fix: do not fill compound lib with invalid compounds and atoms

Reading the BIRD data from prd-all.cif.gz which doesn't contain any
compound would result in a compound lib filled with dummy compounds and
atoms, containing no useful data. This commit skips compounds with no
_chem_comp.id (key data item) and non-loop atoms without an
_chem_comp_atom.atom_id, with a warning.
The result of reading prd-all.cif.gz is now an empty compound lib.