{"id":19339505,"url":"https://github.com/becksteinlab/mdpow","last_synced_at":"2025-06-30T06:04:12.392Z","repository":{"id":2908028,"uuid":"44999898","full_name":"Becksteinlab/MDPOW","owner":"Becksteinlab","description":"Calculation of water/solvent partition coefficients with Gromacs.","archived":false,"fork":false,"pushed_at":"2024-10-14T20:03:58.000Z","size":775340,"stargazers_count":26,"open_issues_count":32,"forks_count":9,"subscribers_count":4,"default_branch":"develop","last_synced_at":"2025-04-09T20:08:04.937Z","etag":null,"topics":["free-energy","gromacs","gromacswrapper","molecular-dynamics","python","science"],"latest_commit_sha":null,"homepage":"https://mdpow.readthedocs.io","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Becksteinlab.png","metadata":{"files":{"readme":"README.rst","changelog":"CHANGES","contributing":null,"funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-10-26T21:58:15.000Z","updated_at":"2025-01-03T11:42:29.000Z","dependencies_parsed_at":"2024-11-10T03:34:49.734Z","dependency_job_id":null,"html_url":"https://github.com/Becksteinlab/MDPOW","commit_stats":{"total_commits":557,"total_committers":14,"mean_commits":"39.785714285714285","dds":"0.37163375224416517","last_synced_commit":"4a46ac2e696030e30d13f5815a7c4409d29eaf5a"},"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FMDPOW","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FMDPOW/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FMDPOW/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FMDPOW/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Becksteinlab","download_url":"https://codeload.github.com/Becksteinlab/MDPOW/tar.gz/refs/heads/develop","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248103872,"owners_count":21048245,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["free-energy","gromacs","gromacswrapper","molecular-dynamics","python","science"],"created_at":"2024-11-10T03:22:32.726Z","updated_at":"2025-04-09T20:08:14.389Z","avatar_url":"https://github.com/Becksteinlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"===================\n README for MDPOW\n===================\n\n|build| |cov| |docs| |black| |zenodo|\n\n.. |P_ow| replace:: *P*\\ :sub:`OW`\n.. |P_cw| replace:: *P*\\ :sub:`CW`\n.. |P_tw| replace:: *P*\\ :sub:`TW`  \n\n*MDPOW* is a python package that automates the calculation of\nsolvation free energies via molecular dynamics (MD) simulations. In\nparticular, it facilitates the computation of partition\ncoefficients. Currently implemented:\n\n- *water-octanol* partition coefficient (|P_ow|)\n- *water-cyclohexane* partition coefficient (|P_cw|)\n- *water-toluene* partition coefficient (|P_tw|)\n  \nCalculations are performed with the Gromacs_ MD software package\n[#GromacsWrapperNote]_. Currently, *OPLS-AA*, *CHARMM/CGENFF*, and\n*AMBER/GAFF* parameters are supported.\n\nAs *input*, the user only needs to provide a structure file (PDB or\nGRO) and a Gromacs ITP file containing the parametrization of the\nsmall molecule (e.g. from LigandBook_ or ParamChem_).\n\n.. _Gromacs: http://www.gromacs.org\n.. _GromacsWrapper: http://gromacswrapper.readthedocs.org/en/latest/\n.. _LigandBook: http://ligandbook.org/\n.. _ParamChem: https://cgenff.paramchem.org/\n\n\nDocumentation\n-------------\n\n* https://mdpow.readthedocs.io\n* `Tutorial`_ : computing the octanol-water partition coefficient of\n  benzene (uses the `example files`_)\n\n\n.. _Tutorial: http://mdpow.readthedocs.io/en/latest/init.html#tutorial-using-the-mdpow-scripts-to-compute-logpow-of-benzene\n.. _example files: https://github.com/Becksteinlab/MDPOW/tree/develop/doc/examples\n\nInstallation\n------------\n\nSee `INSTALL`_ for detailed instructions. MDPOW currently supports and\nis tested with Python 3.10 to 3.12.\n\nYou will also need `Gromacs`_ (currently tested with versions 4.6.5,\n2018, 2020, 2021, 2022, 2023, 2024 but 2016 and 2019 should also work).\n\n\nDevelopment version\n~~~~~~~~~~~~~~~~~~~\n\nIf you want to install the development version, get the sources from\nGitHub (the development branch) ::\n\n  git clone https://github.com/Becksteinlab/MDPOW.git\n\nand Install from the checked out source::\n\n  pip install MDPOW/\n\n(Note the trailing slash ``/`` to indicate the directory.)\n\n\n\nSource code\n-----------\n\n*MDPOW* is open source and published under the `GNU General Public License\nv3`_. Source code is available at https://github.com/Becksteinlab/MDPOW .\n\nWe use `black`_ for uniform code formatting.\n\n.. _`GNU General Public License v3`:\n   http://www.gnu.org/licenses/gpl-3.0.html\n\n.. _`black`: https://github.com/psf/black\n\n\nFootnotes\n---------\n\n.. [#GromacsWrapperNote] The package is built on top of the GromacsWrapper_\n                         framework (which is automatically installed).\n\n.. |build| image:: https://github.com/Becksteinlab/MDPOW/actions/workflows/ci.yaml/badge.svg?branch=develop\n   :alt: Build Status\n   :target: https://github.com/Becksteinlab/MDPOW/actions/workflows/ci.yaml\n\n.. |cov| image:: https://codecov.io/github/Becksteinlab/MDPOW/coverage.svg?branch=develop\n   :alt: Coverage Status\n   :target: https://codecov.io/github/Becksteinlab/MDPOW?branch=develop\n\n.. |docs| image:: https://readthedocs.org/projects/mdpow/badge/?version=latest\n   :target: http://mdpow.readthedocs.org/en/latest/?badge=latest\n   :alt: Documentation\n   \n.. |zenodo| image:: https://zenodo.org/badge/44999898.svg\n   :target: https://zenodo.org/badge/latestdoi/44999898\n   :alt: Zenodo\n\n.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg\n   :target: https://github.com/psf/black\t \n   :alt: black   \n\n.. _INSTALL: INSTALL.rst\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fmdpow","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecksteinlab%2Fmdpow","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fmdpow/lists"}