Hi Greg,
Thanks for the python-full reply!
> # let's test the reaction to make sure it works.
> # due to a (already reported) bug in the way atom properties
> are handled, nrxn cannot be directly used, # so we use a hack
> and reparse it:
> >>> nrxn = AllChem.ReactionFromSmarts(AllChem.ReactionToSmarts(nrxn))
> >>> nrxn.Validate()
> # now we can run a molecule through to make sure it works:
> >>> nmol = Chem.MolFromSmiles('c1ccccc1C') nps =
> >>> nrxn.RunReactants((nmol,)) print Chem.MolToSmiles(nps[0][0])
> # output is: BrCc1ccccc1
>
> Is that what you're looking for?
It certainly allows me to do what I want - which is get a mapped RXN
out. And this can even be done with coordinates - which I have added
below as a reminder to anyone (which included me until about 10 mins
ago!) who had forgotten:
AllChem.Compute2DCoordsForReaction(nrxn)
rxnBlock = AllChem.ReactionToRxnBlock(nrxn)
So Thanks very much! : )
- and thanks for the reminder about sanitizing products from
reactions...
> The molecules that come back from reactions have not been
> sanitized, so all you need to do is add a call to
> Chem.SanitizeMol first:
>
> >>> Chem.SanitizeMol(prod)
Kind regards
James
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