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comparison CADDSuite/data/OpenBabel/atomtyp.txt @ 3:ff6df146c0d5

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author marcel
date Sun, 26 Jun 2011 13:53:57 -0400
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1 ##############################################################################
2 # #
3 # Open Babel file: atomtyp.txt #
4 # #
5 # #
6 # Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
7 # Some portions Copyright (c) 2001-2008 Geoffrey R. Hutchison #
8 # Part of the Open Babel package, under the GNU General Public License (GPL)#
9 # #
10 # SMARTS patterns for atom typing (used by typer.cpp:OBAtomTyper) #
11 # #
12 # INTHYB: used to assign the internal hybridization values for atoms #
13 # IMPVAL: used to assign the implicit valence of an atom #
14 # EXTTYP: used to assign the external type of an atom for translation to #
15 # package specific types (i.e. Sybyl Mol2) #
16 # (these should correspond to INT type names in types.txt too.) #
17 # #
18 # The LAST PATTERN MATCHED is used to assign values with the corresponding #
19 # INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed #
20 # in the EXTRA DEFINITIONS section (to separate from original patterns.) #
21 # #
22 ##############################################################################
23
24 INTHYB [D4] 3 #any 4-valent atom -- tetrahedral
25 INTHYB [D5] 5 #any 5-valent atom -- trigbipy
26 INTHYB [D6] 6 #any 6-valent atom -- oct
27 INTHYB [C] 3 #sp3 carbon
28 INTHYB [c,$(C=*)] 2 #sp2 carbon
29 # INTHYB [$([#6]([#8D1])[#8D1])] 2 # Commented out after PR#3089597
30 INTHYB [$(C#*),$(C(=*)=*)] 1 #sp carbon
31
32 INTHYB [N] 3 #sp3 nitrogen
33 INTHYB [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen
34 INTHYB [ND1,ND2,ND3]a 2 #sp2 nitrogen
35 INTHYB [$(N#*),$([ND2](=*)=*)] 1 #sp nitrogen
36
37 INTHYB [O] 3 #sp3 oxygen
38 INTHYB [o,$(O=*),$(O[#6,#7,#8]=,:*)] 2 #sp2 oxygen
39 INTHYB [$([#8D1][#6][#8D1])] 2 #sp2 oxygen
40 INTHYB [$(O#*)] 1 #sp oxygen
41
42 INTHYB [P] 3 #sp3 phosphorus
43 INTHYB [#15;$([PD1]=*)] 2 #sp2 phosphorus
44 INTHYB [PD5] 5 #sp3d phosphorus, as in PF5
45 INTHYB [Pv5] 5 #sp3d phosphorus, as in H3PO4
46 INTHYB [S] 3 #sp3 sulfur
47 INTHYB [#16;s,$([SD1]=*)] 2 #sp2 sulfur
48 INTHYB [SD6] 6 #sp3d2 sulfur, as in SF6
49 INTHYB [B] 2 #sp2 boron
50 INTHYB [BD4] 3 #sp3 boron
51
52 INTHYB [Al] 2 # typical sp2 Al (and family)
53 INTHYB [Ga] 2
54 INTHYB [In] 2
