MDSynthesis
MDSynthesis copied to clipboard
a logistics and persistence engine for the analysis of molecular dynamics trajectories
============================================================= MDSynthesis: a persistence engine for molecular dynamics data
|zen| |docs| |build| |cov|
Development of MDSynthesis has stopped. For new projects we recommend
you use datreant
_ directly.
As computing power increases, it is now possible to produce hundreds of molecular dynamics simulation trajectories that vary widely in length, system size, composition, starting conditions, and other parameters. Managing this complexity in ways that allow use of the data to answer scientific questions has itself become a bottleneck. MDSynthesis is an answer to this problem.
Built on top of datreant
, MDSynthesis gives a Pythonic interface to
molecular dynamics trajectories using MDAnalysis
, giving the ability to work
with the data from many simulations scattered throughout the filesystem
with ease. It makes it possible to write analysis code that can work across
many varieties of simulation, but even more importantly, MDSynthesis allows
interactive work with the results from hundreds of simulations at once without
much effort.
Efficiently store intermediate data from individual simulations for easy recall
The MDSynthesis Sim object gives an interface to raw simulation data
through MDAnalysis
_. Data structures generated from raw trajectories (pandas
objects, numpy arrays, or any pure python structure) can then be stored and
easily recalled later. Under the hood, datasets are stored in the efficient
HDF5 format when possible.
.. _MDAnalysis: http://www.mdanalysis.org
Powered by datreant
under the hood
MDSynthesis is built on top of the general-purpose datreant
_ library. The
Sim is a Treant
_ with special features for working with molecular dynamics
data, but every feature of datreant applies to MDSynthesis.
.. _Treant: http://datreant.readthedocs.org/en/latest/treants.html
Documentation
A brief user guide is available on Read the Docs <http://mdsynthesis.readthedocs.org/>
__.
Contributing
This project is still under heavy development, and there are certainly rough edges and bugs. Issues and pull requests welcome!
MDSynthesis follows the development model of datreant
; see the
contributor's guide
to learn how to get started with contributing back.
.. _datreant: http://datreant.readthedocs.org/
.. _contributor's guide
: http://datreant.readthedocs.org/en/latest/contributing.html
.. |docs| image:: https://readthedocs.org/projects/mdsynthesis/badge/?version=develop :alt: Documentation Status :scale: 100% :target: https://readthedocs.org/projects/mdsynthesis
.. |build| image:: https://travis-ci.org/datreant/MDSynthesis.svg?branch=develop :alt: Build Status :target: https://travis-ci.org/datreant/MDSynthesis
.. |cov| image:: http://codecov.io/github/datreant/MDSynthesis/coverage.svg?branch=develop :alt: Code Coverage :scale: 100% :target: http://codecov.io/github/datreant/MDSynthesis?branch=develop
.. |zen| image:: https://zenodo.org/badge/13742/datreant/MDSynthesis.svg :alt: Citation :target: https://zenodo.org/badge/latestdoi/13742/datreant/MDSynthesis