.. -*- coding: utf-8 -*-
.. MDAnalysis documentation master file, created by
.. sphinx-quickstart on Mon Sep 27 09:39:55 2010.
.. You can adapt this file completely to your liking, but it should at least
.. contain the root `toctree` directive.

###############################
MDAnalysis documentation
###############################


:Release: |release|
:Date: |today|

**MDAnalysis** (`www.mdanalysis.org`_) is an object-oriented python
toolkit to analyze molecular dynamics trajectories generated by
CHARMM_, Gromacs_, Amber_, NAMD_, LAMMPS_, or `DL_POLY`_; it also reads
other formats (e.g. PDB_ files and `XYZ format`_ trajectories; see
:ref:`Supported coordinate formats` for the full list). It can write
most of these formats, too, together with atom selections for use in
Gromacs_, CHARMM_, VMD_ and PyMol_ (see :ref:`Selection exporters`).

It 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. Fairly complete
atom :ref:`selection-commands-label` are implemented. Trajectories can
also be manipulated (for instance, fit to a reference structure) and
written out in a range of formats.

**Source code** is available from
https://github.com/MDAnalysis/mdanalysis/ under the `GNU Public
Licence, version 2`_, together with some additional documentation.

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

.. _`www.mdanalysis.org`: http://www.mdanalysis.org
.. _GNU Public Licence, version 2: http://www.gnu.org/licenses/old-licenses/gpl-2.0.html
.. _Issue Tracker: https://github.com/MDAnalysis/mdanalysis/issues
.. _`mdnalysis-discussion mailing list`:
   http://groups.google.com/group/mdnalysis-discussion
.. _NumPy: http://numpy.scipy.org
.. _CHARMM:  http://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/
.. _`DL_POLY`: http://www.scd.stfc.ac.uk//44516.aspx
.. _VMD: http://www.ks.uiuc.edu/Research/vmd/
.. _PyMol: http://www.pymol.org/
.. _PDB: http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html
.. _XYZ format: http://openbabel.org/wiki/XYZ_%28format%29


Citation
========

When using MDAnalysis in published work, please cite

*   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`_

.. _`10.1002/jcc.21787`: http://dx.doi.org/10.1002/jcc.21787

MDAnalysis also contains specific algorithms and whole analysis
modules whose algorithms have also been published in the scientific
literature. Please make sure to also reference any
:ref:`references-components` in published work.

Thank you!


Contents
========

.. toctree::
   :maxdepth: 1
   :numbered:		
   
   ./documentation_pages/overview
   ./documentation_pages/selections
   ./documentation_pages/analysis_modules
   ./documentation_pages/topology_modules
   ./documentation_pages/coordinates_modules
   ./documentation_pages/selections_modules
   ./documentation_pages/core_modules
   ./documentation_pages/visualization_modules
   ./documentation_pages/lib_modules
   ./documentation_pages/version
   ./documentation_pages/units
   ./documentation_pages/exceptions
   ./documentation_pages/references
	

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

