Just to add:
- IMP::multifit FFT sampling was rewritten to work faster.
- IMP::domino efficient assignment tables have been added, including a heap and cluster tables
On Aug 21, 2011, at 2:35 PM, Daniel Russel wrote:
> - the IMP::core::MonteCarlo optimizers now support incremental evaluation. This can be a lot faster when only a few particles are moved each step.
> - all the plural types in IMP have moved to bounds checked vectors when using debug builds with gcc. If you get a non-imp error about an invalid access, it is probably some code that walks off the end of an array. Please report it.
> - IMP::rmf::KeyCategory was renamed to IMP::rmf::Category
> - The deprecated constructors for various rmf/hdf5 things from files have been removed. Now use the methods IMP::rmf::open_rmf_file(), IMP::rmf::create_rmf_file(), IMP::rmf::open_rmf_file_read_only(), IMP::rmf::open_hdf5_file(), IMP::rmf::create_hdf5_file().
> - IMP::rmf broke backward compatibility in order to accelerate loading times of files and use a more compact storage for strings.
> - The IMP::core::MoverBase was changed to move it off of the IMP::SingletonContainer. This resulted in the IMP::core::BallMover and IMP::core::NormalMover having new constructors. Now create them from a list of particles, a list of float keys and a radius/standard deviation. This removes some complexity and inefficiencies as well is removes some scope for errors.
> - Temp and non-temp decorator lists have been merged in C++. This was done to simplifity code since no one was using the non-temp variants. Now all decorator lists are temp (non-reference counted) variants.
> - restraints and restraint sets are now evaluated only using "canonical" weights. That is, each restraint has one weight for the model (the total over all the restraint sets it is contained in and will always be evaluated with that weight). This allows the evaluation of simple restraints to be faster.
> - The IMP_LIST() macros have been changed slightly. If your usage needs to take action upon addition, removal or changes to the list, use the IMP_LIST_ACTION() variant in your header. The IMP_LIST_IMPL() macro no longer takes the actions, and the last three (generally empty arguments) will have to be removed from the call to get it to work. This is needed to move towards more flexible and efficient passing of lists of values.
> - IMP::rmf::create_hdf5_file() and IMP::rmf::open_hdf5_file() were added to avoid the dangerous and unclear bool paramter on the HDF5Group constructor. That constructor has been deprecated.
> - IMP::domino uses the new IMP::Model::evaluate_if_good() support to accelerate computations
> - IMP::core::MonteCarlo can use the IMP::Model::evaluate_if_good() support to more quickly reject
> very bad conformations. See IMP::core::MonteCarlo::set_maximum_difference().
> - IMP::core::ExcludedVolumeRestraint has been rewritten to be faster. It is especially
> faster when used with IMP::Model::evaluate_if_good()
> - a new evaluation mode IMP::Model::evaluate_if_good() and IMP::Model::evaluate_if_below() has been added. It allows restraints to shortcut score computation when the score can be shown to be worse than a maximum value.
> - as part of moving towards more efficient use of evaluate_if_good() various deprecated methods have been removed from IMP::core::ExcludedVolumeRestraint and IMP::core::RigidClosePairsFinder.
> - incremental evaluation support was removed from \imp. The reason for doing this was that the code was complicated, created overhead even when incremental support was not used and was not commonly used. Further, decomposing the restraints and using the dependency graph yields similar results and is more transparent.
>
>
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