- 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