.. Summary for PyPI
.. https://pypi.python.org/project/MDAnalysis/

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MDAnalysis_ is an object-oriented python toolkit to analyze molecular
dynamics trajectories generated by CHARMM_, Gromacs_, Amber_, NAMD_,
or LAMMPS_; it also reads other formats (e.g. PDB_ files and `XYZ
format`_ trajectories; see the `Table of Supported Coordinate
Formats`_ and `Table of Supported Topology Formats`_ for details). It
can write most of the coordinate formats, too, together with atom
selections for use in Gromacs_, CHARMM_, VMD_ and PyMOL_ (see
`Selection exporters`_).

MDAnalysis allows one to read molecular dynamics trajectories and
access the atomic coordinates through NumPy_ arrays. This provides a
flexible and relatively fast framework for complex analysis tasks that
integrates well with the wider Python ecosystem. Fairly complete `atom
selection commands`_ are implemented. Trajectories can also be
manipulated (for instance, fit to a reference structure) and written
out in a range of formats.


Availability
============

**Source code** is available from https://www.mdanalysis.org under the `GNU
Public Licence, version 2`_, together with the `online
documentation`_. **Packages** can be downloaded from
https://pypi.org/project/MDAnalysis/ or installed/upgraded via PyPI using `pip`_::

  pip install --upgrade MDAnalysis

By default MDAnalysis does not install every dependency needed to run every
analysis available in the analysis module or read netcdf Amber_ trajectories.
To install and update these dependencies as well run ::

  pip install --upgrade 'MDAnalysis[analysis,AMBER]

Please report **bugs** or **enhancement requests** through the `Issue
Tracker`_. Questions can also be asked on the `mdnalysis-discussion mailing
list`_.

In order to run the `Unit Tests`_ it is also necessary to install a
separate package MDAnalysisTests_ containing the test and test
data. As it contains about 70 MB of molecular dynamics trajectories
and simulation system structures it is not included with the library
itself.


Citation
========

When using MDAnalysis in published work, please cite the following
two papers:

*   R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy,
    M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski,
    S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis:
    A Python package for the rapid analysis of molecular
    dynamics simulations. In S. Benthall and S. Rostrup,
    editors, Proceedings of the 15th Python in Science
    Conference, pages 102-109, Austin, TX, 2016. SciPy.

*   N. Michaud-Agrawal, E. J. Denning, T. B. Woolf,
    and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular
    Dynamics Simulations. *J. Comput. Chem.* **32** (2011), 2319--2327.
    doi:`10.1002/jcc.21787`_

For citations of included algorithms and sub-modules please see the references_.


.. Links

.. _MDAnalysis: https://www.mdanalysis.org
.. _`10.1002/jcc.21787`: https://dx.doi.org/10.1002/jcc.21787
.. _references: https://docs.mdanalysis.org/documentation_pages/references.html
.. _GNU Public Licence, version 2: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
.. _Issue Tracker: https://github.com/mdanalysis/mdanalysis/issues
.. _`mdnalysis-discussion mailing list`:
   https://groups.google.com/group/mdnalysis-discussion
.. _`online documentation`:
   https://docs.mdanalysis.org
.. _`Table of Supported Coordinate Formats`:
   https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1
.. _`Table of Supported Topology Formats`:   
   https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats
.. _`atom selection commands`:
   https://docs.mdanalysis.org/documentation_pages/selections.html#selection-commands
.. _`Selection exporters`:
   https://docs.mdanalysis.org/documentation_pages/selections_modules.html#selection-exporters
.. _NumPy: https://numpy.scipy.org
.. _CHARMM:  https://www.charmm.org/
.. _Amber:   http://ambermd.org/
.. _LAMMPS:  http://lammps.sandia.gov/
.. _NAMD:    http://www.ks.uiuc.edu/Research/namd/
.. _Gromacs: http://www.gromacs.org/
.. _VMD: http://www.ks.uiuc.edu/Research/vmd/
.. _PyMOL: https://www.pymol.org/
.. _PDB: https://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html
.. _XYZ format: https://openbabel.org/wiki/XYZ_%28format%29

.. _Unit Tests: https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests
.. _MDAnalysisTests: https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysisTests

.. _`pip`: https://www.pip-installer.org/en/latest/index.html


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