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MDTraj
======
Read, write and analyze MD trajectories with only a few lines of Python
code.
MDTraj is a python library that allows users to manipulate `molecular
dynamics (MD) <http://en.wikipedia.org/wiki/Molecular_dynamics>`_
trajectories. Features include:
- Wide MD format support, including ``pdb``, ``xtc``,
``trr``, ``dcd``, ``netcdf``, ``mdcrd``, ``prmtop``, and
more.
- Extremely fast RMSD calculations (4x the speed of the original `Theobald
QCP <http://theobald.brandeis.edu/qcp/>`_).
- Extensive :ref:`analysis <analysis>` functions including those that
compute bonds, angles, dihedrals, hydrogen bonds, secondary structure,
and NMR observables.
- Lightweight, Pythonic API.
MDTraj includes a command-line application, ``mdconvert`` (renamed to
``mdconvert-mdtraj`` on Debian systems), for converting
trajectories between formats.
.. toctree::
:maxdepth: 1
installation
new_to_python
notebook-examples/index
whatsnew
.. examples/index
API Reference
-------------
.. toctree::
:maxdepth: 1
load_functions
analysis
atom_selection
api/trajectory_files
api/reporters
api/utils
mdconvert
Developing
----------
.. toctree::
:maxdepth: 1
hdf5_format
Citation |DOI for Citing MDTraj|
--------------------------------
MDTraj is research software. If you make use of MDTraj in scientific
publications, please cite it. The BibTeX reference is
::
@article{McGibbon2015MDTraj,
title = {MDTraj: A Modern Open Library for the Analysis of
Molecular Dynamics Trajectories},
author = {McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan,
Matthew P. and Klein, Christoph and Swails, Jason M. and
Hern{\'a}ndez, Carlos X. and Schwantes, Christian R. and Wang,
Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
journal = {Biophysical Journal},
volume = {109},
number = {8},
pages = {1528 -- 1532},
year = {2015},
doi = {10.1016/j.bpj.2015.08.015}
}
License
-------
MDTraj is licensed under the Lesser GNU General Public License (LGPL
v2.1+).
.. |DOI for Citing MDTraj| image:: https://img.shields.io/badge/DOI-10.1016%2Fj.bpj.2015.08.015-blue.svg
:target: http://doi.org/10.1016/j.bpj.2015.08.015
.. vim: tw=75
|
