trunk/forceFields/atomtyp.txt

##############################################################################
#                                                                            #
#                       Open Babel file: atomtyp.txt                         #
#                                                                            #
#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
#  Some portions Copyright (c) 2001-2003 Geoffrey R. Hutchison               #
#  Part of the Open Babel package, under the GNU General Public License (GPL)#
#                                                                            #
# SMARTS patterns for atom typing (used by typer.cpp:OBAtomTyper)            #
#                                                                            #
# INTHYB: used to assign the internal hybridization values for atoms         #
# IMPVAL: used to assign the implicit valence of an atom                     #
# EXTTYP: used to assign the external type of an atom for translation to     #
#         package specific types (i.e. Sybyl Mol2)                           #
#        (these should correspond to INT type names in types.txt too.)       #
#                                                                            #
# The LAST PATTERN MATCHED is used to assign values with the corresponding   #
# INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed #
# in the EXTRA DEFINITIONS section (to separate from original patterns.)     #
#                                                                            #
##############################################################################

INTHYB  [C]                             3       #sp3 carbon
INTHYB  [c,$(C=*)]                      2       #sp2 carbon
INTHYB  [$([#6]([#8D1])[#8D1])]         2       #sp2 carbon
INTHYB  [$(C#*),$(C(=*)=*)]             1       #sp  carbon
INTHYB  [N]                             3       #sp3 nitrogen
INTHYB  [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2       #sp2 nitrogen
INTHYB  [ND1,ND2,ND3]a                  2       #sp2 nitrogen
INTHYB  [$(N#*),$([ND2](=*)=*)]         1       #sp  nitrogen
INTHYB  [O]                             3       #sp3 oxygen
INTHYB  [o,$(O=*),$(O[#6,#7,#8]=,:*)]   2       #sp2 oxygen
INTHYB  [$([#8D1][#6][#8D1])]           2       #sp2 oxygen
INTHYB  [$(O#*)]                        1       #sp  oxygen
INTHYB  [D4]                            3       #any 4 valent atom

INTHYB  [P]                             3       #sp3 phosphorus
INTHYB  [#15;$([PD1]=*)]                2       #sp2 phosphorus
INTHYB  [S]                             3       #sp3 sulfur
INTHYB  [#16;s,$([SD1]=*)]              2       #sp2 sulfur
INTHYB  [B]                             2       #sp2 boron
INTHYB  [BD4]                           3       #sp3 boron
#
#IMPLICIT VALENCE RULES
#
IMPVAL  [#6^3]                  4
IMPVAL  [#6^2]                  3
IMPVAL  [#6^1]                  2
IMPVAL  [#6^3-]                 3
IMPVAL  [#6^2-]                 2
IMPVAL  [#6^1-]                 1 #CM for isocyanides
IMPVAL  [c+]                    2

IMPVAL  [#8^3]                          2
IMPVAL  [#8^2]                          2
IMPVAL  [$([#8]=*)]                     1
IMPVAL  [#8-]                           1
IMPVAL  [$([#8D1]~[#7D3]~[#8D1])]       1
IMPVAL  [$([#8D1]~[#6]~[#8D1])]         1
# This is from JOELib -- add H to acidic oxygens
IMPVAL  [$([#8D1]-[#6]=[#8D1])]         2
# But don't add an H for pH-corrected formal-charge = -1 oxygens
IMPVAL  [$([#8D1-]-[#6]=[#8D1])]        1

IMPVAL  [N^3]                   3
IMPVAL  [N^3+]                  4
IMPVAL  [N^2]                   3
IMPVAL  [N^2-,N^3-]             2
IMPVAL  [ND1^1]                 1
IMPVAL  [ND2^1]                 2
IMPVAL  [$(N([OD1])*)]          3
IMPVAL  [$(NC=O)]               3
IMPVAL  [$(N(~[OD1])~[OD1])]    3
IMPVAL  [$([Nr0]C=[Nr0])]       3
IMPVAL  [$(N=*)]                2
#IMPVAL [$([Nr0]=C[Nr0])]       3 
IMPVAL  [$([Nr0]=C[Nr0])]       2
IMPVAL  [$([#7D1-]=*)]          1
IMPVAL  [n]                     2
IMPVAL  [n-]                    2
IMPVAL  [n+]                    3

