Re: [Rdkit-discuss] atom index changes after embedding

Hi Pablo, You could loop over the atoms and use SetProp to add a relevant property to each one. That should survive the embedding. Cheers, Dave On Mon, 29 Mar 2021 at 11:18, Pablo Ramos wrote: > Dear community, > > > > I want to embed a molecule. For my personal application, I really need

[Rdkit-discuss] atom index changes after embedding

Dear community, I want to embed a molecule. For my personal application, I really need the atom indices to be respected, even if they are indistinguishable. The problem is that, because of symmetry, some atoms may be indistinguishable. This is something you can see by using