finding isomorphisms.">openbabel/isomorphism.h</a>></span> <span class="comment">// Automorphisms</span>
<a name="l00029"></a>00029 <span class="preprocessor">#include <vector></span>
<a name="l00030"></a>00030 <span class="preprocessor">#include <map></span>
<a name="l00031"></a>00031 <span class="preprocessor">#include <set></span>
<a name="l00032"></a>00032 <span class="preprocessor">#include <climits></span> <span class="comment">// UINT_MAX</span>
<a name="l00033"></a>00033
<a name="l00034"></a>00034 <span class="keyword">namespace </span>OpenBabel {
<a name="l00035"></a>00035
<a name="l00038"></a>00038
<a name="l00075"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml">00075</a> <span class="keyword">struct </span>OBAPI <a class="code" href="structOpenBabel_1_1OBStereo.shtml" title="Placeholder for enums & Ref/Refs related functions.">OBStereo</a>
<a name="l00076"></a>00076 {
<a name="l00080"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7">00080</a> <span class="keyword">enum</span> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7">Type</a> {
<a name="l00081"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7abf2462b166f389c17adccf7a95941396">00081</a> CisTrans = (1<<0),
<a name="l00082"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7a3115cb247d1cb271c7157b4db2407932">00082</a> ExtendedCisTrans = (1<<1),
<a name="l00083"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7a793d15fd6e6d225fcddc0cf4b65259d3">00083</a> SquarePlanar = (1<<2),
<a name="l00084"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7a398755acaa38c780e5a4dc5db1c205be">00084</a> Tetrahedral = (1<<3),
<a name="l00085"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7a8c2578d01eef213503d0894e8be33ad3">00085</a> ExtendedTetrahedral = (1<<4),
<a name="l00086"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7a7cadd5a7e8d25d88807992426f62a397">00086</a> TrigonalBipyramidal = (1<<5),
<a name="l00087"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7a48563b1c184d9fab3497e3e519ce50af">00087</a> Octahedral = (1<<6)
<a name="l00088"></a>00088 };
<a name="l00089"></a>00089
<a name="l00094"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a90087c9021331c97c28e9a8329f41e97">00094</a> <span class="keyword">enum</span> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a90087c9021331c97c28e9a8329f41e97">BondDirection</a> { <span class="comment">// Values taken from MDL format</span>
<a name="l00095"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a90087c9021331c97c28e9a8329f41e97ad207f41315a26ce638464caf613b60a1">00095</a> NotStereo = 0,
<a name="l00096"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a90087c9021331c97c28e9a8329f41e97af4cfb1f053e0e8a980850336a1dcdab1">00096</a> UpBond = 1,
<a name="l00097"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a90087c9021331c97c28e9a8329f41e97a6b3b36219bd6afd10e935be8526cb4ea">00097</a> DownBond = 6,
<a name="l00098"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a90087c9021331c97c28e9a8329f41e97a3d121ce0cfdbe400c4a41e185030d262">00098</a> UnknownDir = 4
<a name="l00099"></a>00099 };
<a name="l00100"></a>00100
<a name="l00108"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">00108</a> <span class="keyword">enum</span> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">Shape</a> {
<a name="l00109"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37ca0ab366e13e0cfd59ccb06cd77b673bca">00109</a> ShapeU = 1,
<a name="l00110"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37cacbf3a0dadf9e3e7a8dd4f0a81f8b010d">00110</a> ShapeZ = 2,
<a name="l00111"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37cafb39b2d794a5fd22489031455416fa31">00111</a> Shape4 = 3
<a name="l00112"></a>00112 };
<a name="l00113"></a>00113
<a name="l00119"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#af1dfb9e747d80437422fdb5fba87c2c7">00119</a> <span class="keyword">enum</span> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#af1dfb9e747d80437422fdb5fba87c2c7">View</a>
