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Viewing changes to src/org/openscience/cdk/config/data/hybridization_atomtypes.xml

  • Committer: Bazaar Package Importer
  • Author(s): Paul Cager
  • Date: 2008-04-09 21:17:53 UTC
  • Revision ID: james.westby@ubuntu.com-20080409211753-46lmjw5z8mx5pd8d
Tags: upstream-1.0.2
Import upstream version 1.0.2

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src/org/openscience/cdk/config/data/hybridization_atomtypes.xml
 
1
<atomTypeList xmlns="http://www.xml-cml.org/schema"
 
2
              xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 
3
              xsi:schemaLocation="http://www.xml-cml.org/schema ../../io/cml/data/cml23.xsd"
 
4
 
 
5
              xmlns:cvs="https://www.cvshome.org/"
 
6
              xmlns:cdk="http://cdk.sf.net/dict/cdk/"
 
7
 
 
8
              id="valency" title="Hybridization AtomTypes">
 
9
 
 
10
    <metadataList>
 
11
        <metadata name="cvs:last-change-by" content="$Author: kaihartmann $"/>
 
12
        <metadata name="cvs:date" content="$Date: 2006-05-03 11:58:38 +0200 (Wed, 03 May 2006) $"/>
 
13
        <metadata name="cvs:revision" content="$Revision: 6128 $"/>
 
14
    </metadataList>
 
15
 
 
16
    <atomType id="H">
 
17
        <atom elementType="H" formalCharge="0">
 
18
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
19
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">1.0</scalar>
 
20
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">1</scalar>
 
21
        </atom>
 
22
    </atomType>
 
23
    <atomType id="Hplus">
 
24
        <atom elementType="H" formalCharge="1">
 
25
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">0.0</scalar>
 
26
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">0.0</scalar>
 
27
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">0</scalar>
 
28
        </atom>
 
29
    </atomType>
 
30
    <atomType id="Hminus">
 
31
        <atom elementType="H" formalCharge="-1">
 
32
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">0.0</scalar>
 
33
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">0.0</scalar>
 
34
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">0</scalar>
 
35
        </atom>
 
36
    </atomType>
 
37
    <atomType id="C.sp3">
 
38
        <atom elementType="C" formalCharge="0">
 
39
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
40
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
 
41
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
 
42
        </atom>
 
43
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar>
 
44
    </atomType>
 
45
    <atomType id="C.sp2">
 
46
        <atom elementType="C" formalCharge="0">
 
47
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
48
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
 
49
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">3</scalar>
 
50
        </atom>
 
51
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
 
52
    </atomType>
 
53
    <atomType id="C.sp">
 
54
        <atom elementType="C" formalCharge="0">
 
55
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">3.0</scalar>
 
56
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
 
57
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">2</scalar>
 
58
        </atom>
 
59
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp1</scalar>
 
60
    </atomType>
 
61
    <atomType id="C.default">
 
62
        <atom elementType="C" formalCharge="0">
 
63
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">3.0</scalar>
 
64
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
 
65
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
 
66
        </atom>
 
67
    </atomType>
 
68
    <atomType id="Cplus.sp2">
 
69
        <atom elementType="C" formalCharge="1">
 
70
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
71
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">3.0</scalar>
 
72
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">2</scalar>
 
73
        </atom>
 
74
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
 
75
    </atomType>
 
76
    <atomType id="Cminus.sp2">
 
77
        <atom elementType="C" formalCharge="-1">
 
78
            <!-- for example in cyclopentadienyl anion -->
 
79
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">3.0</scalar>
 
80
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">3.0</scalar>
 
81
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">3</scalar>
 
82
        </atom>
 
83
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
 
84
    </atomType>
 
85
    <atomType id="Caromatic.sp2">
 
86
        <atom elementType="C" formalCharge="0">
 
87
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.5</scalar>
 
88
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
 
89
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">3</scalar>
 
90
        </atom>
 
91
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
 
92
    </atomType>
 
93
    <atomType id="Cminus">
 
94
        <atom elementType="C" formalCharge="-1">
 
95
            <!-- for example in cyclopentadienyl anion -->
 
96
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">3.0</scalar>
 
97
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">3.0</scalar>
 
98
        </atom>
 
99
    </atomType>
 
100
    <atomType id="N">
 
101
        <atom elementType="N" formalCharge="0">
 
102
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
103
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">3.0</scalar>
 