IMPVAL  [#9D0]            1

IMPVAL  [#15D4]                 4
IMPVAL  [#15D3]                 3
IMPVAL  [#15D2]                 3
IMPVAL  [#15D1^3]               3
IMPVAL  [#15D1^2]               3
IMPVAL  [#15D0]     3
IMPVAL  [$([#15]=[#6])]         2
IMPVAL  [pD2]                   2

IMPVAL  [#16D4]                 4
IMPVAL  [#16D3]                 3
IMPVAL  [#16D2]                 2
IMPVAL  [$([#16D1]-*)]          2
IMPVAL  [#16D1^2]               1
IMPVAL  [s]                     2
IMPVAL  [#16D1-]                1

IMPVAL  [#16D0]           2
IMPVAL  [#17D0]           1
IMPVAL  [#35D0]           1
IMPVAL  [#53D0]           1

IMPVAL  [#5]                    3
IMPVAL  [as]                    3
#
#EXTERNAL TYPE RULES
#
EXTTYP  [#7^3]                                  N3
EXTTYP  [#7X4+]                                 N3+
EXTTYP  [#7^2]                                  Npl
EXTTYP  [#7^1]                                  N1
EXTTYP  [$(N=*)]                                N2
EXTTYP  [$([Nr0]C(=[Nr0])[Nr0])]                Ng+
EXTTYP  [$([Nr0]=C([Nr0])[Nr0])]                Ng+
EXTTYP  [$([ND1]=C[ND1])]                       Ng+
EXTTYP  [$([ND1]C=[ND1])]                       Ng+
EXTTYP  [$(N(O)*)]                              Nox
EXTTYP  [$(NC=[O,S])]                           Nam
EXTTYP  [$(N(~[OD1])~[OD1])]                    Ntr
EXTTYP  [n]                                     Nar

EXTTYP  [#6^3]                                  C3
EXTTYP  [#6^2]                                  C2
EXTTYP  [$(C(=O)[OD1])]                         Cac
EXTTYP  [c]                                     Car
EXTTYP  [#6^1]                                  C1
EXTTYP  [#6+]                                   C+
EXTTYP  [#6-]                                   C-

EXTTYP  [#8^3]                                  O3
EXTTYP  [#8^2]                                  O2
EXTTYP  [$(Oa)]                                 O2
#The following 2 lines used for correct Sybyl atom typing
EXTTYP  [$([OD2]C=[O,S])]                       O3      #ester oxygen
EXTTYP  [$(Oa)]                                 O3      #aromatic ether
EXTTYP  [#8-]                                   O-
EXTTYP  [$([#8D1]~[#6]~[#8D1])]                 O.co2  

EXTTYP  [#15]                                   P
EXTTYP  [#15X4+]                                P3+
EXTTYP  [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])]  Pac
EXTTYP  [#15;$([#15D3](~[OD1])~[OD1])]          Pac

EXTTYP  [#16]                                   S3
EXTTYP  [#16D3+,#16X3+]                         S3+
EXTTYP  [#16;s,$([SD1]=*)]                      S2
EXTTYP  [#16D4;$(S(=O)(=O))]                    So2
EXTTYP  [#16D3;$(S(=O))]                        Sox
EXTTYP  [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])]  Sac
EXTTYP  [#16;$([#16D3](~[OD1])~[OD1])]          Sac