<a name="l00120"></a>00120 {
<a name="l00121"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#af1dfb9e747d80437422fdb5fba87c2c7ad67cd67454910029af59ecf137366d0e">00121</a> ViewFrom = 1,
<a name="l00122"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#af1dfb9e747d80437422fdb5fba87c2c7a82407be1a15d633a8bf5df6eaecad155">00122</a> ViewTowards = 2
<a name="l00123"></a>00123 };
<a name="l00124"></a>00124
<a name="l00130"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#ac3e0e8e3a194037cdf6103a95a1c6d31">00130</a> <span class="keyword">enum</span> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#ac3e0e8e3a194037cdf6103a95a1c6d31">Winding</a> {
<a name="l00131"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#ac3e0e8e3a194037cdf6103a95a1c6d31adc82829d52b935bb1ba087f98f44dac7">00131</a> Clockwise = 1,
<a name="l00132"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#ac3e0e8e3a194037cdf6103a95a1c6d31a6bf12c9b9fea555c370c5f75629cd609">00132</a> AntiClockwise = 2,
<a name="l00133"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#ac3e0e8e3a194037cdf6103a95a1c6d31a7c3b131410d13135cf3b0f159a6cb899">00133</a> UnknownWinding = 3
<a name="l00134"></a>00134 };
<a name="l00135"></a>00135
<a name="l00137"></a>00137
<a name="l00138"></a>00138
<a name="l00145"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#aff913cc7d694153b33e2b3ac168a6350">00145</a> <span class="keyword">typedef</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#aff913cc7d694153b33e2b3ac168a6350">Ref</a>;
<a name="l00149"></a>00149 <span class="keyword">enum</span> {
<a name="l00150"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#aba01db17f4a2bfbc3db60dc172972a25a7295d9aeb6e0e6f3a5b77aa0ce7ed0db">00150</a> NoRef = UINT_MAX,
<a name="l00151"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#aba01db17f4a2bfbc3db60dc172972a25a02b1798105615b9c057d777fd19f1015">00151</a> ImplicitRef = UINT_MAX - 1
<a name="l00152"></a>00152 };
<a name="l00156"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">00156</a> <span class="keyword">typedef</span> std::vector<Ref> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">Refs</a>;
<a name="l00160"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1380cd3ca593dd317be63064b47e14db">00160</a> <span class="keyword">typedef</span> Refs::iterator <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1380cd3ca593dd317be63064b47e14db">RefIter</a>;
<a name="l00164"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a6f0021eb4868fb5540a2cedde823ada1">00164</a> <span class="keyword">typedef</span> Refs::const_iterator <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a6f0021eb4868fb5540a2cedde823ada1">ConstRefIter</a>;
<a name="l00166"></a>00166
<a name="l00168"></a>00168
<a name="l00169"></a>00169
<a name="l00175"></a><a class="code" href="structOpenBabel_1_1OBStereo.shtml#a677b4acc48f3ee3d31f35e20b62ea534">00175</a> <span class="keyword">static</span> Refs MakeRefs(Ref ref1, Ref ref2, Ref ref3, Ref ref4 = NoRef)
<a name="l00176"></a>00176 {
<a name="l00177"></a>00177 Refs refs(3);
<a name="l00178"></a>00178 refs[0] = ref1;
<a name="l00179"></a>00179 refs[1] = ref2;
<a name="l00180"></a>00180 refs[2] = ref3;
<a name="l00181"></a>00181 <span class="keywordflow">if</span> (ref4 != NoRef)
<a name="l00182"></a>00182 refs.push_back(ref4);
<a name="l00183"></a>00183 <span class="keywordflow">return</span> refs;
<a name="l00184"></a>00184 }
<a name="l00197"></a>00197 <span class="keyword">static</span> <span class="keywordtype">bool</span> ContainsSameRefs(<span class="keyword">const</span> Refs &refs1, <span class="keyword">const</span> Refs &refs2);
<a name="l00201"></a>00201 <span class="keyword">static</span> <span class="keywordtype">bool</span> ContainsRef(<span class="keyword">const</span> Refs &refs, <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> ref);
<a name="l00203"></a>00203
