Hi, Thanks for your reply. I'm running version 2019.03.1.
Am 30.04.2019 05:24 schrieb Greg Landrum:
Hi, I’m out-of-office this week and don’t have access to a computer, but I suspect that that is a bug. The drawing code should not generate errors like that. Which version of the rdkit are you running? -greg On Mon, 29 Apr 2019 at 15:55, Jasmin <[email protected]> wrote: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 [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss [1]Links: ------ [1] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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