55 INTHYB [Tl] 2
56 INTHYB [AlD4] 3 # sp3 Al
57 INTHYB [Si] 3 # sp3 Si (and family)
58 INTHYB [Ge] 3
59 INTHYB [Sn] 3
60 INTHYB [Pb] 3
61 INTHYB [As] 3 # sp3 hybridization As (and family)
62 INTHYB [Sb] 3
63 INTHYB [Bi] 3
64
65 INTHYB [se] 2 # aromatic sp2 Se
66 INTHYB [Se] 3 # sp3 hybridization Se (and family)
67 INTHYB [Te] 3
68 INTHYB [Po] 3
69
70 INTHYB [Be] 1 # Alkaline earth, like sp hybrids
71 INTHYB [Mg] 1
72 INTHYB [Ca] 1
73 INTHYB [Sr] 1
74 INTHYB [Ba] 1
75 INTHYB [Ra] 1
76
77 #INTHYB [Pt] 4 # normally square planar
78 #INTHYB [Pd] 4
79 #INTHYB [Cu] 4
80 #INTHYB [Ag] 4
81 #INTHYB [Au] 4
82
83 #
84 #IMPLICIT VALENCE RULES
85 #
86 #IMPVAL [#3,#11,#19,#37,#55,#87] 1 # Alkali metals
87 #IMPVAL [#4,#12,#20,#38,#56,#88] 2 # Alkaline earth
88
89 IMPVAL [#5] 3 # Generic boron
90 IMPVAL [$([#6+]=*)] 2
91 IMPVAL [$([#6+]#*)] 1 # just for InChI C2
92
93 IMPVAL [#6^3] 4
94 IMPVAL [#6^2] 3
95 IMPVAL [#6^1] 2
96 IMPVAL [#6^3-] 3
97 IMPVAL [#6^2-] 2
98 IMPVAL [#6^1-] 1 # isocyanides, CO (valence=1, bond order=3)
99 IMPVAL [c+] 2
100
101 IMPVAL [N^3] 3
102 IMPVAL [N^3+] 4
103 IMPVAL [N^2] 3
104 #IMPVAL [N^2-,N^3-] 2
105 IMPVAL [ND1^1] 1
106 IMPVAL [ND2^1] 2
107 IMPVAL [$(N([OD1])*)] 3
108 IMPVAL [$(NC=O)] 3
109 #IMPVAL [$(n(c=O)c=O)] 3 # aromatic diimide
110 IMPVAL [$(N(~[OD1])~[OD1])] 3
111 IMPVAL [$([Nr0]C=[Nr0])] 3
112 IMPVAL [$(N=*)] 2
113 #IMPVAL [$([Nr0]=C[Nr0])] 3
114 IMPVAL [$([Nr0]=C[Nr0])] 2
115 IMPVAL [$([N+r0]=C[Nr0])] 3 # patch from Steve Constable
116 IMPVAL [$([#7D1-]=*)] 1
117 IMPVAL [N^1-] 1 # N2O [N-]=[N+]=O (valence=1, bondorder=2)
118 IMPVAL [N-] 2
119 IMPVAL [n] 2
120 IMPVAL [n-] 2
121 IMPVAL [n+] 3
122 IMPVAL [$([#7-]=*)] 1
123 IMPVAL [$([#7+]#*)] 2
124
125 IMPVAL [$([#8+]#*)] 1
126
127 IMPVAL [#8] 2 # Generic O
128 IMPVAL [#8-] 1
129 IMPVAL [#8-2] 0
130 IMPVAL [#8+] 3
131 IMPVAL [$([#8]=*)] 1
132 IMPVAL [#8^1+] 1 # carbon monoxide
133
134 IMPVAL [#9D0] 1
135 IMPVAL [#9D0-] 0 #[F-]
136
137 IMPVAL [#13] 3 # generic Al
138
139 IMPVAL [#14] 4 # regular sp3 Si
140 IMPVAL [#14^2] 2 # silylenes
141 IMPVAL [$([#14]=*)] 3 # e.g., Si=O
142 IMPVAL [$([#14](=*)=*)] 0 # e.g., Si(=O)=O
143 IMPVAL [$([#14+]#*)] 1 # just for InChI Si2
144 IMPVAL [$([#14-]#*)] 1 # just for InChI Si2
145
146 IMPVAL [#15D4] 4
147 IMPVAL [#15D3] 3
148 IMPVAL [#15D2] 3
149 IMPVAL [#15D1^3] 3
150 IMPVAL [#15D1^2] 3
151 IMPVAL [#15D0] 3
152 IMPVAL [$([#15]=[#6])] 2
153 IMPVAL [pD2] 2
154 IMPVAL [$([#15]=[#8])] 4 # phosphinate (double bond = one valence)
