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 :-)