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salilab
The Integrative Modeling Platform
Drawing from some of the tricks used in probabilistic programming packages, I'm proposing a reimplementation to `IMP.isd.Nuisance` in IMP that should enable better sampling. The beginnings of an implementation can...
If the X parameter `IMP.isd.Nuisance` has upper and/or lower bounds and if any of the other parameters are themselves Nuisances, then the missing normalization factor from the truncation is non-constant...
and how they compare to handwritten scores
http://www.mcs.anl.gov/research/projects/tao/
e.g. CHARMM sterochemistry, anything that uses a list of pairs/triples of particles should all be trivially parallelizable with OpenMP.
Hi, For me `IMP.em.FitRestraint` is much slower with `use_rigid_bodies = True`, while the doc says it should be faster. For example, running `imp/modules/em/test/expensive_test_resample_by_rigid_bodies.py` test like this: `python -m unittest expensive_test_resample_by_rigid_bodies.Tests.test_resample`...
Release builds still include a lot of `USAGE` checks in performance-critical parts of the code that make the builds substantially slower than fast builds (with no checks at all). Many...
I think this has been reported before but when generating a map from a model using IMP::em::SampledDensityMap, the model and the map are not align. I attached a code snippet...
When adding all the restraint scores reported in the stat file (i.e. excluded volume, connectivity, xls) they do not add to the total score reported in the stat file. For...