155 IMPVAL [$([#15](=[#8])=[#8])] 3 # metaphosphate (double bond = one valence)
156 IMPVAL [$([#15+](=[#8])([#8]))] 0 # R-P+O2
157
158 IMPVAL [#16] 2 #revised CM April 2008
159 IMPVAL [$([#16D1]=*)] 1
160 IMPVAL [$([#16D3](=O)(=O)-O)] 4 #e.g. O[S](=O)=O
161 IMPVAL [$([#16D2](=O)-O)] 3 # e.g. O[S]=O
162 IMPVAL [#16D1-] 1
163
164 IMPVAL [#17D0] 1
165 IMPVAL [#17D0-] 0 #[Cl-]
166
167 IMPVAL [#31] 3
168 IMPVAL [#32] 4
169
170 IMPVAL [#33] 3
171 IMPVAL [as] 3
172
173 IMPVAL [#34] 2
174
175 IMPVAL [#35D0] 1
176 IMPVAL [#35D0-] 0 #[Br-]
177
178 #IMPVAL [#49,#81] 3 # In, Tl, like Ga
179 #IMPVAL [#50,#82] 4 # Sn, Pb, like Ge
180 #IMPVAL [#51,#83] 3 # Sb, Bi, like As
181
182 IMPVAL [#52] 2
183 IMPVAL [#53D0] 1
184 IMPVAL [#53D0-] 0 #[I-]
185
186 #
187 #EXTERNAL TYPE RULES
188 #
189
190 # Tinker OH hydrogens for MM2
191 # Fixes PR# 1839274
192 EXTTYP [#1][#8] HO
193
194 EXTTYP [#7^3] N3
195 EXTTYP [#7X4] N3+
196 EXTTYP [#7^2] Npl
197 EXTTYP [#7^1] N1
198 EXTTYP [$(N=*)] N2
199 EXTTYP [$([Nr0]C(=[Nr0])[Nr0])] Ng+
200 EXTTYP [$([Nr0]=C([Nr0])[Nr0])] Ng+
201 EXTTYP [$([ND1]=C[ND1])] Ng+
202 EXTTYP [$([ND1]C=[ND1])] Ng+
203 EXTTYP [$(N(O)*)] Nox
204 EXTTYP [$(NC=[O,S])] Nam
205 EXTTYP [$(N(~[OD1])~[OD1])] Ntr
206 EXTTYP [n] Nar
207
208 EXTTYP [#6^3] C3
209 EXTTYP [#6^2] C2
210 EXTTYP [$(C(=O)[OD1])] Cac
211 EXTTYP [c] Car
212 EXTTYP [#6^1] C1
213 EXTTYP [#6+] C+
214 EXTTYP [#6-] C-
215
216 EXTTYP [#8^3] O3
217 EXTTYP [#8^2] O2
218 EXTTYP [$(Oa)] O2
219 #The following 2 lines used for correct Sybyl atom typing
220 EXTTYP [$([OD2]C=[O,S])] O3 #ester oxygen
221 EXTTYP [$(Oa)] O3 #aromatic ether
222 EXTTYP [#8-] O-
223 EXTTYP [$([#8D1]~[#6^2]~[#8D1])] O.co2
224
225 EXTTYP [#15] P
226 EXTTYP [#15X4+] P3+
227 EXTTYP [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])] Pac
228 EXTTYP [#15;$([#15D3](~[OD1])~[OD1])] Pac
229
230 EXTTYP [#16] S3
231 EXTTYP [#16D3+,#16X3+] S3+
232 EXTTYP [#16;s,$([SD1]=*)] S2
233 EXTTYP [#16D4;$(S(=O)(=O))] So2
234 EXTTYP [#16D3;$(S(=O))] Sox
235 EXTTYP [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])] Sac
236 EXTTYP [#16;$([#16D3](~[OD1])~[OD1])] Sac
237
238 EXTTYP [#5] B2
239 EXTTYP [#5D4] B3
240
241 ######################## Add Extra Definitions Here ##########################
242
243 #INTHYB [U] 3
244 #INTHYB [W] 3
245 #INTHYB [Mo] 6 # for development
246 #INTHYB [Cr] 5 # for development
247
248 ############################# End Extra Definitions ##########################
249