Hi,
If any atoms specified in a reaction happen to form a ring, RDKit will break it
open:
>>> rxn =
AllChem.ReactionFromSmarts('[C:1][C:2][O:3][C:4][C:5]>>[C:1][C:2][C:3][C:4][C:5]')
>>> mol = Chem.MolFromSmiles('C1CCOC1')
>>> prod = rxn.RunReactants((mol,))[0][0]
>>> Chem.MolToSmiles(prod)
'CCCCC'
Is this a bug, or "expected behaviour"?
It is possible to avoid this by specifying the ring manually in the reactants
and the products:
>>> rxn =
>>> AllChem.ReactionFromSmarts('[C:1]1[C:2][O:3][C:4][C:5]1>>[C:1]1[C:2][C:3][C:4][C:5]1')
But then this won't work if there is no ring, i.e. for CCOCC.
Is it possible to ensure that ring bonds are not broken if they are not
explicitly referenced in the reactants SMARTS?
Matt
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