Hi Dan,
On Fri, 6 Apr 2018 at 00:24, Dan Nealschneider <
dan.nealschnei...@schrodinger.com> wrote:
>
> What is the correct treatment of bond stereochemistry at centers for which
> a hydrogen is required in order to specify the bond stereochemistry? For
> example, an imine with a hydrogen substituent (trivial example, F/C=N/[H]).
>
In these cases the H cannot be implicit. The double bond stereochemistry is
always defined relative to atoms bonded to the double-bonded atoms (more
complex to write than it actually is) and there’s just no way to do this if
either of those atoms is implicit.
I notice that when I use the smiles constructor, or if I read from an SDF
> file using the SDMolSupplier, the C=N bond in the example shown above is
> not recognized as having stereochemistry. However, if I use
> removeHydrogens=False in the SDMolSupplier, the bond *is* recognized as
> Z.
>
I need to confirm it (I’m on my phone at the moment), but I think this is a
bug: removeHs() should not remove atoms that determine stereochemistry.
This might be something I can get fixed before the next release.
*At core, I have 2 questions:* Is RDKit able to represent stereochemistry
> about this bond if the hydrogen is implicit?
>
Nope. Not at the moment.
-greg
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