MSMTools is a Python library for the estimation, validation and analysis Markov state models.

It supports the following main features:

  • Markov state model (MSM) estimation and validation.
  • Computing Metastable states and structures with Perron-cluster cluster analysis (PCCA).
  • Systematic coarse-graining of MSMs to transition models with few states.
  • Extensive analysis options for MSMs, e.g. calculation of committors, mean first passage times, transition rates, experimental expectation values and time-correlation functions, etc.
  • Transition Path Theory (TPT).

For a high-level interface to these functionalities, we encourage you to use PyEMMA.

Technical features:

  • Code is implemented in Python (supports 2.7, 3.3/3.4) and C.
  • Runs on Linux (64 bit), Windows (32 or 64 bit) or MacOS (64 bit).

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