Hi
There appears to be an issue with the DeleteSubstructs method when deleting
groups from an aromatic N. The H-count is not reset properly leading to a
kekulise error.
The workaround is to Kekulise the molecule first. Of course, this would require
more extensive SMARTS based substructures to use the Kekule form.
Here is an example
import rdkit
from rdkit import Chem
print(rdkit.__version__)
smiles = 'c1cccn1C'
mol = Chem.MolFromSmiles(smiles)
Chem.Kekulize(mol,clearAromaticFlags=True)
sub = Chem.MolFromSmarts('[CH3]')
newmol = Chem.rdmolops.DeleteSubstructs(mol,sub)
Chem.SanitizeMol(newmol)
print("1: {}".format(Chem.MolToSmiles(newmol)))
mol = Chem.MolFromSmiles(smiles)
sub = Chem.MolFromSmarts('[CH3]')
newmol = Chem.rdmolops.DeleteSubstructs(mol,sub)
print("2: {}".format(Chem.MolToSmiles(newmol)))
Chem.SanitizeMol(newmol)
print("3: {}".format(Chem.MolToSmiles(newmol)))
With output
2021.03.2
1: c1cc[nH]c1
2: c1ccnc1
[09:50:41] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
Traceback (most recent call last):
File "test.py", line 21, in <module>
Chem.SanitizeMol(newmol)
rdkit.Chem.rdchem.KekulizeException: Can't kekulize mol. Unkekulized atoms: 0
1 2 3 4
Thanks
Stephen
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