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salilab
The Integrative Modeling Platform
A user may need to read in a PDB file but want several positions mutated. Doing this by hand in external programs can be time-consuming. It'd be nice if, after...
The current version of the EM and EM2D modules uses the KernelParameters.h file to sample the density at a given resolution and angstrom per pixel (apix). However both uses the...
referring to #927, we have an ISDRestraint class working and passing tests. Now we want the LogWrapper get the probabilities from a IMP::isd::ISDRestraintsTemp. (we couldn't commit the LogWrapper code and...
Currently the base type is assumed to be IMP.atom.BALLS, but that shouldn't be required. Maybe we want to represent a fragment with only density. Also, any objections if I just...
CMake provides a macro `generate_export_header` that generates a header file with the necessary `#define`s to export symbols. See, for example, salilab/mdt@e329212ce36c. May make sense to use that rather than our...
For example, we link all of `module/foo/include/*.h` from the source directory into `include/IMP/foo/` in the build directory. We can probably avoid this and modify our install rules and compile-time `-I`...
Primarily so we can easily select things when the whole system is properly tagged with StructureSource. Type ideas (I'm open to better names) IMP.atom.XRAY, IMP.atom.MODEL, IMP.atom.EM, and something to represent...
Consider the following: ``` lopt = IMP.core.ConjugateGradients(model) opt = IMP.core.MonteCarloWithLocalOptimization(lopt, 1000) opt.set_scoring_function(sf) opt.optimize(100) ``` The local optimizer `lopt` will actually use `model`'s implicit scoring function by default. In most cases,...
the problem is that in Hierarchy.cpp we check whether a hierarchy is well built. For instance: ``` if (!h.get_as_xyzr()) { TEST_FAIL("Leaf "