Charles Greenberg

Build error on Mac OS X

2

scons is giving me this error: g++ -o test-arac src/cpp/tests/test_datasets.o src/cpp/tests/test_main.o src/cpp/tests/test_optimzation.o src/cpp/tests/test_structure.o src/cpp/tests/test_utilities.o -L/usr/lib -L. -L/usr/local/lib -larac -lgtest scons: **\* [src/python/arac/_cppbridge.so] Source file: src/swig/cppbridge.i is static and is not...

ValueError: Expected 2D array, got 1D array instead

1

Using continuous variables. Took a simple input matrix X and target variable y. It seems to run in a problem using sklearn's preprocessing even though the matrix dimensions are correctly...

Currently the only way to get ALL leaves of all representations is a bit clunky, you have to use selection: ``` python selB = IMP.atom.Selection(hsel,resolution=IMP.atom.ALL_RESOLUTIONS, representation_type=IMP.atom.BALLS) selD = IMP.atom.Selection(hsel,resolution=IMP.atom.ALL_RESOLUTIONS, representation_type=IMP.atom.DENSITIES)...

Representation decorator needs a base_type

1

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...

Add StructureSourceType

1

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...

A common operation in PMI is gathering frames from many RMF files and writing them to a summary RMF file. Currently this can only be done on a single CPU...

Speed up SampledDensityMap by taking advantage of separability

1

The value of a (diagonal) 3D gaussian at some voxel is the product of the x,y, and z 1D gaussians. That means for an NxNxN grid, you don't have to...

SampledDensityMap should natively handle core::Gaussians

3

Currently if you create a SampledDensityMap it treats all Gaussians as point particles and just uses whatever kernel was requested. I will add a CoreGaussianKernel which directly uses the covariance...

Documentation about PairScores vs Restraints etc

5

There doesn't appear to be any documentation explaining what a PairScore (or TripletScore etc), why you would use it, and under what situations, which solution could be faster.