BioSim Extractor Documentation
==============================

``biosim-extractor`` is available at http://github.com/CCPBioSim/biosim-extractor

.. image:: /_static/logos/biosim-extractor-logo-dark-text.png
   :width: 250px
   :align: center
   :class: only-light

.. image:: /_static/logos/biosim-extractor-logo-light-text.png
   :width: 250px
   :align: center
   :class: only-dark

A toolkit for extracting standardised metadata from molecular dynamics (MD) simulations.

Overview
--------

BioSim Extractor provides tools to parse, extract, and standardize metadata from MD simulation outputs (AMBER, GROMACS, etc.), and validate against `biosim-schema <https://github.com/CCPBioSim/biosim-schema>`_.

Features
--------

- Parse log files from multiple MD engines
- Extract topology and trajectory metadata
- Standardise units and schema
- Validate metadata against biosim-schema `biosim-schema <https://github.com/CCPBioSim/biosim-schema>`_

Getting Started
---------------

See :doc:`installation` for setup instructions and :doc:`usage` for examples.

API Reference
-------------

The full API documentation is available in :doc:`api`.

Contents
--------

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   installation
   usage
   contributing
   api

Funding
=======

Contributors to biosim-extractor were supported by

.. image::  _static/logos/psdi-logo.png
   :height: 100px
   :target: https://www.psdi.ac.uk/

.. image:: _static/logos/cosec-logo.png
   :height: 100px
   :target: https://www.cosec.ac.uk/

.. image:: _static/logos/CCPBioSim-logo.png
   :height: 100px
   :target: https://www.ccpbiosim.ac.uk/

Indices and tables
------------------

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