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[Open Babel] obgrep error
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From: remy d1 <re...@gm...> - 2011-04-21 14:00:13
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Hi,
I have a problem with obgrep search method.
obgrep do not find a triazole in this molecule :
-ISIS- 04211115172D
35 38 0 0 0 0 0 0 0 0999 V2000
2.5875 -0.0042 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
2.0167 0.4208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2417 1.0958 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.9500 1.0958 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.1625 0.4208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3042 0.4208 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
0.3625 -0.3542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5167 -0.7042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1625 1.0083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8667 0.9708 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.4458 -1.1667 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.9917 -1.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3333 -0.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0667 -0.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6917 -0.9792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7667 -1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1625 1.6333 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
0.1917 -1.4875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2375 -2.4417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1833 0.3833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.6792 -1.0917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9292 -2.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8208 1.3708 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.1542 -1.6292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1792 -2.3167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.7792 0.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3542 -2.8667 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.3917 -1.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3708 2.3083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5417 1.7208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3292 -2.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3667 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0542 -2.8292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5375 -1.9375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0042 -2.4042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 2 2 0 0 0 0
4 5 2 0 0 0 0
5 1 1 0 0 0 0
6 2 1 0 0 0 0
7 14 1 0 0 0 0
8 1 1 0 0 0 0
9 10 1 0 0 0 0
10 6 1 0 0 0 0
11 13 1 0 0 0 0
12 8 1 0 0 0 0
13 7 2 0 0 0 0
6 14 1 1 0 0 0
15 7 1 0 0 0 0
16 12 2 0 0 0 0
17 9 1 0 0 0 0
18 15 1 0 0 0 0
19 16 1 0 0 0 0
20 9 2 0 0 0 0
21 12 1 0 0 0 0
22 24 1 0 0 0 0
23 17 1 0 0 0 0
24 21 2 0 0 0 0
25 16 1 0 0 0 0
26 5 1 0 0 0 0
27 22 1 0 0 0 0
28 15 2 0 0 0 0
29 17 1 0 0 0 0
30 17 1 0 0 0 0
31 18 2 0 0 0 0
32 25 1 0 0 0 0
33 27 1 0 0 0 0
34 28 1 0 0 0 0
35 34 2 0 0 0 0
4 3 1 0 0 0 0
19 22 2 0 0 0 0
11 18 1 0 0 0 0
31 35 1 0 0 0 0
M END
$$$$
obgrep -c 'Cc1nnc(C)[nH]1' sdf-1-3500-match-triazole-result1.sdf
0
If you import it in a drawing chemical software you will see a reverse
triazole.
Moreover, on debian linux, I have seen that openbabel 2.2.3 includes
libopenbabel.so.3 but obgrep needs libopenbabel.so.4
Even if I install it manually, it does not change anything. However, the
install warn me about my python bindings for openbabel with the last version
of openbabel, so I downgrade openbabel to openbabel 2.2.3 for
python-openbabel package compatibility (but I keep the libopenbabel.so.4
library for obgrep in my /usr/lib directory).
Is it a bug ?
I need it to work for "mychem" software and my database of molecules.
Thanks.
Regards.
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