104
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">3</scalar>
 
105
        </atom>
 
106
    </atomType>
 
107
    <atomType id="N">
 
108
        <atom elementType="N" formalCharge="0">
 
109
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
110
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">5.0</scalar>
 
111
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">3</scalar>
 
112
        </atom>
 
113
    </atomType>
 
114
    <atomType id="N.sp">
 
115
        <atom elementType="N" formalCharge="0">
 
116
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">3.0</scalar>
 
117
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">3.0</scalar>
 
118
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">1</scalar>
 
119
        </atom>
 
120
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp</scalar>
 
121
    </atomType>
 
122
    <atomType id="N.sp2">
 
123
        <atom elementType="N" formalCharge="0">
 
124
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
125
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">3.0</scalar>
 
126
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">2</scalar>
 
127
        </atom>
 
128
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
 
129
    </atomType>
 
130
 
 
131
    <atomType id="N.sp3">
 
132
        <atom elementType="N" formalCharge="0">
 
133
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
134
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">3.0</scalar>
 
135
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">3</scalar>
 
136
        </atom>
 
137
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar>
 
138
    </atomType>
 
139
 
 
140
    <atomType id="Nplus">
 
141
        <atom elementType="N" formalCharge="1">
 
142
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">3.0</scalar>
 
143
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
 
144
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
 
145
        </atom>
 
146
    </atomType>
 
147
    <atomType id="Nminus">
 
148
        <atom elementType="N" formalCharge="-1">
 
149
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
150
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
 
151
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">1</scalar>
 
152
        </atom>
 
153
    </atomType>
 
154
    <atomType id="Nplus.sp3">
 
155
        <atom elementType="N" formalCharge="1">
 
156
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
157
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
 
158
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
 
159
        </atom>
 
160
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar>
 
161
    </atomType>
 
162
    <atomType id="O.sp2">
 
163
        <atom elementType="O" formalCharge="0">
 
164
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
165
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
 
166
        </atom>
 
167
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
 
168
    </atomType>
 
169
    <atomType id="O.sp3">
 
170
        <atom elementType="O" formalCharge="0">
 
171
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
172
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
 
173
        </atom>
 
174
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar>
 
175
    </atomType>
 
176
    <atomType id="Oplus">
 
177
        <atom elementType="O" formalCharge="1">
 
178
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
179
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">3.0</scalar>
 
180
        </atom>
 
181
    </atomType>
 
182
    <atomType id="Ominus">
 
183
        <atom elementType="O" formalCharge="-1">
 
184
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
185
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">1.0</scalar>
 
186
        </atom>
 
187
    </atomType>
 
188
    <atomType id="P3">
 
189
        <atom elementType="P" formalCharge="0">
 
190
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">3.0</scalar>
 
191
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">3.0</scalar>
 
192
        </atom>
 
193
    </atomType>
 
194
    <atomType id="Pplus">
 
195
        <atom elementType="P" formalCharge="1">
 
196
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">4.0</scalar>
 
197
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">1.0</scalar>
 
198
        </atom>
 
199
    </atomType>
 
200
    <atomType id="P4">
 
201
        <atom elementType="P" formalCharge="0">
 
202
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">3.0</scalar>
 
203
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">5.0</scalar>
 
204
        </atom>
 
205
    </atomType>
 
206
    <atomType id="S2">
 
207
        <atom elementType="S" formalCharge="0">
 
208
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
209
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
 
210
        </atom>
 
211
    </atomType>
 
212
    <atomType id="S2-">
 
213
        <atom elementType="S" formalCharge="-1">
 
214
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
215
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">1.0</scalar>
 
216
        </atom>
 
217
    </atomType>
 
218
    <atomType id="Splus">
 
219
        <atom elementType="S" formalCharge="1">
 
220
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
221
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">5.0</scalar>
 
222
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
 
223
        </atom>
 
224
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
 
225
    </atomType>
 
226
    <atomType id="S3">
 
227
        <atom elementType="S" formalCharge="0">
 
228
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
229
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
 
