Hi,
I'm interested in converting a SMILES string into a 3D structure using
another similar molecule as a scaffold. The molecule to be converted
may be a substructure of the scaffold molecule with a few
modifications (e.g. amines changed to imines), or be protonated at an
alternative site (e.g. 4-a
> You could probably code something like this using the OBBuilder code, but it
> would take some work (i.e, it sounds like you'd need to remove or mutate some
> atoms, adjust bond lengths, grow new fragments).
>
> I assume the idea is to do this in an automated fashion, or I'd suggest doing
> it