-
-
Notifications
You must be signed in to change notification settings - Fork 403
/
bondtyp.txt
255 lines (237 loc) · 12.1 KB
/
bondtyp.txt
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
##############################################################################
# #
# Open Babel file: bondtyp.txt #
# #
# Copyright (c) 2002-2005 by Geoffrey R Hutchison #
# Part of the Open Babel package, under the GNU General Public License (GPL)#
# #
# Used by bondtyper.cpp::OBBondTyper (and thus OBMol::PerceiveBondOrders() #
# #
# List of functional groups with double, triple (etc.) bond orders #
# Pattern Atom1 Atom2 Bond Order (repeat as needed) #
# * = Any atom (for setting non-multiple bonds) #
# #
# NOTE: These are applied in order, first to last. #
# So it's generally better to have a long (specifc) SMARTS first. #
# (all bonds must be single bonds to match) #
# #
##############################################################################
# Porphyrin / phthalocyanine (3 patterns for three separate bonding motifs)
# this one has explicit bonds to all four nitrogens (e.g., metal bond or hydrogens)
# X2,X3 is needed to avoid mis-typing coproporphyrinogen
#0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
[X2,X3]1[#6]([#7D3]2)[#6][#6][#6]2[X2,X3][#6]([#7D3]3)[#6][#6][#6]3[X2,X3][#6]([#7D3]4)[#6][#6][#6]4[X2,X3][#6]([#7D3]5)[#6][#6][#6]51 0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
# this one has explicit bonds to two nitrogens (12 and 14)
#0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
[X2,X3]1[#6]([#7D3]2)[#6][#6][#6]2[X2,X3][#6]([#7]3)[#6][#6][#6]3[X2,X3][#6]([#7D3]4)[#6][#6][#6]4[X2,X3][#6]([#7]5)[#6][#6][#6]51 0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
# and this one doesn't have any explicit bonds to the nitrogens
#0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
[X2,X3]1[#6]([#7]2)[#6][#6][#6]2[X2,X3][#6]([#7]3)[#6][#6][#6]3[X2,X3][#6]([#7]4)[#6][#6][#6]4[X2,X3][#6]([#7]5)[#6][#6][#6]51 0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
# N-methylmethanesulfinimidic-acid
[#6X4][#7X2][#16X3] 0 1 1 1 2 2
# amino--diaminomethylideneamino-methylidene--ethylazanium and analogs
[#6X3]([#7X3])([#7X3])([#7X2][#6X3]([#7X3])([#7X3]([#6]))) 0 1 1 0 2 1 0 3 2 3 4 1 4 5 1 4 6 2 6 7 1
# cyanoimino-methylene-azanide N#C-N-C#N
[#7X1][#6X2][#7X2][#6X2][#7X1] 0 1 3 1 2 1 2 3 1 3 4 3
# fulvene analogs
[#6X3]1([#6X3]([#1])([#1]))([#6X3][#6X3][#6X3][#6X3]1) 0 1 2 1 2 1 1 3 1 0 4 1 4 5 2 5 6 1 6 7 2 0 7 1
[#6X3]1([#7X2])([#6X3][#6X3][#6X3][#6X3]1) 0 1 2 0 2 1 2 3 2 3 4 1 4 5 2 0 5 1
# CR3-N=N-CH=CH
[#6X4][#7X2][#7X2][#6X3][#6X3] 0 1 1 1 2 2 2 3 1 3 4 2
#CR2=N-N=CH2
