- IMP::display::PlaneGeometry was added to display planes
- the optimize methods on optimizers was moved to a "non-virtual interface". Usage has not changed, but optimizers should implement IMP::Optimizer::do_optimize() instead of IMP::Optimizer::optimize() to
benifit from better checking.
- the two-vector constructor for IMP::algebra::Plane3D now expects the second vector to be a unit vector as otherwise one could switch the order around without noticing.
- the io functions in the kernel have been cleaned up a bit (the old ones are there for backwards compatibility). See IMP::write_particles(), IMP::write_particles_binary(), IMP::write_particles_to_buffer() and IMP::read_particles(), IMP::read_particles_binary(), IMP::read_particles_from_buffer()
- IMP::core::WriteModelOptimizerState is going away as it duplicated IMP::WriteParticlesOptimizerState.
- the IMP::algebra::Grid3D has been changed to make it support any (fixed) dimension when used with sparse storage. The template arguments have also been changed to remove a redundant one. See IMP::algebra::GridD.
- the biological systems specification has been improved a little adding ability to run some rudamentary tests to make sure the scripts are ok and to not require that everything be run from the svn directory.
- A new method IMP::atom::create_compatible_rigid_body() which creates a rigid body from a hierarchy which has the same internal coordinates as another rigid body. A way to make the rigid body construction more canonical would be nice (so we don't need this function), but I'm not sure how to do that.