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Project Description

What is it?

PyEMMA (EMMA = Emma’s Markov Model Algorithms) is an open source Python/C package for analysis of extensive molecular dynamics simulations. In particular, it includes algorithms for estimation, validation and analysis of:

  • Clustering and Featurization
  • Markov state models (MSMs)
  • Hidden Markov models (HMMs)
  • Multi-ensemble Markov models (MEMMs)
  • Time-lagged independent component analysis (TICA)
  • Transition Path Theory (TPT)

PyEMMA can be used from Jupyter (former IPython, recommended), or by writing Python scripts. The docs, can be found at http://pyemma.org.

Citation

If you use PyEMMA in scientific work, please cite:

M. K. Scherer, B. Trendelkamp-Schroer, F. Paul, G. Pérez-Hernández, M. Hoffmann, N. Plattner, C. Wehmeyer, J.-H. Prinz and F. Noé: PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models, J. Chem. Theory Comput. 11, 5525-5542 (2015)

Installation

With pip:

pip install pyemma

with conda:

conda install -c 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/suggestions/complaints please file an issue on GitHub.

Or start a discussion on our mailing list: pyemma-users@lists.fu-berlin.de

External Libraries

Release History

Release History

2.4

This version

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2.3.2

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2.3.1

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2.3

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2.2.7

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2.2.6

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2.2.4

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2.2.3

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2.2.2

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2.2.1

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2.2

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2.1.1

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2.1

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2.1rc3

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2.1rc2

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2.1rc1

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2.0.4

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2.0.3

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2.0.2

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2.0.1

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2.0

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1.2.2

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1.2.1

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Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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1.2

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Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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1.1.2

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Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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1.1.1

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Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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1.1

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Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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1.0.2

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Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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1.0.1

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TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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1.0

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Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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1.0a3

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Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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1.0a2

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Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
pyEMMA-2.4.tar.gz (1.6 MB) Copy SHA256 Checksum SHA256 Source May 20, 2017

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