pyEMMA 2.0

EMMA: Emma's Markov Model Algorithms

What is it?

EMMA is an open source collection of algorithms implemented mostly in NumPy and SciPy to analyze trajectories generated from any kind of simulation (e.g. molecular trajectories) via Markov state models (MSM).

It provides APIs for estimation and analyzing MSM and various utilities to process input data (clustering, coordinate transformations etc). For documentation of the API, please have a look at the sphinx docs in doc directory or online.

For some examples on how to apply the software, please have a look in the ipython directory, which shows the most common use cases as documentated IPython notebooks.

Installation

With pip:

pip install pyemma

with conda:

conda install -c https://conda.binstar.org/omnia pyemma

or install latest devel branch with pip:

pip install git+https://github.com/markovmodel/PyEMMA.git@devel

For a complete guide to installation, please have a look at the version online or offline in file doc/source/INSTALL.rst

To build the documentation offline you should install the requirements with:

pip install -r requirements-build-doc.txt

Then build with make:

cd doc; make html

Support and development

For bug reports/sugguestions/complains please file an issue on GitHub.

Or start a discussion on our mailing list: [e-mail]

External Libraries

• mdtraj (LGPLv3): https://mdtraj.org