PyEMMA: Emma's Markov Model Algorithms
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
If you want to use Miniconda on Linux or OSX, you can run this script to download and install everything:
curl -s https://raw.githubusercontent.com/markovmodel/PyEMMA/devel/install_miniconda%2Bpyemma.sh | bash
If you have Anaconda/Miniconda installed, use the following:
conda install -c conda-forge pyemma
With pip:
pip install 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
mdtraj (LGPLv3): https://mdtraj.org
bhmm (LGPLv3): http://github.com/bhmm/bhmm
msmtools (LGLPv3): http://github.com/markovmodel/msmtools
thermotools (LGLPv3): http://github.com/markovmodel/thermotools
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
File details
Details for the file pyEMMA-2.5.10.tar.gz.
File metadata
- Download URL: pyEMMA-2.5.10.tar.gz
- Upload date:
- Size: 2.4 MB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/0.0.0 importlib_metadata/4.8.2 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.7.12
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 23a5d719cbc7df8355c6e7533aeade8499964c465cc5578697821eb9863e15f4 |
|
| MD5 | dedb82456fe441e3cc2c9f44b8b71c63 |
|
| BLAKE2b-256 | 4ddba8d56cf87e94b7b1f1b16b68b619b8bcc9cfea9b7527b38f58e6dfc7e227 |
