msmbuilder-legacy
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msmbuilder
Legacy release of MSMBuilder
I can cluster by RMSD fine. But clustering by contact fails on multiple data sets. I get all sorts of different errors depending on settings and clustering algorithm. Anyone know...
Does any body have an idea how can I get a human readable of the Assignments.h5? Thanks in advance for your help.
The test that fails is `test_msm_analysis.test_msm_acf.test_2`, but in the most recent run it only fails for python3.3 I can't reproduce the failure for either python2.7 or python3.3 on my mac.
Our scripting system has a bunch of code in the `entry_point()`, that isn't currently tested by `test_wrappers`, which will only run the `.main(*args)` function. This can mean that bugs slip...
Is there currently any inbuilt functionality within MSMB for bootstrapping to assign variance to implied timescales calculated for a particular state representation? I'd like to achieve something similar to what...
Added a package in Extras for mapping MSM populations to a 3-D free energy PMF that can be viewed in OpenDX format in VMD. Also can estimate free energy differences...
The docstring notes that msm_analysis.sample should take dense or sparse matrices, but it throws an error for dense. Sparse or compressed sparse matrices are fine.
LPRMSD no longer worked when we moved mdtraj into msmbuilder. It's still necessary because the `altindices` behavior is not available in mdtraj (at least to my knowledge). I attempted to...
These should be the same changes as simtk/msmbuilder#360 redone so that it will be able to be merged.
Basically it doesn't make sense to save a single file for an entire dataset because the result of mdtraj.geometry.sasa.shrake_rupley is an array with SASA for each ATOM in the trajectory....