================================
MDAnalysis Repository README
================================, numfocus, build, cov, [*], docs, devdocs, usergroup, developergroup, anaconda, mybinder, 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 a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many other — see the lists of supported trajectory formats_ and topology formats.
MDAnalysis also includes widely used analysis algorithms in the MDAnalysis.analysis module.
.. _numfocus-fiscal-sponsor-attribution:
The MDAnalysis project uses an open governance model_ and is fiscally sponsored by NumFOCUS. Consider making
a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
.. image:: https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png
:height: 60px
:target: https://numfocus.org/project/mdanalysis
:align: center
:alt: NumFOCUS
This project is bound by a Code of Conduct_.
Example analysis script
.. code:: python
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())
There are a number of tutorials_ on the MDAnalysis homepage that explain
how to conduct RMSD calculations, Alignment and many more features of MDAnalysis.
Source code
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_).
This is the top level of the master repository. It contains
-
the MDAnalysis toolkit source files in the directory ::
package/
-
the unit tests together with any input files required for
running those tests in the directory ::testsuite/
The directory maintainer contains scripts only needed for
maintaining releases and are not generally useful for the user or the
typical developer.
(For more details on the directory layout see Issue 87_ on the
MDAnalysis issue tracker.)
Guide for Developers
To setup a development environment and run the testsuite you can use this
guide_. If you are a new developer who would like to start contributing to
MDAnalysis as a start you can increase our code coverage, the guides explain how
to find uncovered code.
.. Footnotes
.. [*] build: Unit testing is for the whole package; coverage is
shown for the core library modules and the analysis modules.
.. _NumFOCUS: https://numfocus.org/
.. _open governance model: https://www.mdanalysis.org/about/#governance
.. _tax-deductible donation: https://numfocus.org/donate-to-mdanalysis
.. _Code of Conduct: https://www.mdanalysis.org/pages/conduct/
.. _trajectory formats: https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1
.. _topology formats: https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats
.. _Issue 87: https://github.com/MDAnalysis/mdanalysis/issues/87
.. _MDAnalysis: https://www.mdanalysis.org
.. _LICENSE: https://github.com/MDAnalysis/mdanalysis/blob/master/LICENSE
.. _#286: https://github.com/MDAnalysis/mdanalysis/issues/286
.. _MDAnalysis.analysis: https://docs.mdanalysis.org/documentation_pages/analysis_modules.html
.. _tutorials: https://www.mdanalysis.org/pages/learning_MDAnalysis/
.. _guide: https://github.com/MDAnalysis/mdanalysis/wiki/Guide-for-Developers
.., usergroup, image:: https://img.shields.io/badge/Google%20Group-Users-lightgrey.svg
:alt: User Google Group
:target: http://users.mdanalysis.org
.., developergroup, image:: https://img.shields.io/badge/Google%20Group-Developers-lightgrey.svg
:alt: Developer Google Group
:target: http://developers.mdanalysis.org
.., docs, image:: https://img.shields.io/badge/docs-latest-brightgreen.svg
:alt: Documentation (latest release)
:target: https://docs.mdanalysis.org
.., devdocs, image:: https://img.shields.io/badge/docs-development-yellow.svg
:alt: Documentation (development version)
:target: https://www.mdanalysis.org/mdanalysis/
.., numfocus, image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A
:alt: Powered by NumFOCUS
:target: https://www.numfocus.org/
.., build, image:: https://travis-ci.com/MDAnalysis/mdanalysis.svg?branch=develop
:alt: Build Status
:target: https://travis-ci.com/MDAnalysis/mdanalysis
.., cov, image:: https://codecov.io/gh/MDAnalysis/mdanalysis/branch/develop/graph/badge.svg
:alt: Coverage Status
:target: https://codecov.io/gh/MDAnalysis/mdanalysis
.., anaconda, image:: https://anaconda.org/conda-forge/mdanalysis/badges/version.svg
:alt: Anaconda
:target: https://anaconda.org/conda-forge/mdanalysis
.., mybinder, image:: https://mybinder.org/badge.svg
:alt: My Binder
:target: https://mybinder.org/v2/gh/MDAnalysis/binder-notebook/master
