Hi Thomas,
OB does not sanitize molecules when reading from SMILES (or any other
format). By default it writes aromatic SMILES though, but it sounds like
you want Kekule SMILES - see the obabel -Hsmi for the list of options. In
this case you want 'k':
$ obabel -:"O=C1C=COC(=C1(O))C" -xk -osmi
O=C1C=COC(=C1O)C
In Python, this is something like mol.write(opt={"k:" True}).
Neither does it add Hs. A SMILES string exactly specifies the number of Hs
on each atom; this is preserved on reading/writing. If you could provide
information on a specific case, we could explain what's happening more
clearly.
Regards
Noel
On Fri, 17 Feb 2023 at 16:18, Thomas <[email protected]> wrote:
> Is there an option to avoid sanitization of a molecule when reading from
> SMILES?
> For example I'd like the SMILES to remain unchanged if I read and write it:
>
> mol = pybel.readstring('smi', 'O=C1C=COC(=C1(O))C')
> mol.write()
> O=c1ccoc(c1O)C
>
> Beside kekulization issues, other unwanted sanitizations are the addition
> of Hs if I generate the molecule from SMILES fragments (partial SMILES)
>
> Thank you
> Thomas
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