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The normalization pattern for pyridine N-oxide is not specific enough #4281

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ptosco opened this issue Jun 24, 2021 · 0 comments
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The normalization pattern for pyridine N-oxide is not specific enough #4281

ptosco opened this issue Jun 24, 2021 · 0 comments
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ptosco commented Jun 24, 2021

Reported by JP Ebejer:

from rdkit import Chem
from rdkit.Chem.MolStandardize import rdMolStandardize

m = Chem.MolFromSmiles('Cn1c(=O)c2nc[nH][n+](=O)c2n(C)c1=O')
m

image

rdMolStandardize.Cleanup(m)
RDKit ERROR: [19:20:42] Can't kekulize mol.  Unkekulized atoms: 0 3 4 6 7

The molecule is not actually a pyridine N-oxide, rather the oxy tautomer of a N-hydroxypyridinium ion, but it hits the pyridine N-oxide normalization pattern because the latter is not sufficiently specific.

@ptosco ptosco added the bug label Jun 24, 2021
@ptosco ptosco self-assigned this Jun 24, 2021
ptosco pushed a commit to ptosco/rdkit that referenced this issue Jun 24, 2021
ptosco pushed a commit to ptosco/rdkit that referenced this issue Jun 24, 2021
@greglandrum greglandrum added this to the 2021_03_4 milestone Jul 1, 2021
greglandrum pushed a commit that referenced this issue Jul 9, 2021
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
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