Skip to content
This repository has been archived by the owner on Sep 11, 2023. It is now read-only.

Service release

Compare
Choose a tag to compare
@marscher marscher released this 20 Sep 13:10
· 2650 commits to devel since this 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