Documentation

PyEMMA is a Python library and can be used through python or ipython. See Tutorials for examples and getting started. The API (Application Programming Interface) is currently divided into two main packages:

• Coordinates package (pyemma.coordinates)
  • User API
  • Classes
  • Implementation
• Markov State Models package (pyemma.msm)
  • User Functions
  • MSM classes
  • MSM functions (low-level API)
• Thermo package (pyemma.thermo)
  • User-Functions
  • Thermo classes

Plotting functions for aiding in the scientific analysis are found here:

• Plotting package
  • plots - Plotting tools (pyemma.plots)

For saving and loading in PyEMMA take a brief look here:

• Model serialization