EXTTYP  [#5]                                    B2
EXTTYP  [#5D4]                                  B3

######################## Add Extra Definitions Here ##########################


############################# End Extra Definitions ##########################

Revision:	760
Committed:	Mon Nov 21 14:59:34 2005 UTC (19 years, 5 months ago) by tim
Content type:	text/plain
File size:	5154 byte(s)
Log Message:	adding openbabel data files
#	User	Rev	Content
1	tim	760	##############################################################################
2			# #
3			# Open Babel file: atomtyp.txt #
4			# #
5			# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
6			# Some portions Copyright (c) 2001-2003 Geoffrey R. Hutchison #
7			# Part of the Open Babel package, under the GNU General Public License (GPL)#
8			# #
9			# SMARTS patterns for atom typing (used by typer.cpp:OBAtomTyper) #
10			# #
11			# INTHYB: used to assign the internal hybridization values for atoms #
12			# IMPVAL: used to assign the implicit valence of an atom #
13			# EXTTYP: used to assign the external type of an atom for translation to #
14			# package specific types (i.e. Sybyl Mol2) #
15			# (these should correspond to INT type names in types.txt too.) #
16			# #
17			# The LAST PATTERN MATCHED is used to assign values with the corresponding #
18			# INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed #
19			# in the EXTRA DEFINITIONS section (to separate from original patterns.) #
20			# #
21			##############################################################################
22
23			INTHYB [C] 3 #sp3 carbon
24			INTHYB [c,$(C=*)] 2 #sp2 carbon
25			INTHYB [$([#6]([#8D1])[#8D1])] 2 #sp2 carbon
26			INTHYB [$(C#),$(C(=)=*)] 1 #sp carbon
27			INTHYB [N] 3 #sp3 nitrogen
28			INTHYB [n,$(N=),$(N[#6,#7,#8]=,:,#)] 2 #sp2 nitrogen
29			INTHYB [ND1,ND2,ND3]a 2 #sp2 nitrogen
30			INTHYB [$(N#),$([ND2](=)=*)] 1 #sp nitrogen
31			INTHYB [O] 3 #sp3 oxygen
32			INTHYB [o,$(O=),$(O[#6,#7,#8]=,:)] 2 #sp2 oxygen
33			INTHYB [$([#8D1][#6][#8D1])] 2 #sp2 oxygen
34			INTHYB [$(O#*)] 1 #sp oxygen
35			INTHYB [D4] 3 #any 4 valent atom
36
37			INTHYB [P] 3 #sp3 phosphorus
38			INTHYB [#15;$([PD1]=*)] 2 #sp2 phosphorus
39			INTHYB [S] 3 #sp3 sulfur
40			INTHYB [#16;s,$([SD1]=*)] 2 #sp2 sulfur
41			INTHYB [B] 2 #sp2 boron
42			INTHYB [BD4] 3 #sp3 boron
43			#
44			#IMPLICIT VALENCE RULES
45			#
46			IMPVAL [#6^3] 4
47			IMPVAL [#6^2] 3
48			IMPVAL [#6^1] 2
49			IMPVAL [#6^3-] 3
50			IMPVAL [#6^2-] 2
51			IMPVAL [#6^1-] 1 #CM for isocyanides
52			IMPVAL [c+] 2
53
54			IMPVAL [#8^3] 2
55			IMPVAL [#8^2] 2
56			IMPVAL [$([#8]=*)] 1
57			IMPVAL [#8-] 1
58			IMPVAL [$([#8D1]~[#7D3]~[#8D1])] 1
59			IMPVAL [$([#8D1]~[#6]~[#8D1])] 1
