Paolo's gist includes a vocabulary mistake[1] that I think is confusing
things here.
In the RDKit the stereochemistry of a double bond can be unspecified,
unknown, or known. Unspecified means that you haven't said anything about
what the stereo is; unknown means that you've actively provided the
Hi Theo,
The atom label placement in drawings turns out to be very tricky to do in a
cross platform way.
You're using the RDKit's old drawing code which we haven't been maintaining
for a while now, I'd recommend either switching to using one of the
convenience functions likes Draw.MolToImage() or
Hi Adelene,
I have updated the gist
https://gist.github.com/ptosco/1e1c23ad24c90444993fa1db21ccb48b
to account for your questions.
Cheers,
p.
On Tue, Oct 20, 2020 at 2:08 PM Adelene LAI wrote:
> Hi Dave and Pablo,
>
>
> Thanks for your helpful replies.
>
>
> @Dave, issue created:
Hi Dave and Pablo,
Thanks for your helpful replies.
@Dave, issue created: https://github.com/rdkit/rdkit/issues/3514
@Pablo, your gist shows that the internal representation of the mol does indeed
factor in undefined stereo, contrary to the way it is depicted.
But why then does this
Hi Adelene,
this gist
https://gist.github.com/ptosco/1e1c23ad24c90444993fa1db21ccb48b
shows how to add stereo annotations to RDKit 2D depictions, and also how to
access the double bond stereochemistry programmatically.
Cheers,
p.
On Tue, Oct 20, 2020 at 12:24 PM Adelene LAI wrote:
> Hi
Dear RDKit-ers,
this sounds like a simple problem, however, I haven't found a link to the
corresponding documentation.
When I draw a structure with:
from.rdkit.Chem import Draw
Draw.MolToQPixmap(mol)
The non-Carbon atom labels are not centered to the bonds, but typically shifted
downwards.
Hi RDKit Community,
Is there a way to preserve undefined stereochemistry aka unspecified
stereochemistry when doing MolFromSmiles?
I'm working with a bunch of molecules, some with stereochemistry defined, some
without.
If stereochemistry is undefined in the SMILES, I would like it to stay
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