Using mapping instead of beads to specify coarse-graining rules doesn't fill in the complete topology information in the output GSD file.

[chrisjonesBSU]

The issue arises in CG_System because the _set_mapping method is called when you pass in beads, but it isn't called when passing in mapping instead.

        if beads is not None:
            # get compounds
            self._get_compounds(
                beads=beads,
                allow_overlap=allow_overlap,
                length_scale=length_scale,
                conversion_dict=conversion_dict,
                add_hydrogens=add_hydrogens,
                aniso_beads=aniso_beads,
            )

            # calculate the bead mappings for the entire trajectory
            self._set_mapping()
        elif mapping is not None:
            if not isinstance(mapping, dict):
                with open(mapping, "r") as f:
                    mapping = json.load(f)
            self.mapping = mapping

Inside the _set_mapping method, the bond information is populated, and this information is needed to infer angles and dihedrals as well.