Hello!
When running the following Code:
testmol = Chem.MolFromSmiles('c1cccn2cccc12')
info = {}
fp = AllChem.GetMorganFingerprintAsBitVect(testmol, 2, nBits=1024,
bitInfo=info)
drawing = []
for key in info:
drawing.append((testmol, key, {key: info[key]}))
Draw.DrawMorganBits(drawing)
I get the following error:
ValueError: Sanitization error: Can't kekulize mol. Unkekulized atoms:
0 1 2 6 7
I can track the problem down to bit 470: ((3, 2), (5, 2))
There seems to be a problem with this somewhat unusual aromatic
structure. The problem also appears with other similar structures like
1,2,4-Triazolo[1,5-a]pyrimidine and Pyroxsulam.
Any ideas how to fix this? Can I somehow sanitize the molecule before
creating the fingerprint?
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
