- new methods IMP::atom::add_radii() and IMP::atom::add_bonds();
- Hierarchys to IMP::atom::Hierarchies
- IMP::Particles has been changed to a new type. It no longer plays
quite so well with python lists (you can't create a part one from an
arbitrary python list).
- The contains for multiple decorators have been revised to make them
more useful. See IMP::Decorators. You can now implicitly convert, for
example, a IMP::core::XYZs to an IMP::Particles (as well as use
IMP::Decorators::get_particles()). All methods that take a collection
of particles with a certain type now instead take a IMP::Decorators.
- A method that has expectations about the particles it takes should
take decorators rather than particles. That is, anything which expects
IMP::core::XYZ particles, should take an IMP::core::XYZs instead of
IMP::Particles.
- IMP_LIST() now takes an extra argument (the name of the plural container)
- In C++ IMP::Decorator objects are implicitly convertible to
IMP::Particle* objects. Unfortunately, making this work in Python is
problematic.
- More methods take and return decorators rather than IMP::Particles.
This means it is clearer what their expectations are and what they
produce.