Re: [Rdkit-discuss] problem with MolToSmiles with 6-valenced sulfur

[Christian M. <chr...@un...>]

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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