<a name="l00205"></a>00205
<a name="l00206"></a>00206
<a name="l00226"></a>00226 <span class="keyword">static</span> <span class="keywordtype">int</span> NumInversions(<span class="keyword">const</span> Refs &refs);
<a name="l00236"></a>00236 <span class="keyword">static</span> <span class="keywordtype">void</span> Permutate(Refs &refs, <span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j);
<a name="l00248"></a>00248 <span class="keyword">static</span> Refs Permutated(<span class="keyword">const</span> Refs &refs, <span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j);
<a name="l00250"></a>00250
<a name="l00251"></a>00251 };
<a name="l00252"></a>00252
<a name="l00258"></a><a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml">00258</a> <span class="keyword">struct </span><a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml" title="Struct representing a single stereogenic unit.">OBStereoUnit</a>
<a name="l00259"></a>00259 {
<a name="l00264"></a><a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml#ad200dcf5a41b516d592daf60cab1fd0e">00264</a> <a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml" title="Struct representing a single stereogenic unit.">OBStereoUnit</a>() : type(static_cast<<a class="code" href="structOpenBabel_1_1OBStereo.shtml" title="Placeholder for enums & Ref/Refs related functions.">OBStereo</a>::Type>(0)), id(<a class="code" href="structOpenBabel_1_1OBStereo.shtml" title="Placeholder for enums & Ref/Refs related functions.">OBStereo</a>::NoRef), para(false)
<a name="l00265"></a>00265 {
<a name="l00266"></a>00266 }
<a name="l00267"></a>00267
<a name="l00271"></a><a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml#a65527f1c8d53729db66c6fdc5e43e46b">00271</a> <a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml" title="Struct representing a single stereogenic unit.">OBStereoUnit</a>(<a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7">OBStereo::Type</a> _type, <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> _id, <span class="keywordtype">bool</span> _para = <span class="keyword">false</span>) :
<a name="l00272"></a>00272 type(_type), id(_id), para(_para)
<a name="l00273"></a>00273 {
<a name="l00274"></a>00274 }
<a name="l00275"></a>00275
<a name="l00276"></a><a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml#aeecb8f40f1a4fa558dbf6383d1b72771">00276</a> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7">OBStereo::Type</a> <a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml#aeecb8f40f1a4fa558dbf6383d1b72771" title="the type for this stereogenic unit">type</a>;
<a name="l00277"></a><a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml#af17b8bd946e0f93c6550050f9e8aa349">00277</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml#af17b8bd946e0f93c6550050f9e8aa349">id</a>;
<a name="l00278"></a><a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml#a85967158ea10743b1e69bfe4edbcb6a1">00278</a> <span class="keywordtype">bool</span> <a class="code" href="structOpenBabel_1_1OBStereoUnit.shtml#a85967158ea10743b1e69bfe4edbcb6a1" title="the atom/bond (depends on type) unique id">para</a>;
<a name="l00279"></a>00279 };
<a name="l00287"></a><a class="code" href="group__stereo.shtml#ga042299211c7a52f5aee1975d32820af7">00287</a> <span class="keyword">typedef</span> std::vector<OBStereoUnit> <a class="code" href="group__stereo.shtml#ga042299211c7a52f5aee1975d32820af7" title="A single set of OBStereoUnit objects.">OBStereoUnitSet</a>;
<a name="l00294"></a><a class="code" href="group__stereo.shtml#ga75c7c66edf2555b974417a77968ebb57">00294</a> <span class="keyword">typedef</span> std::vector<OBStereoUnitSet> <a class="code" href="group__stereo.shtml#ga75c7c66edf2555b974417a77968ebb57" title="A set of sets of OBStereoUnit objects.">OBStereoUnitSetOfSets</a>;
<a name="l00295"></a>00295
<a name="l00296"></a>00296
<a name="l00297"></a>00297 <span class="comment">// fwd decl</span>
