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salilab
The Integrative Modeling Platform
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...
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...
Some IMP headers are conditionally compiled with `IMP_SWIG_WRAPPER`. This is defined only when the SWIG Python wrappers are being compiled. This is used, for example, to do different checks at...
Each module's Python wrapper imports (via SWIG's `%import` directive) any module dependencies. This is done so that any classes in the module that derive from those in other modules get...
If the rigid body we're looking at has no symmetries, the axes for its inertial tensor are uniquely defined. I understand a `algebra::ReferenceFrame3D` as a set of three unitary orthogonal...
Need to be careful since CHARMM dihedral parameters have special treatment of wildcards and order is important... but should be possible to speed things up with some maps.
@pellarin reports that running https://github.com/salilab/mediator/tree/master/mediator_modeling/template/modeling.py generates RMF files that look like: ``` % rmf_show -v ... + "med3" [representation] molecule (sequence): 1(s) + "Beads" [representation] rigid body index (IMP): 262099(s)...
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...
And the method docs are a bit thin too.
I found / fixed the problem in test_linear. In test_harmonic the numbers still do not match - I put fake fixes for now just so that the test would be...