[#6X3][#7X2][#7X2][#6X3]([#1])([#1]) 0 1 2 1 2 1 2 3 2 3 4 1 3 5 1
# C2=N-NO2
[#6X3][#7X2][#7X3]([#8X1])([#8X1]) 0 1 2 1 2 1 2 3 1 2 4 2
#1-3-oxazole analogs
[#8X2]1[#6X3][#7X2][#6X3][#6X3]1 0 1 1 1 2 2 2 3 1 3 4 2 0 4 1
#N=C=N-C#N
[#7X1][#6X2][#7X2][#6X2][#7X1] 0 1 2 1 2 2 2 3 1 3 4 3
#pyridinium analogs
[#7X3]1([#6])([#6X3][#6X3][#6X3][#6X3][#6X3]1) 0 1 1 0 2 1 2 3 2 3 4 1 4 5 2 5 6 1 0 6 2
[#7X3]1([#1])([#6X3][#6X3][#6X3][#6X3][#6X3]1) 0 1 1 0 2 2 2 3 1 3 4 2 4 5 1 5 6 2 0 6 1
#Pyrrol-imine analogs
[#6X3]1([#7X2][#1,#6])([#7X2][#6X3][#6X3][#6X3]1) 0 1 2 1 2 1 0 3 1 3 4 2 4 5 1 5 6 2 0 6 1
#1H-pyrimidin-2-one analogs
[#6X3]1([#8X1])([#7X3][#6X3][#6X3][#6X3][#7X2]1) 0 1 2 0 2 1 2 3 1 3 4 2 4 5 1 5 6 2 0 6 1
# 5-methylideneimidazol-2-one analogs, 5-methylimidazol-4-one analogs
[#6X3]1([#8X1])([#7X3][#6X3]([#6X3])[#6X3][#7X2]1) 0 1 2 0 2 1 2 3 1 3 4 2 3 5 1 5 6 2 0 6 1
[#6X3]1([#8X1])([#7X2][#6X3][#7X2][#6X3]1) 0 1 2 0 2 1 2 3 2 3 4 1 4 5 2 0 5 1
# C/N-N=CH2
[#6X3]([#1])([#1])[#7X2][#7X2,#7X3,#6X3,#6X4] 0 1 1 0 2 1 0 3 2 3 4 1
# Imines
[#6X3]([#7X2][#1])([#7X3][#6X3]([#1])[#6X3]) 0 1 2 1 2 1 0 3 1 3 4 1 4 5 1 4 6 2
[#6X3]([#7X2][#1])([#7X2][#6X3]([#1])[#6X3]) 0 1 2 1 2 1 0 3 1 3 4 2 4 5 1 4 6 1
[#6X3]([#7X2][#1,#6])([#7X3])([*]) 0 1 2 1 2 1 0 3 1 0 4 1
# Azide
[#7D2][#7D2^1][#7D1] 0 1 2 1 2 2
# Nitro
# [#8D1][#7D3^2]([#8D1])* 0 1 2 1 2 2 1 3 1; old code
[#8D1][#7D3^2]([#8D1])* 0 1 1 1 2 2 1 3 1
# nitronium
[#8X1][#7X2]([#8X1]) 0 1 2 1 2 2
# Dimethyl(methylidene)azanium and analogs
[#7X3]([#6X4])([#6X4])([#6X3]([#1])([#1])) 0 1 1 0 2 1 0 3 2 3 4 1 3 5 1
[#7X3]([#6X3]([#7X3])([#7X3]))([#6X4])([#6X4]) 0 1 2 1 2 1 1 3 1 0 4 1 0 5 1
# N2O
[#7X1][#7X2][#8X1] 0 1 3 1 2 1
# nitroso R-N=O
[#8X1][#7X2][#7X2][#6X3] 0 1 2 1 2 1 2 3 2
[#8X1][#7X2]([*;!#6]) 0 1 2 1 2 1
[#8X1][#7X2]([#6X3]([*])([*])) 0 1 2 1 2 1 2 3 1 2 4 1
# H-N=P(-O)3
[#7X2]([#1])([#15X4]([#8X1])([#8X1])([#8X1])) 0 1 1 0 2 2 2 3 1 2 4 1 2 5 1
# NR2-C=C-C=O
[#7X3][#6X3][#6X3][#6X3][#8X1] 0 1 1 1 2 2 2 3 1 3 4 2
# NR2-C=C-C
[#7X3][#6X3][#6X3]([#6X4,#1])[#6X2] 0 1 1 1 2 2 2 3 1 2 4 1
# C=CH-NR-CR=O
[#6X3][#6X3]([#1])[#7X3][#6X3][#8X1] 0 1 2 1 2 1 1 3 1 3 4 1 4 5 2
# bis-methylamino-methylidene-methylazaniumyl--sulfate analogs
[#7X3]([#8X2])([#6X4])([#6X3]([#7X3])([#7X3])) 0 1 1 0 2 1 0 3 2 3 4 1 3 5 1
# NO2H=CH-CR3
[#7X3]([#8X2])([#8X1])([#6X3][#6X4]) 0 1 1 0 2 1 0 3 2 3 4 1
# CR2=N-N(CR3)2
[#6X3][#7X2][#7X3]([#6X4])([#6X4]) 0 1 2 1 2 1 2 3 1 2 4 1
#1-2-4-thiadiazole
[#6X3]1([#7X2][#6X3]([#1])[#7X2][#16X2]1) 0 1 2 1 2 1 2 3 1 2 4 2 4 5 1 0 5 1
# cyanoimino-methylene-azanide N#C-N-C#N
#[#7X1][#6X2][#7X2][#6X2][#7X1] 0 1 3 1 2 1 2 3 1 3 4 3
