- create_* functions (helper functions for rigid bodies and covers) now require you to add the score state to the model yourself. Whether the rigid body is enforced or not can be controlled by adding or removing the returned score state.

- All previously deprecated code has been removed. Removed functionality includes indexes in particles, the no-argument constructor for particles and the functionality that was moved from core to atom.

- The rigid body decorators have been simplified by removing the traits classes. There is now only one type of rigid body and it stores the list of member particles internally.

- NameDecorator has been deprecated as Particles have built in names.

- a ChainDecorator added to IMP.atom to store the chain id