230
        </atom>
 
231
    </atomType>
 
232
    <atomType id="S4">
 
233
        <atom elementType="S" formalCharge="0">
 
234
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
235
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">6.0</scalar>
 
236
        </atom>
 
237
    </atomType>
 
238
    <atomType id="S">
 
239
        <atom elementType="S" formalCharge="0">
 
240
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
241
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
 
242
        </atom>
 
243
    </atomType>
 
244
    <atomType id="F">
 
245
        <atom elementType="F" formalCharge="0">
 
246
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
247
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">1.0</scalar>
 
248
        </atom>
 
249
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp1</scalar>
 
250
    </atomType>
 
251
    <atomType id="Fminus">
 
252
        <atom elementType="F" formalCharge="-1">
 
253
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">0.0</scalar>
 
254
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">0.0</scalar>
 
255
        </atom>
 
256
    </atomType>
 
257
    <atomType id="Fplus">
 
258
        <atom elementType="F" formalCharge="1">
 
259
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
260
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
 
261
        </atom>
 
262
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
 
263
    </atomType>
 
264
    <atomType id="Cl">
 
265
        <atom elementType="Cl" formalCharge="0">
 
266
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
267
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">1.0</scalar>
 
268
        </atom>
 
269
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp1</scalar>
 
270
    </atomType>
 
271
    <atomType id="Cl-">
 
272
        <atom elementType="Cl" formalCharge="-1">
 
273
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">0.0</scalar>
 
274
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">0.0</scalar>
 
275
        </atom>
 
276
    </atomType>
 
277
    <atomType id="Clplus">
 
278
        <atom elementType="Cl" formalCharge="1">
 
279
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
280
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
 
281
        </atom>
 
282
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
 
283
    </atomType>
 
284
    <atomType id="Br">
 
285
        <atom elementType="Br" formalCharge="0">
 
286
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
287
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">1.0</scalar>
 
288
        </atom>
 
289
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp1</scalar>
 
290
    </atomType>
 
291
    <atomType id="Brminus">
 
292
        <atom elementType="Br" formalCharge="-1">
 
293
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">0.0</scalar>
 
294
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">0.0</scalar>
 
295
        </atom>
 
296
    </atomType>
 
297
    <atomType id="Brplus">
 
298
        <atom elementType="Br" formalCharge="1">
 
299
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
300
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
 
301
        </atom>
 
302
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
 
303
    </atomType>
 
304
    <atomType id="I">
 
305
        <atom elementType="I" formalCharge="0">
 
306
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
307
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">1.0</scalar>
 
308
        </atom>
 
309
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp1</scalar>
 
310
    </atomType>
 
311
    <atomType id="I-">
 
312
        <atom elementType="I" formalCharge="-1">
 
313
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">0.0</scalar>
 
314
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">0.0</scalar>
 
315
        </atom>
 
316
    </atomType>
 
317
    <atomType id="Iplus">
 
318
        <atom elementType="I" formalCharge="1">
 
319
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">2.0</scalar>
 
320
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">2.0</scalar>
 
321
        </atom>
 
322
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp2</scalar>
 
323
    </atomType>
 
324
 
 
325
    <atomType id="Si.sp3">
 
326
        <atom elementType="Si" formalCharge="0">
 
327
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
328
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
 
329
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
 
330
        </atom>
 
331
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar>
 
332
    </atomType>
 
333
 
 
334
    <atomType id="Sn.sp3">
 
335
        <atom elementType="Sn" formalCharge="0">
 
336
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
337
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
 
338
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
 
339
        </atom>
 
340
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar>
 
341
    </atomType>
 
342
 
 
343
    <atomType id="Asplus.sp3">
 
344
        <atom elementType="As" formalCharge="1">
 
345
            <scalar dataType="xsd:double" dictRef="cdk:maxBondOrder">1.0</scalar>
 
346
            <scalar dataType="xsd:double" dictRef="cdk:bondOrderSum">4.0</scalar>
 
347
            <scalar dataType="xsd:integer" dictRef="cdk:formalNeighbourCount">4</scalar>
 
348
        </atom>
 
349
        <scalar dataType="xsd:string" dictRef="cdk:hybridization">sp3</scalar>
 
350
    </atomType>
 
351
 
 
352
</atomTypeList>