# CR2=CH2
[#6X3]([#1])([#1])[#6X3] 0 1 1 0 2 1 0 3 2
#R-C#N-S
[#16X1][#7X2][#6X2] 0 1 1 1 2 3
# R(RO)S=O
[#16X3]([#8X1])([#8X2])([*!#8]) 0 1 2 0 2 1 0 3 1
#R-N=S=O
[#8X1][#16X2][#7X2][*] 0 1 2 1 2 2 2 3 1
[#8X1][#16X4]([#7X2][#1])([*])([*]) 0 1 2 1 2 2 2 3 1 1 4 1 1 5 1
# Sulfones
[#16D4]([#8D1])([#8D1])([*!#8])([*!#8]) 0 1 2 0 2 2 0 3 1 0 4 1
# Sulfates
[#16D4]([#8D1])([#8D1])([#8-,#8D1])([#8-,#8D1]) 0 1 2 0 2 2 0 3 1 0 4 1
# Thiosulfates
#[#16D4]([#16D1])([#8D1])([#8-,#8])([#8-,#8]) 0 1 2 0 2 2 0 3 1 0 4 1
[#16D4]([#16D1])([#8D1])([#8])([#8-,#8]) 0 1 1 0 2 2 0 3 2 0 4 1
# Sulfonyl analogs
[#16X3]([#8X1])([#8X1])([#6^2,#7^2]) 0 1 2 0 2 2 0 3 2
# Sulfinic acid and analogs
[#16X3]([#8X1])([#8X1,#8X2])([#6]) 0 1 2 0 2 1 0 3 1
# Sulfoxides
[#16D3]([#8D1])([*!#8])([*!#8]) 0 1 2 0 2 1 0 3 1
# Sulfite
[#16D3]([#8D1])([#8D1-])([#8D1-]) 0 1 2 0 2 1 0 3 1
# Sulfur trioxide
[#16D3^2]([#8D1])([#8D1])([#8D1]) 0 1 2 0 2 2 0 3 2
# Sulfites
[#16D3]([#8D1])([#8])([#8]) 0 1 2 0 2 1 0 3 1
# 1-Sulfinylethane and analogs C=S=O
[#8X1][#16X2][#6X3] 0 1 2 1 2 2
#H2C=S=O
[#16X4]([#8X1])([#6X3]([#1])([#1])) 0 1 2 0 2 2 2 3 1 2 4 1
# Sulfonic acid and sulfonic ester
[#16X4]([#8X1])([#8X1])([#8])* 0 1 2 0 2 2 0 3 1 0 4 1
# Disulfur monoxide
[#16D2]([#8D1])([#16D1]) 0 1 2 0 2 2
# Sulfmonoxides
[#16D2]([#8D1])([*!#8]) 0 1 2 0 2 1
# S=N-H
[#16X2,#16X4][#7X2][#1] 0 1 2 1 2 1
# Sulfur dioxide
[#16D2]([#8D1])([#8D1]) 0 1 2 0 2 2
# S=S=S, S=S
[#16X1][#16X2][#16X1] 0 1 2 1 2 2
[#16X1][#16X1] 0 1 2
# S=CH2
[#16X2][#6X3]([#1])([#1]) 0 1 2 1 2 1 1 3 1
# dimethyl-oxido-sulfanylidene-lambda5-phosphane and analogs
[#16X1][#15] 0 1 2
# dihydroxy-sulfanylidene--lambda4-sulfane and analogs
[#16X1;!-][#16X3,#16X4] 0 1 2
# thiopyrylium
[#16X2]1[#6X3][#6X3][#6X3]([#1])[#6X3][#6X3]1 0 1 1 1 2 2 2 3 1 3 4 1 3 5 2 5 6 1 0 6 2
# dithiol-1-ium analogs
[#16X2]1[#6X3][#6X3][#6X3][#16X2]1 0 1 2 1 2 1 2 3 2 3 4 1 0 4 1
# O=S=CR2
[#8X1][#16X2][#6X3] 0 1 2 1 2 2
# 4-methylidenetriphosphole
[#6X3]1([#6X3])([#15X2][#15X2][#15X2][#6X3]1) 0 1 2 0 2 1 2 3 2 3 4 1 4 5 2 0 5 1
# C=P-H
[#6X3]1([#15X2][#1])([#6X3][#15X2][#6X3][#15X2]1) 0 1 2 1 2 1 0 3 1 3 4 2 4 5 1 5 6 2 0 6 1
[#6X3]1[#15X2][#6X3][#6X3][#6X3]1 0 1 1 1 2 2 2 3 1 3 4 2 0 4 1
[#6X3,#6X2,#16X2][#15X2][#1] 0 1 2 1 2 1
# 3-4-dihydrophosphol-2-one analogs
[#6X3]1[#15X2][#6X3][#6X4][#6X4]1 0 1 1 1 2 2 2 3 1 3 4 1 0 4 1
# C=P-C
[#6X3][#15X2][#6;!r6] 0 1 2 1 2 1
#Phosphite
[#15D3]([#8D1])([#8D1])([#8D2]) 0 1 2 0 2 2 0 3 1
#Methylphosphinate and analogs
[#15X3^2]([#8X1;!-])([#8X1;!-])([#6]) 0 1 2 0 2 2 0 3 1
#oxophosphane
[#15D2]([#8D1])([#1]) 0 1 2 0 2 1
#phosphaalkene and analogs
[#15X2;!R]([#6X3,#6X4])([#6X3]) 0 1 1 0 2 2
