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) `_ trajectories. Features include: - Wide MD format support, including ``pdb``, ``xtc``, ``trr``, ``dcd``, ``binpos``, ``netcdf``, ``mdcrd``, ``prmtop``, and more. - Extremely fast RMSD calculations (4x the speed of the original `Theobald QCP `_). - Extensive :ref:`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``, for converting trajectories between formats. .. toctree:: :maxdepth: 1 installation new_to_python examples/index whatsnew 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