Code for Markov state modeling of weighted ensemble trajectories.

• Authors: John Russo, Jeremy Copperman
• Free software: MIT license
• Documentation: https://jdrusso.github.io/msm_we/ .

• Compute a history-augmented Markov state model from WESTPA weighted ensemble data
• Estimate steady-state distributions
• Estimate flux profiles
• Estimate committors

• Provide option for user to override dimReduce() in case they want to do something other than PCA/VAMP
• Add TICA option to dimReduce()
• Add monkey-patching directly into msm_we code. I.e., add a function like register_featurization(func) which takes the featurization function as input and overloads msm_we.processCoordinates() with it. Right now, this has to be done manually.

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.