Metadata-Version: 2.1
Name: pyEMMA
Version: 2.5.8
Summary: PyEMMA: Emma's Markov Model Algorithms
Home-page: http://github.com/markovmodel/PyEMMA
Author: The Emma team
Author-email: info@emma-project.org
Maintainer: Martin K. Scherer
Maintainer-email: m.scherer@fu-berlin.de
License: LGPLv3+
Keywords: Markov State Model Algorithms
Platform: Windows
Platform: Linux
Platform: Solaris
Platform: Mac OS-X
Platform: Unix
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Environment :: MacOS X
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
Requires-Dist: bhmm (<0.7,>=0.6)
Requires-Dist: decorator (>=4.0.0)
Requires-Dist: h5py (>=2.7.1)
Requires-Dist: matplotlib
Requires-Dist: mdtraj (>=1.9.2)
Requires-Dist: msmtools (>=1.2)
Requires-Dist: numpy (>=1.8.0)
Requires-Dist: pathos
Requires-Dist: psutil (>=3.1.1)
Requires-Dist: pyyaml
Requires-Dist: scipy (>=0.11)
Requires-Dist: tqdm (>=4.23)
Requires-Dist: deeptime

=====================================
EMMA (Emma's Markov Model Algorithms)
=====================================

.. image:: https://img.shields.io/travis/markovmodel/PyEMMA/master.svg
   :target: https://travis-ci.org/markovmodel/PyEMMA
.. image:: https://img.shields.io/pypi/v/pyemma.svg
   :target: https://pypi.python.org/pypi/pyemma
.. image:: https://anaconda.org/conda-forge/pyemma/badges/downloads.svg
   :target: https://anaconda.org/conda-forge/pyemma
.. image:: https://anaconda.org/conda-forge/pyemma/badges/installer/conda.svg
   :target: https://conda.anaconda.org/conda-forge
.. image:: https://img.shields.io/codecov/c/github/markovmodel/PyEMMA/devel.svg
   :target: https://codecov.io/gh/markovmodel/PyEMMA/branch/devel


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 <http://www.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 <http://www.emma-project.org/latest/INSTALL.html>`__ 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 <http://github.com/markovmodel/PyEMMA>`__.

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


