Hi,
I have this molfile (CHEMBL265667):
11280714432D 1 1.00000 0.00000 0
25 27 0 0 0 999 V2000
3.8042 -1.6000 0.0000 C 0 0 0 0 0 0 0 0 0
4.3167 -1.9000 0.0000 N 0 0 3 0 0 0 0 0 0
3.8042 -1.0000 0.0000 N 0 0 0 0 0 0 0 0 0
4.8417 -1.6000 0.0000 N 0 0 0 0 0 0 0 0 0
4.3167 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0
4.3167 -3.6917 0.0000 C 0 0 0 0 0 0 0 0 0
4.8417 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0
4.3167 -0.7000 0.0000 C 0 0 0 0 0 0 0 0 0
3.7917 -3.3917 0.0000 C 0 0 0 0 0 0 0 0 0
4.8375 -3.3917 0.0000 C 0 0 0 0 0 0 0 0 0
3.8000 -2.7917 0.0000 C 0 0 0 0 0 0 0 0 0
4.8375 -2.7917 0.0000 C 0 0 0 0 0 0 0 0 0
4.3167 -4.2917 0.0000 C 0 0 3 0 0 0 0 0 0
3.2875 -1.8917 0.0000 O 0 0 0 0 0 0 0 0 0
4.8375 -4.5917 0.0000 C 0 0 0 0 0 0 0 0 0
4.3167 -0.0917 0.0000 O 0 0 0 0 0 0 0 0 0
4.8292 -5.1917 0.0000 C 0 0 0 0 0 0 0 0 0
5.3500 -4.2917 0.0000 C 0 0 0 0 0 0 0 0 0
5.8667 -5.1917 0.0000 C 0 0 0 0 0 0 0 0 0
3.7917 -4.5917 0.0000 O 0 0 0 0 0 0 0 0 0
5.8667 -4.5917 0.0000 C 0 0 0 0 0 0 0 0 0
5.3542 -5.4917 0.0000 C 0 0 0 0 0 0 0 0 0
6.3917 -5.4917 0.0000 Cl 0 0 0 0 0 0 0 0 0
3.2750 -3.6917 0.0000 C 0 0 0 0 0 0 0 0 0
5.3542 -3.6917 0.0000 C 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0
3 1 1 0 0 0
4 2 1 0 0 0
5 2 1 0 0 0
6 10 1 0 0 0
7 8 1 0 0 0
8 3 1 0 0 0
9 11 1 0 0 0
10 12 2 0 0 0
11 5 2 0 0 0
12 5 1 0 0 0
13 6 1 0 0 0
14 1 2 0 0 0
15 13 1 0 0 0
16 8 2 0 0 0
17 15 2 0 0 0
18 15 1 0 0 0
19 21 1 0 0 0
20 13 1 0 0 0
21 18 2 0 0 0
22 17 1 0 0 0
23 19 1 0 0 0
24 9 1 0 0 0
25 10 1 0 0 0
4 7 2 0 0 0
9 6 2 0 0 0
22 19 2 0 0 0
M END
and this smarts: [OH1]-C(-c1ccccc1)c2ccccc2
I'm using this code to find a substructure:
mol = Chem.MolFromMolBlock(str(molstring), sanitize=False)
mol.UpdatePropertyCache(strict=False)
patt = Chem.MolFromSmarts(str(smarts))
Chem.GetSSSR(patt)
Chem.GetSSSR(mol)
match = mol.HasSubstructMatch(patt)
and the `match` is empty.
But with indigo code:
mol = indigoObj.loadMolecule(str(molstring))
patt = indigoObj.loadSmarts(str(smarts))
match = indigoObj.substructureMatcher(mol).match(patt)
match is valid and I can render this to image:
I'm I missing some flag or doing something wrong?
--
Michal
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