Hi Thomas,
My first reaction is that this looks like a bug, but these things are
subtle and tricky, so I’m going to have to dig into it a bit to be sure.
Best,
-greg
On Fri, 8 Jun 2018 at 19:12, Thomas Duigou <[email protected]> wrote:
> Hi RDKiters,
>
> I am trying to build reaction SMARTS that encode inversion of chirality.
>
> However, I get different results (inversion of chirality done, vs. fail)
> depending of the order in which the atoms are given in the SMARTS reaction
> string. Below a toy example:
>
> # 2 different ways to depict a same reaction (L-lactate to D-lactate)
> rsmarts1 = '[#8:6]-[#6@
> :2](-[#1:8])(-[#6:3](-[#8-:5])=[#8:4])-[#6:1]>>[#8:6]-[#6@
> @:2](-[#1:8])(-[#6:3](-[#8-:5])=[#8:4])-[#6:1]'
> rsmarts2 = '[#1:8]-[#6@
> @:2](-[#6:1])(-[#8:6])-[#6:3](-[#8-:5])=[#8:4]>>[#1:8]-[#6@
> :2](-[#6:1])(-[#8:6])-[#6:3](-[#8-:5])=[#8:4]'
> rxn1 = AllChem.ReactionFromSmarts(rsmarts1)
> rxn2 = AllChem.ReactionFromSmarts(rsmarts2)
> rxn1.Initialize()
> rxn2.Initialize()
>
> # Reactions SMILES of the reactions are the same
> assert AllChem.ReactionToSmiles(rxn1) == AllChem.ReactionToSmiles(rxn2)
> # OK
>
> # Let's apply the reaction on L- and D-lactate
> llac = Chem.MolFromSmiles('C[C@H](O)C([O-])=O')
> llac = Chem.AddHs(llac)
>
> # rsmarts1 depiction: successful inversion of chirality
> ps = rxn1.RunReactants((llac,))
> print('rxn1', len(ps))
> print('Sub ', Chem.MolToSmiles(llac))
> print('Prod', Chem.MolToSmiles(ps[0][0]))
> # Sub [H]O[C@]([H])(C(=O)[O-])C([H])([H])[H]
> # Prod [H]O[C@@]([H])(C(=O)[O-])C([H])([H])[H]
>
> # rsmarts2 depiction: inversion of chirality fail
> ps = rxn2.RunReactants((llac,))
> print('rxn2', len(ps))
> print('Sub ', Chem.MolToSmiles(llac))
> print('Prod', Chem.MolToSmiles(ps[0][0]))
> # Sub [H]O[C@]([H])(C(=O)[O-])C([H])([H])[H]
> # Prod [H]O[C@]([H])(C(=O)[O-])C([H])([H])[H]
>
> Did I make a mistake somewhere, or is there something additional to do in
> order to make inversion of chirality working in all cases? I am using the
> last stable conda version of rdkit (2018.03.2.0).
>
> Thank you by advance for any clue,
> Best wishes,
> Thomas
>
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