Metadata-Version: 2.4
Name: mdtraj
Version: 1.11.2
Summary: MDTraj: A modern, open library for the analysis of molecular dynamics trajectories
Author-email: Robert McGibbon <rmcgibbo@gmail.com>
License-Expression: LGPL-2.1-or-later
Project-URL: download, https://github.com/mdtraj/mdtraj/releases/latest
Project-URL: homepage, https://mdtraj.org
Project-URL: issues, https://githubcom/mdtraj/mdtraj/issues
Project-URL: source, https://github.com/mdtraj/mdtraj
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Programming Language :: C
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy~=2.0
Requires-Dist: packaging
Requires-Dist: pyparsing!=3.3.3
Requires-Dist: scipy
Provides-Extra: all
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Requires-Dist: mdtraj[tests]; extra == "all"
Provides-Extra: optional
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Dynamic: license-file


# MDTraj: an open-source library for analysis of molecular dynamics trajectories

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MDTraj is a python library that allows users to manipulate molecular dynamics
(MD) trajectories and perform a variety of analyses, including fast RMSD,
solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj
is the wide variety of molecular dynamics trajectory file formats which are
supported, including RCSB pdb, GROMACS xtc, and trr, CHARMM / NAMD dcd, AMBER
AMBER NetCDF, AMBER mdcrd, TINKER arc and MDTraj HDF5."

Read, write and analyze MD trajectories with only a few lines of Python code.

##  Features

With MDTraj, you can:

- Read and write from **every MD format imaginable** (`pdb`, `xtc`, `trr`, `dcd`, `netcdf`, `mdcrd`, `prmtop`, `gsd`, ...)
- Run **blazingly** fast RMSD calculations (4x the speed of the original Theobald QCP).
- Use tons of analysis functions like bonds/angles/dihedrals, hydrogen bonding identification, secondary structure assignment, NMR observables.
- Use a **lightweight API**, with a focus on **speed** and vectorized operations.

For details, see the [documentation](https://mdtraj.readthedocs.io/en/latest/). To get involved,
take a look at the [GitHub issue tracker](https://github.com/mdtraj/mdtraj/issues)
and/or the [Discussions](https://github.com/mdtraj/mdtraj/discussions) section.

##  Citation

MDTraj is research software. If you make use of MDTraj in scientific publications, please cite it. The BibTeX reference is
```
@article{McGibbon2015MDTraj,
    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.},
    title = {MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
    journal = {Biophysical Journal},
    volume = {109},
    number = {8},
    pages = {1528 -- 1532},
    year = {2015},
    doi = {10.1016/j.bpj.2015.08.015}
}
```

## License

GNU LGPL version 2.1, or at your option a later version of the license.
Various sub-portions of this library may be independently distributed under
different licenses. See those files for their specific terms.

## Project Status
MDTraj is actively maintained by community members and representatives from Folding@Home, The Molecular Sciences Software Institute, and Open Force Field Initiative. We welcome new users and contributors!

If you are interested in contributing, please check out the [repository issue tracker](https://github.com/mdtraj/mdtraj/issues). For feature ideas or general questions, please post in the [repository discussions](https://github.com/mdtraj/mdtraj/discussions).
