Hi,
I just ran into a small gotcha and thought I'd share it. I have a molecule
with a fragment of 6 carbons, 5 of which form a ring, and I am deleting
fragments that match "CCCCCC". I thought that if I were working in SMILES
the ring fragment would be spared, but not if it was a SMARTS. However as
the following code shows it gets deleted either way.
>>> import rdkit
>>> from rdkit import Chem
>>> query = Chem.MolFromSmiles('C.CC1CCCC1')
>>> remove_as_smiles = Chem.MolFromSmiles('CCCCCC')
>>> remove_as_smarts = Chem.MolFromSmarts('CCCCCC')
>>> print Chem.MolToSmiles(Chem.DeleteSubstructs(query, remove_as_smiles,
onlyFrags=True))
C
>>> print Chem.MolToSmiles(Chem.DeleteSubstructs(query, remove_as_smarts,
onlyFrags=True))
C
So now I know to use "[C!r][C!r][C!r][C!r][C!r][C!r]" explicitly if that's
what I mean. Hope this saves someone else from stumbling into my mistakes.
Yours,
Toby Wright
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