[#15X2]([#6X3;!H,#6X4])([#6X3;!H]) 0 1 1 0 2 2
# P=O
[#15X2][#8X1] 0 1 2
#Nitrosyl Hydride
[#7D2]([#8D1])([#1]) 0 1 2 0 2 1
#Nitrite
[#8X1][#7X2][#8X2][*] 0 1 2 1 2 1 2 3 1
# chloro-hydroxy-dioxidophosphanium; not working right now
#[#15X4]([#8X1])([#8X1])([#8X2])([*]) 0 1 1 0 2 1 0 3 1 0 4 1
#[#15X4]([#8X1])([#8X1])([#17])([*]) 0 1 1 0 2 1 0 3 1 0 4 1
# Phosphone
[#15X4]([#8X1])([*])([*])([*]) 0 1 2 0 2 1 0 3 1 0 4 1
# diphospholes and analogs
[#6][#15X2][#15X2][#6] 0 1 1 1 2 2 2 3 1
# C-P=O
[#15X2]([#8X1])([#6]) 0 1 2 0 2 1
# Carboxylic Acid, ester, etc.
[#6D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1
# Carbon dioxide
[#8D1][#6D2^1][#8D1] 0 1 2 1 2 2
# Carbon monoxide
[#8X1][#6X1] 0 1 3
# Amide C(=O)N - no negative charge on O (2aix_u1k.sdf)
[#6D3^2]([#8D1;!-])([#7])* 0 1 2 0 2 1 0 3 1
# Seleninic acid Se(=O)OH
[#34D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1
# Thioacid / Thioester C(=O)S
[#6D3^2]([#8D1])([#16])* 0 1 2 0 2 1 0 3 1
# dithioacid / dithioester C(=S)S
[#6D3^2]([#16D1])([#16])* 0 1 2 0 2 1 0 3 1
# thioamide C(=S)N
# avoid aromatics (pdb_ligands_sdf/1yry_msg.sdf)
[CD3^2]([#16D1])([N])* 0 1 2 0 2 1 0 3 1
# C=C=C=CH2
[#6X3][#6X2][#6X2][#6X3]([#1])([#1]) 0 1 2 1 2 2 2 3 2 3 4 1 3 5 1
# allene C=C=C
# (this is problematic -- need to make sure the center carbon is sp)
[#6^2][#6D2^1][#6^2] 0 1 2 1 2 2
# ethenolate
[#6X3]([#1])([#1])[#6X3]([#8])([#1]) 0 1 1 0 2 1 0 3 2 3 4 1 3 5 1
# acetylenoate
[#6X2]([#1])[#6X2]([#8]) 0 1 1 0 2 2 2 3 1
# ene-one C=C=O
[#6^2][#6D2^1][#8D1] 0 1 2 1 2 2
# isonitrile / isocyano
[#6D1][#7D2^1]* 0 1 3 1 2 1
# NR2 in ring with hybridized carbon neighbors, do not apply to aromatic N
# valence insted of degree used to fix pdb_ligands_sdf/3dcv_55e.sdf
[Nv2R][#6v3^2][#8v2] 0 1 2 1 2 1
[Nv2R][#6v3^2][Nv2] 0 1 2 1 2 1
# if three N are present in R-N-guanidine-ish, prefer double bond to the
# non-terminal N (i.e. D2 if present)
[#6D3^2;!R]([#7D2;!R])([#7D1;!R])~[#7D1;!R] 0 1 2 0 2 1 0 3 1
# guanidinium and amidine -C(=NH)NH2 without hydrogens
[#6D3^2;!R]([#7D1H0;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1
# and also with hydrogens
# (this can normally be figured out, but is needed to avoid matching the next SMARTS)
[#6D3^2;!R]([#7D2H1;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1
# and also with more hydrogens than normal (protonated)
[#6D3^2;!R]([#7D3H2;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1
# Schiff base, protonated
[#6D3^2;!R]([#1,#6])([#1,#6])[#7D3^2;!R]([#1])[#6] 0 1 1 0 2 1 0 3 2 3 4 1 3 5 1
### other potential functional groups that may (or may not) be useful to add
# imidines ( N=C/N\C=N