MDAnalysis

Yanked

This release has been yanked by its maintainers, and will be ignored by installers, except when explicitly specified.
Consider using release 2.10.0 instead.
Reason given by maintainers: Bad SOURCES.txt

[*]

MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists.

It works with a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many others — see the lists of supported trajectory formats and topology formats. MDAnalysis also includes widely used analysis algorithms in the MDAnalysis.analysis module.

This project is bound by a Code of Conduct.

Example analysis script

import MDAnalysis as mda

# Load simulation results with a single line
u = mda.Universe('topol.tpr','traj.trr')

# Select atoms
ag = u.select_atoms('name OH')

# Atom data made available as Numpy arrays
ag.positions
ag.velocities
ag.forces

# Iterate through trajectories
for ts in u.trajectory:
    print(ag.center_of_mass())

Documentation

New users should read the Quickstart Guide and might want to look at our videos, in which core developers explain various aspects of MDAnalysis.

All users should read the User Guide.

Developers may also want to refer to the MDAnalysis API docs.

A growing number of tutorials_ are available that explain how to conduct RMSD calculations, structural alignment, distance and contact analysis, and many more.

Installation and availability

The latest release can be installed via ``pip`` or ``conda`` as described in the Installation Quick Start.

Source code is hosted in a git repository at https://github.com/MDAnalysis/mdanalysis and is available under the GNU General Public License, version 2 (see the file LICENSE).

Contributing

Please report bugs or enhancement requests through the Issue Tracker. Questions can also be asked on the user mailing list.

If you are a new developer who would like to start contributing to MDAnalysis get in touch on the developer mailing list. To set up a development environment and run the test suite read the developer guide.

Citation

When using MDAnalysis in published work, please cite the following two papers:

R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. doi:10.25080/Majora-629e541a-00e
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

For citations of included algorithms and sub-modules please see the references.

Release files for MDAnalysis 1.1.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for MDAnalysis 1.1.0
File	Size	Uploaded
MDAnalysis-1.1.0.tar.gz	3.9 MB	May 1, 2021	Details

Release files / MDAnalysis-1.1.0.tar.gz

Download URL	MDAnalysis-1.1.0.tar.gz
Size	3.9 MB
Tags	Source
SHA-256 checksum How to use checksums	`17cafb982e4380d62c6e2ba951c7717e9393b4c7b6200b6632763100ea2b0839`
BLAKE2b-256 checksum How to use checksums	`0f5a3f34615abbe7c7758847636167d0caad7bb428c3950da64e7a3003b2c6fc`
Upload date	May 1, 2021
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.4.1 importlib_metadata/4.0.1 pkginfo/1.6.1 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.56.0 CPython/3.8.3`