It seems that converting XYZ files to SDF files (when the molecule is charged) do not seem to be a trivial thing, does anybody know a solution to this? So the SDF gets the right charge value without changing the original bond orders. #compchem #cheminformatics @kjelljorner

@SevenRoldan This is a notoriously difficult problem as you need to deduce the chemical bonding based on only the atomic coordinates. I would recommend openbabel or github.com/jensengroup/xy… but they will probably not be very robust for charged species. @janhjensen might know more.

@SevenRoldan @kjelljorner We usually create an initial SDF file from smiles or inchi and copy the connectivity indices from this file to the final SDF file (obtained from an XYZ file).