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Describe the bug
There is a KekulizationException when canonicalizing tautomers for some types of molecules. This seems to be new since the sprint release. I've seen it in a couple of places, but the commonality seems to be with non-aromatic rings with two nitrogens and one external methyl group.
Here are a couple of examples:
To Reproduce
from rdkit import Chem
from rdkit.Chem.MolStandardize import rdMolStandardize
for smi in ['NC1=NC=NC(C)=C1',
'CC1N=CN(C)C(=O)C=1',
'CC1=CC=CC(=O)N1C']:
mol = Chem.MolFromSmiles(smi)
rdMolStandardize.TautomerEnumerator().Canonicalize(mol)
Expected behavior
some sort of answer :)
Screenshots
If applicable, add screenshots to help explain your problem.
Configuration (please complete the following information):
RDKit version: 2022.09 release. Also tested with a build at adfdeca (head of origin/master on November 20)
OS: Darwin, Linux and Windows
Using an internal Schrödinger build, also built locally
The text was updated successfully, but these errors were encountered:
Would it make sense to catch kekulization errors and continue at this point? I think it would be best if all transformations were guaranteed to always produce valid structures, but that seems like a hard guarantee to make!
Describe the bug
There is a KekulizationException when canonicalizing tautomers for some types of molecules. This seems to be new since the sprint release. I've seen it in a couple of places, but the commonality seems to be with non-aromatic rings with two nitrogens and one external methyl group.
Here are a couple of examples:
To Reproduce
Expected behavior
some sort of answer :)
Screenshots
If applicable, add screenshots to help explain your problem.
Configuration (please complete the following information):
The text was updated successfully, but these errors were encountered: