Dear all,
I've got a question for the community about how chirality should be
handled in reactions.
This morning I managed to fix one of the outstanding reaction
stereochemistry problems in the RDKit: the loss of chirality when one
bond to a stereocenter is to an unmapped atom. Here's a quick demo of
the new behavior (not yet checked in; there are still a couple things
to be cleaned up):
In [7]: rxn = AllChem.ReactionFromSmarts('[C:1]-O>>[C:1]-S')
In [8]: ps = rxn.RunReactants((Chem.MolFromSmiles('F[C@H](O)Cl'),))
In [9]: Chem.MolToSmiles(ps[0][0],True)
Out[9]: 'F[C@H](S)Cl'
It seems nice to be able to preserve chirality in these cases.
The question that comes up is: "*Should* we be preserving chirality in
these cases?". The change makes it impossible to indicate a reaction
that scrambles stereochemistry. That doesn't seem right.
So... the question to you guys: How should stereochemistry
inversion/retention/loss be indicated in Reaction SMARTS?
Bonus points to anyone who can explain to me how the
inversion/retention flags in RXN files should be handled. At the
moment the RDKit uses what's in the products and ignores them in the
reactants.
-greg
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