Dear Colleagues,
DeleteSubstructs usually deletes the specified substructure from a
molecule, AND then caps it with a hydrogen. However, it does not work like
this when the deleted part is next to a charged atom.
*> f = Chem.MolFromSmarts('F')*
*> m = Chem.MolFromSmiles("FN(C)C")*
*> print(Chem.MolToSmiles(AllChem.DeleteSubstructs(m,f)))*
*CNC*
*> f = Chem.MolFromSmarts('F')*
*> m = Chem.MolFromSmiles("F[NH+](C)C")*
*> print(Chem.MolToSmiles(AllChem.DeleteSubstructs(m,f)))*
*C[NH+]C*
In the latter case, the result is a radical. I cannot "normalize" it even
with SanitizeMol().
I do understand that when there is a square bracket, RDKit would try to
minimize any change. I just wonder if there is any hack to get around this?
I do have a successful workaround by using ReplaceSubstructs instead of
DeleteSubstructs. However, ReplaceSubstructs has its own problems,
including my post a few minutes ago.
Thanks again!
Ling
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