A Markov State Model estimation and analysis toolbox for time series data inspired by msmtools and PyEMMA. Written in Python, mostly relying on numpy and scipy.
This package provides the following functionality:
- Basic data clustering (KMeans/KMeans++, Regspace, DBSCAN)
- Estimation of transition matrices from trajectory data
- Analysis functionality (eigenvalues/vectors, transition path theory, aperiodicity, irreducibility) for Markov State Models
- Visualization for clustering and analysis
numpy, msmtools>=1.0, matplotlib, scipy, pandas
Call
python setup.py install
from project directory. Alternatively, call
pip install git+https://github.com/Markov-Schmarkov/mcmm-project
to install from github.