There is a new method IMP::display::create_writer() which creates the appropriate writer based on the file name passed.
- You can now add members to rigid bodies via IMP::core::RigidBody::add_member(). These members can be other rigid bodies (although this functionality is only lightly tested).
- The code to get bounding volumes for IMP::atom::Hierarchy has been moved to the atom module, as as the clone and destroy code. They can be found at IMP::atom::clone(), IMP::atom::destroy(), IMP::atom::get_bounding_box().
- Added IMP::core::VolumeRestraint.
- Several functions have been added to helper in creating restraints. They are create_simple_connectivity_on_rigid_bodies(), create_simple_connectivitiy_on_molecules(), create_simple_distance(), create_simple_diameter(), create_simple_em_fit(), and create_simple_excluded_volume_on_rigid_bodies(). Functions load_em_density_map() and set_rigid_bodies() are added as well. See IMP::helper for more information.
- IMP::ScoreStates are further hidden. Namely, IMP::core::RigidBody constructs the needed score states internally, doing away with the need for the create functions (which have been done away with). In addition there are new decorators IMP::core::Cover and IMP::core::Centroid which manage their respective score states, further doing away with more create methods. The hierarchy-based create method for rigid bodies has been moved to the atom module and is called IMP::atom::rigid_body_setup_hierarchy().
- IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite.
- A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs.
- IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such.
- IMP::core::ClosePairsScoreState and IMP::core::CloseBipartitePairsScoreState have been replaced by IMP::core::ClosePairContainer and IMP::core::CloseBipartitePairContainer. The score states have been marked as deprecated and are mostly still there, but are more limited than they were.
- IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added.