Recent Changes to IMP

Please add notifications of significant changes you have made to IMP.

Week of April 6:

• get_version_info and show were moved into IMP::Object, so all IMP::Object-inheriting classes must have them. This makes things more uniform and allows the methods to be documented in once place.

• Model and Optimizer objects are now RefCounted. As a result, IMP::Object itself is now RefCounted. To facilitate this IMP::Object now inherits from RefCounted (rather than the other way around), and so you can have RefCounted objects which are not IMP::Objects. This means that the former unsupport creation of Model on the stack now doesn't work and it needs to be created on the heap (and preferably stored using a IMP::Pointer).

• The docs now better explain reference counting and our memory management scheme better

• running doxygen produces no warnings, lets try to keep it that way. Run "scons doc > /dev/null" before you check in large blocks of new code to make sure that you didn't introduce warnings.

Week of March 30:

• A helper class has been added to make Modifiers look like functors for C++ and python.

Week of March 20:

• 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. This 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.

• ChainDecorator added to Atom to store the chain id

Week of March 13:

• A new writer, ChimeraWriter has been added which exports geometry to native Chimera constructs. It probably should be used instead of bild and cmm for most purposes as it combines the best of both types.

• compose for transformation is now a free function so compose(rotation, vector) will work.
• the geometry classes have been cleaned up and are now more consistent with IMP standards (and more likely to do what their names/comments suggest)

• ParticleRefiner has been renamed to Refiner since the Particle was long and unnecessary.

Week of March 6:

• Helper functions have been added to set up diameter restraints and covers.
• The new web site has gone live. Please check it out and pass on any comments/problems.
• Several new geometric shapes have been added to the algebra module