Dear All,
I've got a strong suspicion that what I am seeing is related to the open issue
3490 (https://github.com/rdkit/rdkit/issues/3490), but as I can't seem to find
a mention of a non-spiro problem then I thought I would share.
Tested in 2020.09.4 and 2021.03.2 with the same result.
smi_list = ['CC1CCC(CC1)C(N)=O', 'CC12CCC(CC1)(C2)C(N)=O', 'CC1CC(C1)C(N)=O',
'CC12CC(C1)(CC2)C(N)=O']
for smi in smi_list:
mol = Chem.MolFromSmiles(smi)
display(show_mol(mol, size=(450, 200))) # wrapper function for new drawing
code in jupyter
print(list(Chem.FindPotentialStereo(mol)))
print(Chem.FindMolChiralCenters(mol, includeUnassigned=True,
useLegacyImplementation=False))
The 4 cases are:
* Symmetrically-disubstituted 6-membered ring
* A bridged version (using a 1-atom bridge to avoid a completely
symmetrical product)
* Symmetrically-disubstituted 4-membered ring
* A bridged version (this time using a 2-atom bridge to avoid symmetry)
And this is what I see:
[cid:[email protected]]
In the case of the bridged 4-membered ring (or bridged 5-membererd ring,
depending on your viewpoint!), FindPotentialStereo() fails to identify the two
potential stereo atoms.
If anyone can spot if this is the same issue as 3490, or something different,
then that would be appreciated!
Kind regards
James
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