Hi Michał,
Have you tried using AdjustQueryProperties(). I think Greg mentioned it in
his presentation at UGM
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#AdjustQueryProperties
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
[email protected]
2016-11-01 19:20 GMT+01:00 Michał Nowotka <[email protected]>:
> 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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