This repository has been archived by the owner on Sep 11, 2023. It is now read-only.
Service release
New features:
- plots: network plots can now be plotted using a given Axes object.
- thermo: TRAM supports the new parameter equilibrium which triggers a TRAMMBAR estimation.
- thermo: the model_active_set and msm_active_set attributes in estimated MEMMs is deprecated; every
MSM in models now contains its own active_set. - thermo: WHAM and MBAR estimations return MultiThermModel objects; return of MEMMs is reserved for
TRAM/TRAMMBAR/DTRAM estimations.
Fixes:
- coordinates: MiniBatchKmeans with MD-data is now memory efficient
and successfully converges. It used to only one batch during iteration. #887 #890 - coordinates: source and load function accept mdtraj.Trajectory objects to extract topology. #922. Thanks @jeiros
- base: fix progress bars for modern joblib versions.
- plots: fix regression in plot_markov_model with newer NumPy versions #907. Thanks @ghoti687.
- estimation: for n_jobs=1 no multi-processing is used.
- msm: scale transition path times by time unit of MSM object in order to get
physical time scales. #929