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salilab
The Integrative Modeling Platform
As discussed on slack, this PR sets up a github actions CI that builds all of IMP and runs the test suite with code coverage, uploading to codecov.
Test and files added in 2e3590ae7e showing `CoarseCC.cross_correlation_coefficient()` evaluating to > 1.0. I see this when adding two cropped maps together and comparing them to the original map. Failing test...
SampledDensityMap has 3 constructors for its class. ``` (i) SampledDensityMap(KernelType kt = GAUSSIAN); (ii) SampledDensityMap(const DensityHeader &header, KernelType kt = GAUSSIAN); (iii) SampledDensityMap(const ParticlesTemp &ps, emreal resolution, emreal voxel_size, IMP::FloatKey...
`IMP::atom::get_volume_from_residue_type` currently returns no useful value for RNA or DNA. This causes a warning when using PMI to build models containing nucleic acids. We should add appropriate volumes.
When a Random Walk Monte Carlo move is proposed by `IMP::core::MonteCarlo`, `Model::update()` is called during scoring function evaluation. For variables with `ScoreState`s, this causes their score states to be enforced...
I've lost count of how many implementations we have of log-normal restraints. I propose a module with a series of classes that represent probability distributions. I started something like this...
While there are use cases in generic integrative modeling where one might want to use the gradients of a subset of the scoring function, this is dangerous when using MD...
There is an unexpected behavior in EM2D right now when fitting a model to an image. The error shows up when the pixel size is fairly high (~2Å/pix). The error...
`IMP.core.TransformationSymmetry` is an `IMP.SingletonModifier` that updates a list of `IMP.core.XYZ`, `IMP.core.NonRigidMember` and `IMP.core.RigidBody` coordinates/reference frames according to a list of reference particles. A complementary `IMP.SingletonDerivativeModifier` with the proposed name `TransformationSymmetryDerivatives`...
It would be useful to add a two-way interface to [NAMD](https://www.ks.uiuc.edu/Research/namd/) so that 1. IMP `ScoringFunction`s can be added to the NAMD forcefield so that we can use NAMD's integrator....