Metadata-Version: 2.1
Name: MDPOW
Version: 0.8.0
Summary: A library for computing solvation/water partitioning coefficients using molecular dynamics simulations
Home-page: https://github.com/Becksteinlab/MDPOW
Author: Oliver Beckstein
Author-email: orbeckst@gmail.com
License: GPLv3
Description: ===================
         README for MDPOW
        ===================
        
        |build| |cov| |docs|
        
        .. |P_ow| replace:: *P*\ :sub:`OW`
        .. |P_cw| replace:: *P*\ :sub:`CW`
        
        *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|)
        
        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 3.7 to 3.9.
        
        You will also need `Gromacs`_ (currently tested with versions 4.6.5,
        2018, 2020, 2021 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 .
        
        .. _`GNU General Public License v3`:
           http://www.gnu.org/licenses/gpl-3.0.html
        
        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
        
        .. _INSTALL: INSTALL.rst
        
Keywords: science Gromacs analysis 'molecular dynamics'
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Description-Content-Type: text/x-rst
