Hi Christos,
On Mon, May 12, 2014 at 12:35 PM, Christos Kannas <chriskan...@gmail.com>wrote:
>
> I've noticed the following:
> >>> m = Chem.MolFromSmarts("[O]=[O+]-[O-]")
> >>> print Chem.MolToSmarts(m)
> O=[O&+]-[O&-]
> >>> print Chem.MolToSmiles(m)
> O=OO
>
> In order to have a correct SMILES for it I do:
> >>> smiles = Chem.MolToSmarts(m).replace("&". "")
> >>> m1 = Chem.MolFromSmiles(smiles)
> >>> print Chem.MolToSmiles(m1)
> O=[O+]-[O-]
>
Just a general comment: there's really no reason to expect that you should
be able to sensibly and accurately convert a molecule with query features
(which is what you get from MolFromSmarts) into SMILES. Why are you trying
to do this?
The hack you propose above will work in many cases, but it's certainly not
robust.
-greg
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