Hi,
Looking over the documentation and discussion threads I've found solid and
sensible answers for how chiral molecules and reactions in almost every
case, but I've hit what seems to be an issue in a situation I can't find
discussed.
I have atoms in my product that are untagged and do not appear in my
reactants. This is because I'm shortcutting a number of steps in what is
happening in the real chemistry where these extra atoms are added. And
RDKit behaves exactly as I would hope in general when I do this, adding
these new atoms to the product without taking them from any reactant. But
where these new atoms have chiral information it is being lost, as shown by
the following example:
> rxn =
AllChem.ReactionFromSmarts("[F:1][C:2]([C:3])[I:4]>>[F:1][C:2]([C:3][C@H
]([OH])Br)[Cl:4]")
> m = Chem.MolFromSmiles('FC(C)I')
> p = rxn.RunReactants((m,))[0][0]
> Chem.SanitizeMol(p)
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
> Chem.MolToSmiles(p,isomericSmiles=True)
'OC(Br)CC(F)Cl'
The output I was hoping for was O[C@@H](CC(F)Cl)Br but the chiral
information in the unmapped atoms in the product part of the reaction
specification appears to have been lost. Is this a bug or am I going about
my reaction in the wrong way?
Yours,
Toby Wright
--
InhibOx Ltd
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