Molecule-related classes such as ResidueDecorator and AtomDecorator
are now in IMP.atom. The IMP.core versions of most things have been
left for the time being (but marked as deprecated). Unfortunately,
technical difficulties with SWIG prevent that being done easily for
ResidueDecorator and AtomDecorator and anything which uses them. The
fix is just to replace core.AtomDecorator with atom.AtomDecorator
(etc.) (a good excuse to learn sed if you don't already know it :-)