That does seem like a bug. You can also see it without involving
DeleteSubstructs, by starting from different SMILES representations of the
same molecule:
>>> m1 = Chem.MolFromSmiles('FC12C31C32F')
>>> m2 = Chem.MolFromSmiles('C12C31C32')
>>> m3 = Chem.MolFromSmiles('C1CC2C3C(C1)C23')
Hi Tim,
You might also consider using chemfp, which has this sort of functionality
available through its toolkit wrapper API:
from chemfp import rdkit_toolkit as T
import itertools
with T.read_ids_and_molecules("chembl_28.sdf.gz") as reader:
loc = reader.location
for id, mol in
I am needing to access the text of each record of a SDF, as well as
creating a mol instance.
I was successfully doing this using SDMolSupplier.GetItemText().
Then I needed to switch to handling gzipped SD files, and SDMolSupplier can
only take a file name in its constructor.
ForwardSDMolSupplier
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