<a name="l00298"></a>00298 <span class="keyword">class </span><a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>;
<a name="l00321"></a><a class="code" href="classOpenBabel_1_1OBStereoBase.shtml">00321</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBStereoBase.shtml" title="Base class for all stereochemistry classes.">OBStereoBase</a> : <span class="keyword">public</span> <a class="code" href="classOpenBabel_1_1OBGenericData.shtml" title="Base class for generic data.">OBGenericData</a>
<a name="l00322"></a>00322 {
<a name="l00323"></a>00323 <span class="keyword">public</span>:
<a name="l00330"></a><a class="code" href="classOpenBabel_1_1OBStereoBase.shtml#a4e9716db658a2f725a214f4f23b6a68d">00330</a> <a class="code" href="classOpenBabel_1_1OBStereoBase.shtml" title="Base class for all stereochemistry classes.">OBStereoBase</a>(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *mol) :
<a name="l00331"></a>00331 <a class="code" href="classOpenBabel_1_1OBGenericData.shtml" title="Base class for generic data.">OBGenericData</a>(<span class="stringliteral">"StereoData"</span>, OBGenericDataType::<a class="code" href="namespaceOpenBabel_1_1OBGenericDataType.shtml#a06fc87d81c62e9abb8790b6e5713c55ba3f9974bdbccde7c26064d7ec21d570ef" title="Stereochemistry data (see OBStereoBase)">StereoData</a>, <a class="code" href="namespaceOpenBabel.shtml#a87d90c5296e904e126b8520e1daacc14ab1c8706dce6832c9ce173260ba2bf392" title="Perceived by Open Babel library methods.">perceived</a>),
<a name="l00332"></a>00332 m_mol(mol), m_specified(true)
<a name="l00333"></a>00333 {
<a name="l00334"></a>00334 }
<a name="l00338"></a><a class="code" href="classOpenBabel_1_1OBStereoBase.shtml#af79f43b5cb6090d98dac9da71e083499">00338</a> <span class="keyword">virtual</span> <a class="code" href="classOpenBabel_1_1OBStereoBase.shtml#af79f43b5cb6090d98dac9da71e083499">~OBStereoBase</a>() { m_mol = 0; }
<a name="l00339"></a>00339
<a name="l00341"></a>00341
<a name="l00342"></a>00342
<a name="l00346"></a><a class="code" href="classOpenBabel_1_1OBStereoBase.shtml#acd313cc12ec2b66926e4d0102042732a">00346</a> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a>* <a class="code" href="classOpenBabel_1_1OBStereoBase.shtml#acd313cc12ec2b66926e4d0102042732a">GetMolecule</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> m_mol; }
<a name="l00350"></a>00350 <span class="keyword">virtual</span> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7">OBStereo::Type</a> GetType() <span class="keyword">const</span> = 0;
<a name="l00356"></a><a class="code" href="classOpenBabel_1_1OBStereoBase.shtml#aa03f9b7e07be400ad77ba2306a2f1619">00356</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBStereoBase.shtml#aa03f9b7e07be400ad77ba2306a2f1619">SetSpecified</a>(<span class="keywordtype">bool</span> specified) { m_specified = specified; }
<a name="l00360"></a><a class="code" href="classOpenBabel_1_1OBStereoBase.shtml#a1a34764224cb3e3c4f1f84a4a3366617">00360</a> <span class="keywordtype">bool</span> <a class="code" href="classOpenBabel_1_1OBStereoBase.shtml#a1a34764224cb3e3c4f1f84a4a3366617">IsSpecified</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> m_specified; }
<a name="l00362"></a>00362 <span class="keyword">private</span>:
<a name="l00363"></a>00363 <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *m_mol;
<a name="l00364"></a>00364 <span class="keywordtype">bool</span> m_specified;
<a name="l00365"></a>00365 };
<a name="l00366"></a>00366
<a name="l00367"></a>00367 <span class="comment">// fwd decl</span>
<a name="l00368"></a>00368 <span class="keyword">class </span>OBTetrahedralStereo;
<a name="l00369"></a>00369 <span class="keyword">class </span>OBCisTransStereo;
<a name="l00370"></a>00370 <span class="keyword">class </span>OBSquarePlanarStereo;
<a name="l00384"></a><a class="code" href="classOpenBabel_1_1OBStereoFacade.shtml">00384</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBStereoFacade.shtml" title="Facade to simplify retrieval of OBStereoBase derived objects.">OBStereoFacade</a>
