To close the loop on this: the bug fix is now merged onto master. The ring
stereochemistry code now handles spiro centers.
Here's the little demo of that:
In [2]: print(Chem.CanonSmiles('O[C@H]1CC[C@]11CC[C@@](Cl)(Br)CC1'))
O[C@H]1CC[C@]12CC[C@@](Cl)(Br)CC2
Unlike previously (see the bug report)
SetIsotope(0)
>
> sdf.write(mol)
>
>
>
>
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> GIST is updated to include this: https://gist.github.com/jepdavidson/
> fdfbf6366a17f4829de3d4de22f3b442
>
>
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> Kind regards
>
>
>
> James
>
>
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>
>
> *From:* Greg Landrum [mailto:greg
2017 03:45
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral
centres(?)
Hi James,
This is definitely a bug. The problem seems to be connected to the way what the
RDKit calls "ring stereochemistry" i
Hi James,
This is definitely a bug. The problem seems to be connected to the way what
the RDKit calls "ring stereochemistry" is handled when there are spiro
linkages.
Here's the github issue: https://github.com/rdkit/rdkit/issues/1294
I'll take a look.
Best,
-greg
On Tue, Feb 7, 2017 at
Dear All,
I have hit what I think is a problem with stereochemistry perception/handling
for certain types of pseudochiral and/or spirocyclic systems.
Basically I am observing that some types of input tetrahedral stereochemical
information gets lost when an RDKit molecule is generated.
But I
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