[IMP-dev] Recent and coming changes in IMP

[Daniel Russel <>]

I haven't sent such an email in a while. Here is a summary of some of the interesting recent changes:

- Javi added his 2D EM scoring functionality as IMP::em2D

- some new ways to speed up scons have been added. See IMP::core::HarmonicDistancePairScore, IMP::core::SoftSpherePairScore and, for C++ users, the generic restraint support IMP::container::create_restraint() and IMP::core::create_restraint(). These each offer between 2x and 1.2x speedup when using simple scores (like harmonics on distances). In addition, a function IMP::container::get_slack_estimate() has been added which will estimate the correct slack to use with a IMP::container::ClosePairContainer. This will be extended to support IMP::core::ExcludedVolumeRestraint eventually.

- support for dense and sparse grids have been added to IMP::algebra. See the IMP::algebra module page (I'm still working on how to make the docs clearer).

- all write functions now have associated IMP::OptimizerState and IMP::FailureHandler classes. For examples, see IMP::WriteOptimizerState, IMP::WriteBinaryOptimizerState, IMP::WriteFailureHandler, IMP::atom::WritePDBOptimizerState etc.

- functions IMP::write_binary_model(), IMP::read_binary_model() and IMP::read_configurations() have been added to support space and filesystem efficient storage of model configurations. Multiple configuration can be written to a single file. This functionality requires NetCDF be installed (NetCDF is a standard library for reading and writing binary data).

- domino2 has been added. It provides a simpler interface on Keren's domino optimize as well as a number of new optimization and hooks for customizing the optimization process

- a better explaination of how to use reference counted pointers has been added to IMP::Pointer.

- all simple, planar polygons are now supported for display when CGAL is present



Some of the future changes:
- The IMP::algebra::Grid3D will be used to store EM grids and many of the computational kernels for EM will be moved to algebra so that density maps can be used in core and statistics.

- the excluded volume restraint is likely to get faster (and produce better derivatives) as Keren is working on an implementation using grids rather than zillions of atoms