On Wed, Dec 13, 2017 at 10:39 AM, Marina Garcia de Lomana <
m.garciadelom...@gmail.com> wrote:
> Thanks for your answer Paolo!
> But I would need to read in the stereochemistry information from the SD
> file (7th column in the atom block) and not calculate the chirality from
> the coordinates, since this way the information about racemates would get
> lost.
>
> Is there a way to do that?
>
There is not. In this case the RDKit follows the recommendation of the
documentation for Mol files and ignores that field when reading structures.
A standard way to indicate that you don't know the stereochemistry of a
center despite there being 3D coordinates is to make one of the bonds from
it a "squiggly" bond (i.e. bond type 4). The RDKit will recognize this and
avoid assigning stereochemistry there.
A request: please do not post questions both to the mailing list and to
github. It's ok to use either one, but if you pick both it just makes more
work and confusion for those of us who are trying to answer things.
Thanks,
greg
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