Hi Ling,
On 2023-11-17 18:40, Ling Chan wrote:
When I run MolToSmiles on a molecule with a 6-valenced sulfur, it
produced a problematic smiles. Seems it's a bug?
[...]
Running "Chem.MolToSmiles(Chem.MolFromMolFile("mol.sdf"))" on the
following sdf, I got
'C[S@OH16](F)(F)(F)(F)F'
The SMILES looks correct to me. Have a look at the SMILES documentation
[0] regarding the Chiral Specification of octahedral structures (3.3.4).
The OH16 does in fact *not* represent a Hydroxy group or something of
the sort, but is a closer description of the octahedral geometry.
Best,
Chris
[0] https://daylight.com/dayhtml/doc/theory/theory.smiles.html
--
Christian Meyenburg
ZBH - Zentrum für Bioinformatik Hamburg
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e-Mail: christian.meyenb...@uni-hamburg.de
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