trunk/forceFields/bondtyp.txt

##############################################################################
#                                                                            #
#    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)
#0  1    2       3   4   5  6  7     8      9  10  11  12 13   14     15 16   17  18 19  20       21 22  23
*1[#6]([#7D3]2)[#6][#6][#6]2*[#6]([#7D3]3)[#6][#6][#6]3*[#6]([#7D3]4)[#6][#6][#6]4*[#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
*1[#6]([#7D3]2)[#6][#6][#6]2*[#6]([#7]3)[#6][#6][#6]3*[#6]([#7D3]4)[#6][#6][#6]4*[#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
*1[#6]([#7]2)[#6][#6][#6]2*[#6]([#7]3)[#6][#6][#6]3*[#6]([#7]4)[#6][#6][#6]4*[#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

# Azide
[#7D2][#7D2^1][#7D1]            0 1 2 1 2 2
# Nitro
[#8D1][#7D3^2]([#8D1])*         0 1 2 1 2 1 1 3 1
# Sulphone
[#16D4]([#8D1])([#8D1])(*)(*)   0 1 2 0 2 2 0 3 1 0 4 1
# Phosphone
[#15D4]([#8D1])(*)(*)(*)        0 1 2 0 2 1 0 3 1 0 4 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
# Amide C(=O)N
[#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
[#6D3^2]([#16D1])([#7])*                0 1 2 0 2 1 0 3 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

# 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
# sulfoxides
# heme / porphyrin
# phthalocyanine
Revision:	760
Committed:	Mon Nov 21 14:59:34 2005 UTC (20 years, 3 months ago) by tim
Content type:	text/plain
File size:	4308 byte(s)
Log Message:	adding openbabel data files
#	User	Rev	Content
1	tim	760	##############################################################################
2			# #
3			# Open Babel file: bondtyp.txt #
4			# #
5			# Copyright (c) 2002-2005 by Geoffrey R Hutchison #
6			# Part of the Open Babel package, under the GNU General Public License (GPL)#
7			# #
8			# Used by bondtyper.cpp::OBBondTyper (and thus OBMol::PerceiveBondOrders() #
9			# #
10			# List of functional groups with double, triple (etc.) bond orders #
11			# Pattern Atom1 Atom2 Bond Order (repeat as needed) #
12			# * = Any atom (for setting non-multiple bonds) #
13			# #
14			# NOTE: These are applied in order, first to last. #
15			# So it's generally better to have a long (specifc) SMARTS first. #
16			# (all bonds must be single bonds to match)
17			# #
18			##############################################################################
19
20			# Porphyrin / phthalocyanine (3 patterns for three separate bonding motifs)
21			# this one has explicit bonds to all four nitrogens (e.g., metal bond or hydrogens)
22			#0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
23			1[#6]([#7D3]2)[#6][#6][#6]2[#6]([#7D3]3)[#6][#6][#6]3[#6]([#7D3]4)[#6][#6][#6]4[#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
24
25			# this one has explicit bonds to two nitrogens (12 and 14)
26			#0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
27			1[#6]([#7D3]2)[#6][#6][#6]2[#6]([#7]3)[#6][#6][#6]3[#6]([#7D3]4)[#6][#6][#6]4[#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
28
29			# and this one doesn't have any explicit bonds to the nitrogens
30			#0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
31			1[#6]([#7]2)[#6][#6][#6]2[#6]([#7]3)[#6][#6][#6]3[#6]([#7]4)[#6][#6][#6]4[#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
32
33			# Azide
34			[#7D2][#7D2^1][#7D1] 0 1 2 1 2 2
35			# Nitro
36			[#8D1][#7D3^2]([#8D1])* 0 1 2 1 2 1 1 3 1
37			# Sulphone
38			[#16D4]([#8D1])([#8D1])()() 0 1 2 0 2 2 0 3 1 0 4 1
39			# Phosphone
40			[#15D4]([#8D1])()()(*) 0 1 2 0 2 1 0 3 1 0 4 1
41
42			# Carboxylic Acid, ester, etc.
43			[#6D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1
44			# Carbon dioxide
45			[#8D1][#6D2^1][#8D1] 0 1 2 1 2 2
46			# Amide C(=O)N
47			[#6D3^2]([#8D1])([#7])* 0 1 2 0 2 1 0 3 1
48			# Seleninic acid Se(=O)OH
49			[#34D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1
50			# Thioacid / Thioester C(=O)S
51			[#6D3^2]([#8D1])([#16])* 0 1 2 0 2 1 0 3 1
52			# dithioacid / dithioester C(=S)S
53			[#6D3^2]([#16D1])([#16])* 0 1 2 0 2 1 0 3 1
54			# thioamide C(=S)N
55			[#6D3^2]([#16D1])([#7])* 0 1 2 0 2 1 0 3 1
56
57			# allene C=C=C
58			# (this is problematic -- need to make sure the center carbon is sp)
59			[#6^2][#6D2^1][#6^2] 0 1 2 1 2 2
60
61			# guanidinium and amidine -C(=NH)NH2 without hydrogens
62			[#6D3^2;!R]([#7D1H0;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1
63			# and also with hydrogens
64			# (this can normally be figured out, but is needed to avoid matching the next SMARTS)
65			[#6D3^2;!R]([#7D2H1;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1
66			# and also with more hydrogens than normal (protonated)
67			[#6D3^2;!R]([#7D3H2;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1
68
69			# Schiff base, protonated
70			[#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
71
72			### other potential functional groups that may (or may not) be useful to add
73			# imidines ( N=C/N\C=N
74			# sulfoxides
75			# heme / porphyrin
76			# phthalocyanine