=================== README for MDPOW

|build| |cov| |docs| |black| |zenodo|

.. |P_ow| replace:: P\ :sub:OW .. |P_cw| replace:: P\ :sub:CW .. |P_tw| replace:: P\ :sub:TW

MDPOW is a python package that automates the calculation of solvation free energies via molecular dynamics (MD) simulations. In particular, it facilitates the computation of partition coefficients. Currently implemented:

• water-octanol partition coefficient (|P_ow|)
• water-cyclohexane partition coefficient (|P_cw|)
• water-toluene partition coefficient (|P_tw|)

Calculations are performed with the Gromacs_ MD software package [#GromacsWrapperNote]_. Currently, OPLS-AA, CHARMM/CGENFF, and AMBER/GAFF parameters are supported.

As input, the user only needs to provide a structure file (PDB or GRO) and a Gromacs ITP file containing the parametrization of the small molecule (e.g. from LigandBook_ or ParamChem_).

.. _Gromacs: http://www.gromacs.org .. _GromacsWrapper: http://gromacswrapper.readthedocs.org/en/latest/ .. _LigandBook: http://ligandbook.org/ .. _ParamChem: https://cgenff.paramchem.org/

Documentation

• https://mdpow.readthedocs.io
• Tutorial_ : computing the octanol-water partition coefficient of benzene (uses the example files_)

.. _Tutorial: http://mdpow.readthedocs.io/en/latest/init.html#tutorial-using-the-mdpow-scripts-to-compute-logpow-of-benzene .. _example files: https://github.com/Becksteinlab/MDPOW/tree/develop/doc/examples

Installation

See INSTALL_ for detailed instructions. MDPOW currently supports and is tested with Python 3.8 to 3.10.

You will also need Gromacs_ (currently tested with versions 4.6.5, 2018, 2020, 2021, 2022, 2023 but 2016 and 2019 should also work).

Development version

If you want to install the development version, get the sources from
GitHub (the development branch) ::

  git clone https://github.com/Becksteinlab/MDPOW.git

and Install from the checked out source::

  pip install MDPOW/

(Note the trailing slash ``/`` to indicate the directory.)



Source code
-----------

*MDPOW* is open source and published under the `GNU General Public License
v3`_. Source code is available at https://github.com/Becksteinlab/MDPOW .

We use `black`_ for uniform code formatting.

.. _`GNU General Public License v3`:
   http://www.gnu.org/licenses/gpl-3.0.html

.. _`black`: https://github.com/psf/black


Footnotes
---------

.. [#GromacsWrapperNote] The package is built on top of the GromacsWrapper_
                         framework (which is automatically installed).

.. |build| image:: https://github.com/Becksteinlab/MDPOW/actions/workflows/ci.yaml/badge.svg?branch=develop
   :alt: Build Status
   :target: https://github.com/Becksteinlab/MDPOW/actions/workflows/ci.yaml

.. |cov| image:: https://codecov.io/github/Becksteinlab/MDPOW/coverage.svg?branch=develop
   :alt: Coverage Status
   :target: https://codecov.io/github/Becksteinlab/MDPOW?branch=develop

.. |docs| image:: https://readthedocs.org/projects/mdpow/badge/?version=latest
   :target: http://mdpow.readthedocs.org/en/latest/?badge=latest
   :alt: Documentation
   
.. |zenodo| image:: https://zenodo.org/badge/44999898.svg
   :target: https://zenodo.org/badge/latestdoi/44999898
   :alt: Zenodo

.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
   :target: https://github.com/psf/black	 
   :alt: black   

.. _INSTALL: INSTALL.rst