It's possible to get cifs into mdanalysis via openmm's cif reader, though it's not exactly convenient. It's not possible to write them out. prepmd uses mdanalysis to extract hetatms from structure files and write them out as rdfs, and mdanalysis does the conversion to the rdfpy Molecule data structure, so my only options are to find another package that does that (as far as I know, no other python packages read mmcifs and output rdfpy molecules) or re-implement the functionality (way out of scope). For now, these files are written to temporary PDBs and then converted back to mmCif, but this won't work with all structure files, such as those with large numbers of atoms. There is a (very old) open issue on the MDAnalysis issue tracker, but I don't think supporting mmCif is a priority for them.
It's possible to get cifs into mdanalysis via openmm's cif reader, though it's not exactly convenient. It's not possible to write them out. prepmd uses mdanalysis to extract hetatms from structure files and write them out as rdfs, and mdanalysis does the conversion to the rdfpy Molecule data structure, so my only options are to find another package that does that (as far as I know, no other python packages read mmcifs and output rdfpy molecules) or re-implement the functionality (way out of scope). For now, these files are written to temporary PDBs and then converted back to mmCif, but this won't work with all structure files, such as those with large numbers of atoms. There is a (very old) open issue on the MDAnalysis issue tracker, but I don't think supporting mmCif is a priority for them.