<a name="l00385"></a>00385 {
<a name="l00386"></a>00386 <span class="keyword">public</span>:
<a name="l00394"></a><a class="code" href="classOpenBabel_1_1OBStereoFacade.shtml#af8355c7f4c1621336979f3bb83bc48c1">00394</a> <a class="code" href="classOpenBabel_1_1OBStereoFacade.shtml" title="Facade to simplify retrieval of OBStereoBase derived objects.">OBStereoFacade</a>(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *mol, <span class="keywordtype">bool</span> perceive = <span class="keyword">true</span>) :
<a name="l00395"></a>00395 m_mol(mol), m_init(false), m_perceive(perceive)
<a name="l00396"></a>00396 {
<a name="l00397"></a>00397 }
<a name="l00398"></a>00398
<a name="l00401"></a>00401
<a name="l00404"></a>00404 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> NumTetrahedralStereo();
<a name="l00409"></a>00409 <span class="keywordtype">bool</span> HasTetrahedralStereo(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> atomId);
<a name="l00415"></a>00415 <a class="code" href="classOpenBabel_1_1OBTetrahedralStereo.shtml" title="Class for handling and storing tetrahedral atom stereochemistry.">OBTetrahedralStereo</a>* GetTetrahedralStereo(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> atomId);
<a name="l00417"></a>00417
<a name="l00420"></a>00420
<a name="l00423"></a>00423 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> NumCisTransStereo();
<a name="l00428"></a>00428 <span class="keywordtype">bool</span> HasCisTransStereo(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> bondId);
<a name="l00434"></a>00434 <a class="code" href="classOpenBabel_1_1OBCisTransStereo.shtml" title="Class for handling and storing cis/trans stereochemistry.">OBCisTransStereo</a>* GetCisTransStereo(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> bondId);
<a name="l00436"></a>00436
<a name="l00439"></a>00439
<a name="l00442"></a>00442 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> NumSquarePlanarStereo();
<a name="l00447"></a>00447 <span class="keywordtype">bool</span> HasSquarePlanarStereo(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> atomId);
<a name="l00453"></a>00453 <a class="code" href="classOpenBabel_1_1OBSquarePlanarStereo.shtml" title="Class for handling and storing square planar stereochemistry.">OBSquarePlanarStereo</a>* GetSquarePlanarStereo(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> atomId);
<a name="l00455"></a>00455
<a name="l00456"></a>00456 <span class="keyword">template</span><<span class="keywordtype">int</span> StereoType>
<a name="l00457"></a>00457 <span class="keywordtype">bool</span> HasStereo(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <span class="keywordtype">id</span>);
<a name="l00458"></a>00458 <span class="keyword">template</span><<span class="keyword">typename</span> T>
<a name="l00459"></a>00459 <a class="code" href="namespaceOpenBabel_1_1OBResidueIndex.shtml#abc5c98fcc1211af2b80116dd6e0a035da21f40778b7db9343a6ca75ec2c41ccce">T</a>* GetStereo(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <span class="keywordtype">id</span>);
<a name="l00460"></a>00460
<a name="l00461"></a>00461
<a name="l00462"></a>00462 <span class="keyword">private</span>:
<a name="l00466"></a>00466 <span class="keyword">inline</span> <span class="keywordtype">void</span> EnsureInit() { <span class="keywordflow">if</span> (!m_init) InitMaps(); }
<a name="l00472"></a>00472 <span class="keywordtype">void</span> InitMaps();
<a name="l00473"></a>00473
<a name="l00474"></a>00474 OBMol *m_mol;
<a name="l00475"></a>00475 <span class="keywordtype">bool</span> m_init;
<a name="l00476"></a>00476 <span class="keywordtype">bool</span> m_perceive;
<a name="l00477"></a>00477 std::map<unsigned long, OBTetrahedralStereo*> m_tetrahedralMap;
<a name="l00478"></a>00478 std::map<unsigned long, OBCisTransStereo*> m_cistransMap;
