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Describe the bug
Tautomer canonicalization ends up clearing/losing stereo in this case
To Reproduce
from rdkit import Chem
from rdkit.Chem.MolStandardize import rdMolStandardize
rdkit_mol = Chem.MolFromSmiles("O=C(N1)[C@H](CC(N)=O)CC1=O")
assert Chem.MolToSmiles(rdkit_mol) == "NC(=O)C[C@@H]1CC(=O)NC1=O"
enumerator = rdMolStandardize.TautomerEnumerator()
enumerator.SetMaxTautomers(10000)
enumerator.SetMaxTransforms(10000)
enumerator.SetRemoveSp3Stereo(False) # default=True
canon_mol = enumerator.Canonicalize(rdkit_mol)
assert Chem.MolToSmiles(canon_mol) == "NC(=O)Cc1cc(O)[nH]c1O" # but it should not have lost it
Expected behavior
To get "the most canonical" tautomer without losing that bond. Or have some flag to make it happen. In OE toolkits, these transformations can be disallowed.
Configuration (please complete the following information):
RDKit version: 2024.9.2
OS: Ubuntu 20.04.2
Python version (if relevant): 3.9
Are you using conda? No
If you are using conda, which channel did you install the rdkit from? n/a
If you are not using conda: how did you install the RDKit? Built from source
The text was updated successfully, but these errors were encountered:
Describe the bug
Tautomer canonicalization ends up clearing/losing stereo in this case
To Reproduce
Expected behavior
To get "the most canonical" tautomer without losing that bond. Or have some flag to make it happen. In OE toolkits, these transformations can be disallowed.
Configuration (please complete the following information):
The text was updated successfully, but these errors were encountered: