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comparison CADDSuite-1.0/data/OpenBabel/bondtyp.txt @ 14:55c32b55c2c2

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Uploaded Version 1.1
author marcel
date Thu, 12 Jan 2012 11:00:43 -0500
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13:cce3667779c2 14:55c32b55c2c2
1 ##############################################################################
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 2 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