<a name="l00479"></a>00479 std::map<unsigned long, OBSquarePlanarStereo*> m_squarePlanarMap;
<a name="l00480"></a>00480 };
<a name="l00481"></a>00481
<a name="l00482"></a>00482 <span class="comment">// fwd decl</span>
<a name="l00483"></a>00483 <span class="keyword">class </span>OBBond;
<a name="l00486"></a>00486
<a name="l00494"></a>00494 OBAPI <span class="keywordtype">void</span> <a class="code" href="group__stereo.shtml#gae7aedffc6994cf26d16524389c56bdac">PerceiveStereo</a>(OBMol *mol, <span class="keywordtype">bool</span> force = <span class="keyword">false</span>);
<a name="l00526"></a>00526 OBAPI <span class="keywordtype">void</span> <a class="code" href="group__stereo.shtml#ga305c9600a3a336da16683baa395e20f4">StereoFrom2D</a>(OBMol *mol,
<a name="l00527"></a>00527 std::map<OBBond*, enum OBStereo::BondDirection> *updown = NULL, <span class="keywordtype">bool</span> force = <span class="keyword">false</span>);
<a name="l00544"></a>00544 OBAPI <span class="keywordtype">void</span> <a class="code" href="group__stereo.shtml#gaebcf38fd76c5d76fffbae808b8571f9b">StereoFrom3D</a>(OBMol *mol, <span class="keywordtype">bool</span> force = <span class="keyword">false</span>);
<a name="l00560"></a>00560 OBAPI <span class="keywordtype">void</span> <a class="code" href="group__stereo.shtml#ga419e494a34740f1f8003acabfa30a95b">StereoFrom0D</a>(OBMol *mol);
<a name="l00562"></a>00562
<a name="l00565"></a>00565
<a name="l00603"></a>00603 OBAPI std::vector<OBTetrahedralStereo*> <a class="code" href="group__stereo.shtml#ga35e07645a245db366b115f0dc20542fd">TetrahedralFrom3D</a>(OBMol *mol,
<a name="l00604"></a>00604 <span class="keyword">const</span> <a class="code" href="group__stereo.shtml#ga042299211c7a52f5aee1975d32820af7" title="A single set of OBStereoUnit objects.">OBStereoUnitSet</a> &stereoUnits, <span class="keywordtype">bool</span> addToMol = <span class="keyword">true</span>);
<a name="l00649"></a>00649 OBAPI std::vector<OBTetrahedralStereo*> <a class="code" href="group__stereo.shtml#gab85c5ef4c9416ee7af02b21658fe9de2">TetrahedralFrom2D</a>(OBMol *mol,
<a name="l00650"></a>00650 <span class="keyword">const</span> <a class="code" href="group__stereo.shtml#ga042299211c7a52f5aee1975d32820af7" title="A single set of OBStereoUnit objects.">OBStereoUnitSet</a> &stereoUnits, <span class="keywordtype">bool</span> addToMol = <span class="keyword">true</span>);
<a name="l00670"></a>00670 OBAPI std::vector<OBTetrahedralStereo*> <a class="code" href="group__stereo.shtml#gac3049b86debe9059b851825b29b1557c">TetrahedralFrom0D</a>(OBMol *mol,
<a name="l00671"></a>00671 <span class="keyword">const</span> <a class="code" href="group__stereo.shtml#ga042299211c7a52f5aee1975d32820af7" title="A single set of OBStereoUnit objects.">OBStereoUnitSet</a> &stereoUnits, <span class="keywordtype">bool</span> addToMol = <span class="keyword">true</span>);
<a name="l00672"></a>00672
<a name="l00709"></a>00709 OBAPI std::vector<OBCisTransStereo*> <a class="code" href="group__stereo.shtml#ga7e1ba3a4ac33b0c6404b0d960cc53d00">CisTransFrom3D</a>(OBMol *mol,
<a name="l00710"></a>00710 <span class="keyword">const</span> <a class="code" href="group__stereo.shtml#ga042299211c7a52f5aee1975d32820af7" title="A single set of OBStereoUnit objects.">OBStereoUnitSet</a> &stereoUnits, <span class="keywordtype">bool</span> addToMol = <span class="keyword">true</span>);
<a name="l00741"></a>00741 OBAPI std::vector<OBCisTransStereo*> <a class="code" href="group__stereo.shtml#ga98528c3002ed718695ccfaf031ca3f04">CisTransFrom2D</a>(OBMol *mol,
<a name="l00742"></a>00742 <span class="keyword">const</span> <a class="code" href="group__stereo.shtml#ga042299211c7a52f5aee1975d32820af7" title="A single set of OBStereoUnit objects.">OBStereoUnitSet</a> &stereoUnits,
<a name="l00743"></a>00743 <span class="keyword">const</span> std::map<OBBond*, enum OBStereo::BondDirection> *updown = NULL, <span class="keywordtype">bool</span> addToMol = <span class="keyword">true</span>);
