===========
BioSimSpace
===========

.. image:: https://github.com/michellab/BioSimSpace/workflows/Build/badge.svg
   :target: https://github.com/michellab/BioSimSpace/actions?query=workflow%3ABuild)
   :alt: Build status

.. image:: https://anaconda.org/michellab/biosimspace/badges/downloads.svg
   :target: https://anaconda.org/michellab/biosimspace
   :alt: Conda Downloads

.. image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
   :target: https://www.gnu.org/licenses/gpl-3.0.html
   :alt: License

.. image:: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225/status.svg
   :target: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225
   :alt: Paper

`BioSimSpace <https://github.com/michellab/BioSimSpace>`__ is an interoperable
Python framework for biomolecular simulation. With it you can:

* Write robust and portable biomolecular :ref:`workflow components <ref_nodes>` that work on different hardware, with different software packages, and that can be run in different ways, e.g. command-line, `Jupyter <https://jupyter.org>`__.
* Interact with molecular-simulation processes in real time.

Citation |DOI for Citing BioSimSpace|
=====================================

If you use BioSimSpace in any scientific software, please cite the following paper: ::

    @article{Hedges2019,
      doi = {10.21105/joss.01831},
      url = {https://doi.org/10.21105/joss.01831},
      year = {2019},
      publisher = {The Open Journal},
      volume = {4},
      number = {43},
      pages = {1831},
      author = {Lester Hedges and Antonia Mey and Charles Laughton and Francesco Gervasio and Adrian Mulholland and Christopher Woods and Julien Michel},
      title = {BioSimSpace: An interoperable Python framework for biomolecular simulation},
      journal = {Journal of Open Source Software}
    }

.. |DOI for Citing BioSimSpace| image:: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225/status.svg
   :target: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225

Installation
============

.. toctree::
   :maxdepth: 2

   install

Compatibility
=============

.. toctree::
   :maxdepth: 2

   compatibility

Documentation
=============

.. toctree::
   :maxdepth: 2

   api/index

Development
===========
.. toctree::
   :maxdepth: 2

   development
   changelog

Nodes
=====
.. toctree::
   :maxdepth: 2

   nodes

Notebook server
===============
.. toctree::
   :maxdepth: 2

   notebook

Protocols
=========
.. toctree::
   :maxdepth: 2

   protocols

Media
=====
.. toctree::
   :maxdepth: 2

   media

Legal Notices
=============
.. toctree::
   :maxdepth: 1

   legal

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`