EMMA -> Emma’s Markov Model Algorithms

This software is a 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 an API 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 PyEMMA API. To install this software and additional dependencies refer to the Installation Guide. For support/bug reports/sugguestions/complains please visit us at GitHub

Installation

• Installation
  • Anaconda install (Recommended)
  • Python Package Index (PyPI)
  • Building from Source
  • For Developers
  • Frequently Asked Questions (FAQ)
• Runtime Configuration
  • Default configuration file
  • Members

Documentation

• PyEMMA API
  • Coordinates package (pyemma.coordinates)
  • Markov State Models package (pyemma.msm)
  • Plotting API

Tutorials

• IPython Notebook Tutorials
  • MSM estimation and validation

Development

• Changelog
  • 1.2.1 (28-5-2015)
  • 1.2 (4-14-2015)
  • 1.1.2 (3-18-2015)
• Developer’s Guide
  • Contributing
  • Workflow
  • Publish a new release

Indices and tables

• Index
• Module Index
• Search Page