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https://github.com/becksteinlab/mdpow

Calculation of water/solvent partition coefficients with Gromacs.

https://github.com/becksteinlab/mdpow

Science Score: 33.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
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    DOI references
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    Academic publication links
    Links to: acs.org, zenodo.org
  • ✓
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    3 of 14 committers (21.4%) from academic institutions
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    Low similarity (18.0%) to scientific vocabulary

Keywords

free-energy gromacs gromacswrapper molecular-dynamics python science

Keywords from Contributors

computational-chemistry molecular-dynamics-simulation mdanalysis molecular-simulation trajectory-analysis
Last synced: 6 months ago · JSON representation

Repository

Calculation of water/solvent partition coefficients with Gromacs.

Basic Info
  • Host: GitHub
  • Owner: Becksteinlab
  • License: gpl-3.0
  • Language: Python
  • Default Branch: develop
  • Homepage: https://mdpow.readthedocs.io
  • Size: 739 MB
Statistics
  • Stars: 28
  • Watchers: 4
  • Forks: 9
  • Open Issues: 32
  • Releases: 8
Topics
free-energy gromacs gromacswrapper molecular-dynamics python science
Created over 10 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License Authors

README.rst 

===================
 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 3.10 to 3.12.

You will also need `Gromacs`_ (currently tested with versions 4.6.5,
2018, 2020, 2021, 2022, 2023, 2024 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

Owner

  • Name: Becksteinlab
  • Login: Becksteinlab
  • Kind: organization
  • Email: obeckste@asu.edu
  • Location: Tempe, AZ

Computational Biophysics at Arizona State University

GitHub Events

Total
  • Watch event: 3
  • Fork event: 1
Last Year
  • Watch event: 3
  • Fork event: 1

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 557
  • Total Committers: 14
  • Avg Commits per committer: 39.786
  • Development Distribution Score (DDS): 0.372
Past Year
  • Commits: 16
  • Committers: 1
  • Avg Commits per committer: 16.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Oliver Beckstein o****t@g****m 350
Ian Kenney i****y@a****u 96
Alexander Moriarty a****4@g****m 37
VOD555 g****8@h****m 36
Bogdan Iorga b****a@i****r 12
Cade Duckworth 1****h 9
Alia Lescoulie 7****e 9
David Dotson d****l@g****m 2
Cody c****y@q****m 1
Ryan Heilman r****a@a****u 1
Bogdan Iorga i****a@d****r 1
Bogdan Iorga i****a@d****r 1
Bogdan Iorga i****a@p****r 1
Ian Kenney I****y 1
Committer Domains (Top 20 + Academic)
asu.edu: 2 piccolo.icsn.cnrs-gif.fr: 1 datura2.icsn.cnrs-gif.fr: 1 datura.icsn.cnrs-gif.fr: 1 quantifiedcode.com: 1 icsn.cnrs-gif.fr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 75
  • Total pull requests: 67
  • Average time to close issues: 8 months
  • Average time to close pull requests: 2 months
  • Total issue authors: 7
  • Total pull request authors: 6
  • Average comments per issue: 1.75
  • Average comments per pull request: 5.46
  • Merged pull requests: 56
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 9
  • Pull requests: 6
  • Average time to close issues: about 14 hours
  • Average time to close pull requests: about 1 hour
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.78
  • Average comments per pull request: 1.33
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • orbeckst (44)
  • cadeduckworth (14)
  • VOD555 (5)
  • ALescoulie (5)
  • iorga (4)
  • a-ws-m (2)
  • rsexton2 (1)
Pull Request Authors
  • orbeckst (23)
  • VOD555 (14)
  • cadeduckworth (13)
  • ALescoulie (11)
  • a-ws-m (4)
  • ianmkenney (2)
Top Labels
Issue Labels
bug (16) testing (13) refactoring (8) installation (7) docs (7) CI (6) analysis (6) release (5) Python 3 (4) scripts (4) forcefield (4) configuration (3) enhancement (3) workflows (3) wontfix (2) question (1) help wanted (1) work in progress (1)
Pull Request Labels
analysis (3) enhancement (3) work in progress (3) bug (2) configuration (1) testing (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 36 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 5
  • Total maintainers: 1
pypi.org: mdpow

A library for computing solvation/water partitioning coefficients using molecular dynamics simulations

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 36 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 10.9%
Stargazers count: 13.0%
Dependent repos count: 21.6%
Average: 23.8%
Downloads: 63.7%
Maintainers (1)
Oliver.Beckstein
Last synced: 6 months ago

Dependencies

doc/requirements.txt pypi
  • GromacsWrapper >=0.5.1
  • alchemlyb *
  • mdanalysis *
  • numpy *
  • pandas *
  • pyyaml *
  • scipy *
  • six *
setup.py pypi
  • GromacsWrapper >=0.5.1
  • alchemlyb *
  • mdanalysis *
  • numkit *
  • numpy >=1.6
  • pandas *
  • pymbar *
  • pyyaml *
  • scipy *
  • six *
.github/workflows/ci.yaml actions
  • actions/checkout v3 composite
  • codecov/codecov-action v3 composite
  • mamba-org/provision-with-micromamba main composite
.github/workflows/black.yaml actions
  • actions/checkout v3 composite
  • psf/black stable composite
.github/workflows/deploy.yaml actions
  • MDAnalysis/pypi-deployment main composite
  • actions/checkout v4 composite