.. -*- coding: utf-8 -*-
.. MDAnalysis documentation master file, created by
.. sphinx-quickstart on Mon Sep 27 09:39:55 2010.
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###############################
MDAnalysis documentation
###############################


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

**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 :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 http://mdanalysis.googlecode.com 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`_.

.. _GNU Public Licence, version 2: http://www.gnu.org/licenses/old-licenses/gpl-2.0.html
.. _Issue Tracker: http://code.google.com/p/mdanalysis/issues/list
.. _`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/
.. _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`_

.. rubric:: Included algorithms

If you use the RMSD calculation (:mod:`MDAnalysis.analysis.rms`) or
alignment code (:mod:`MDAnalysis.analysis.align`) that uses the
:mod:`~MDAnalysis.core.qcprot` module please also cite

*   Douglas L. Theobald. Rapid calculation of RMSD using a
    quaternion-based characteristic polynomial. *Acta
    Crystallographica A* **61** (2005), 478-480.

*   Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald. Fast
    determination of the optimal rotational matrix for macromolecular
    superpositions. *J. Comput. Chem.* **31** (2010), 1561–1563.

If you use the helix analysis algorithm HELANAL_ in
:mod:`MDAnalysis.analysis.helanal` please cite

*   Bansal M, Kumar S, Velavan R. HELANAL — A program to characterise
    helix geometry in proteins. *J. Biomol. Struct. Dyn.* **17**
    (2000), 811–819

If you use the GNM trajectory analysis code in
:mod:`MDAnalysis.analysis.gnm` please cite

*   Benjamin A. Hall, Samantha L. Kaye, Andy Pang, Rafael Perera, and
    Philip C. Biggin. Characterization of Protein Conformational
    States by Normal-Mode Frequencies. *JACS* **129** (2007), 11394–11401.


Thanks! 

.. _`10.1002/jcc.21787`: http://dx.doi.org/10.1002/jcc.21787
.. _HELANAL: http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html


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/KDTree_modules

	

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

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