60			# This is from JOELib -- add H to acidic oxygens
61			IMPVAL [$([#8D1]-[#6]=[#8D1])] 2
62			# But don't add an H for pH-corrected formal-charge = -1 oxygens
63			IMPVAL [$([#8D1-]-[#6]=[#8D1])] 1
64
65			IMPVAL [N^3] 3
66			IMPVAL [N^3+] 4
67			IMPVAL [N^2] 3
68			IMPVAL [N^2-,N^3-] 2
69			IMPVAL [ND1^1] 1
70			IMPVAL [ND2^1] 2
71			IMPVAL [$(N([OD1])*)] 3
72			IMPVAL [$(NC=O)] 3
73			IMPVAL [$(N(~[OD1])~[OD1])] 3
74			IMPVAL [$([Nr0]C=[Nr0])] 3
75			IMPVAL [$(N=*)] 2
76			#IMPVAL [$([Nr0]=C[Nr0])] 3
77			IMPVAL [$([Nr0]=C[Nr0])] 2
78			IMPVAL [$([#7D1-]=*)] 1
79			IMPVAL [n] 2
80			IMPVAL [n-] 2
81			IMPVAL [n+] 3
82
83			IMPVAL [#9D0] 1
84
85			IMPVAL [#15D4] 4
86			IMPVAL [#15D3] 3
87			IMPVAL [#15D2] 3
88			IMPVAL [#15D1^3] 3
89			IMPVAL [#15D1^2] 3
90			IMPVAL [#15D0] 3
91			IMPVAL [$([#15]=[#6])] 2
92			IMPVAL [pD2] 2
93
94			IMPVAL [#16D4] 4
95			IMPVAL [#16D3] 3
96			IMPVAL [#16D2] 2
97			IMPVAL [$([#16D1]-*)] 2
98			IMPVAL [#16D1^2] 1
99			IMPVAL [s] 2
100			IMPVAL [#16D1-] 1
101
102			IMPVAL [#16D0] 2
103			IMPVAL [#17D0] 1
104			IMPVAL [#35D0] 1
105			IMPVAL [#53D0] 1
106
107			IMPVAL [#5] 3
108			IMPVAL [as] 3
109			#
110			#EXTERNAL TYPE RULES
111			#
112			EXTTYP [#7^3] N3
113			EXTTYP [#7X4+] N3+
114			EXTTYP [#7^2] Npl
115			EXTTYP [#7^1] N1
116			EXTTYP [$(N=*)] N2
117			EXTTYP [$([Nr0]C(=[Nr0])[Nr0])] Ng+
118			EXTTYP [$([Nr0]=C([Nr0])[Nr0])] Ng+
119			EXTTYP [$([ND1]=C[ND1])] Ng+
120			EXTTYP [$([ND1]C=[ND1])] Ng+
121			EXTTYP [$(N(O)*)] Nox
122			EXTTYP [$(NC=[O,S])] Nam
123			EXTTYP [$(N(~[OD1])~[OD1])] Ntr
124			EXTTYP [n] Nar
125
126			EXTTYP [#6^3] C3
127			EXTTYP [#6^2] C2
128			EXTTYP [$(C(=O)[OD1])] Cac
129			EXTTYP [c] Car
130			EXTTYP [#6^1] C1
131			EXTTYP [#6+] C+
132			EXTTYP [#6-] C-
133
134			EXTTYP [#8^3] O3
135			EXTTYP [#8^2] O2
136			EXTTYP [$(Oa)] O2
137			#The following 2 lines used for correct Sybyl atom typing
138			EXTTYP [$([OD2]C=[O,S])] O3 #ester oxygen
139			EXTTYP [$(Oa)] O3 #aromatic ether
140			EXTTYP [#8-] O-
141			EXTTYP [$([#8D1]~[#6]~[#8D1])] O.co2
142
143			EXTTYP [#15] P
144			EXTTYP [#15X4+] P3+
145			EXTTYP [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])] Pac
146			EXTTYP [#15;$([#15D3](~[OD1])~[OD1])] Pac
147
148			EXTTYP [#16] S3
149			EXTTYP [#16D3+,#16X3+] S3+
150			EXTTYP [#16;s,$([SD1]=*)] S2
151			EXTTYP [#16D4;$(S(=O)(=O))] So2
152			EXTTYP [#16D3;$(S(=O))] Sox
153			EXTTYP [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])] Sac
154			EXTTYP [#16;$([#16D3](~[OD1])~[OD1])] Sac
155
156			EXTTYP [#5] B2
157			EXTTYP [#5D4] B3
158
159			######################## Add Extra Definitions Here ##########################
160
161
162			############################# End Extra Definitions ##########################
163