<a name="l00770"></a>00770 OBAPI <span class="keywordtype">bool</span> <a class="code" href="group__stereo.shtml#ga182a53150e1793ac1ec14958afb05f17">TetStereoToWedgeHash</a>(OBMol &mol,
<a name="l00771"></a>00771 std::map<OBBond*, enum OBStereo::BondDirection> &updown,
<a name="l00772"></a>00772 std::map<OBBond*, OBStereo::Ref> &from);
<a name="l00784"></a>00784 OBAPI std::set<OBBond*> <a class="code" href="group__stereo.shtml#ga63e739a42d88ac64ed77c07d73866a45">GetUnspecifiedCisTrans</a>(OBMol& mol);
<a name="l00796"></a>00796 OBAPI <span class="keywordtype">void</span> <a class="code" href="group__stereo.shtml#ga9b44683d071146220a97390283944f70">StereoRefToImplicit</a>(OBMol& mol, <a class="code" href="structOpenBabel_1_1OBStereo.shtml#aff913cc7d694153b33e2b3ac168a6350">OBStereo::Ref</a> atomId);
<a name="l00816"></a>00816 OBAPI std::vector<OBCisTransStereo*> <a class="code" href="group__stereo.shtml#gac74fff254a639ede4d92a59fa44318a6">CisTransFrom0D</a>(OBMol *mol,
<a name="l00817"></a>00817 <span class="keyword">const</span> <a class="code" href="group__stereo.shtml#ga042299211c7a52f5aee1975d32820af7" title="A single set of OBStereoUnit objects.">OBStereoUnitSet</a> &stereoUnits,
<a name="l00818"></a>00818 <span class="keywordtype">bool</span> addToMol = <span class="keyword">true</span>);
<a name="l00820"></a>00820
<a name="l00821"></a>00821
<a name="l00824"></a>00824
<a name="l00904"></a>00904 OBAPI <a class="code" href="group__stereo.shtml#ga042299211c7a52f5aee1975d32820af7" title="A single set of OBStereoUnit objects.">OBStereoUnitSet</a> <a class="code" href="group__stereo.shtml#gaebf264394d502844b99b1dbe031ea185">FindStereogenicUnits</a>(OBMol *mol,
<a name="l00905"></a>00905 <span class="keyword">const</span> std::vector<unsigned int> &symClasses);
<a name="l00982"></a>00982 OBAPI <a class="code" href="group__stereo.shtml#ga042299211c7a52f5aee1975d32820af7" title="A single set of OBStereoUnit objects.">OBStereoUnitSet</a> <a class="code" href="group__stereo.shtml#gaebf264394d502844b99b1dbe031ea185">FindStereogenicUnits</a>(OBMol *mol,
<a name="l00983"></a>00983 <span class="keyword">const</span> std::vector<unsigned int> &symClasses,
<a name="l00984"></a>00984 <span class="keyword">const</span> <a class="code" href="group__substructure.shtml#ga6179e6c11d4f797e8d0ef6ac5c9f25a8" title="A group of automorphic permutations.">Automorphisms</a> &automorphisms);
<a name="l00986"></a>00986
<a name="l01136"></a>01136
<a name="l01137"></a>01137 }
<a name="l01138"></a>01138
<a name="l01139"></a>01139 <span class="preprocessor">#endif</span>
<a name="l01140"></a>01140 <span class="preprocessor"></span>
</pre></div></div>
</div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark"> </span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark"> </span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark"> </span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark"> </span>Friends</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(10)"><span class="SelectionMark"> </span>Defines</a></div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
</div><!-- end content -->
<!--#include file="footer.html" -->
<div id="footer">
<hr size="1">
<img src="http://openbabel.org/babel256.png" width="136" height="127" alt="" style="float: left;" />
<p>This file is part of the documentation for <a href="http://openbabel.org/wiki/">Open Babel</a>, version 2.3.</p>
<div class="bottom">
Documentation copyright © 1998-2007, the <a href="http://openbabel.org/wiki/THANKS">Open Babel Developers</a>.<br>
Open Babel is hosted by: <a href="http://sourceforge.net">
<img src="http://sourceforge.net/sflogo.php?group_id=40728"
width="88" height="31" border="0" alt="SourceForge Logo"></a><br>
Generated on Thu Oct 13 2011 16:08:08 by <a href="http://www.doxygen.org/"><img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.7.5.1.
</div>
</body>
</html>
|
