{"id":18524313,"url":"https://github.com/mdanalysis/mdapackmol","last_synced_at":"2025-04-09T11:32:00.977Z","repository":{"id":66359300,"uuid":"133562584","full_name":"MDAnalysis/MDAPackmol","owner":"MDAnalysis","description":"MDAnalysis wrapper around Packmol","archived":false,"fork":false,"pushed_at":"2023-05-01T03:09:49.000Z","size":29,"stargazers_count":27,"open_issues_count":0,"forks_count":10,"subscribers_count":10,"default_branch":"master","last_synced_at":"2024-10-29T17:22:29.663Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MDAnalysis.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":"docs/contributing.rst","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.rst","dei":null}},"created_at":"2018-05-15T19:18:55.000Z","updated_at":"2024-10-24T02:25:29.000Z","dependencies_parsed_at":"2024-04-12T11:32:26.761Z","dependency_job_id":null,"html_url":"https://github.com/MDAnalysis/MDAPackmol","commit_stats":{"total_commits":36,"total_committers":1,"mean_commits":36.0,"dds":0.0,"last_synced_commit":"fa19c84005f70124bb3f8593e63f1203604756a9"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAPackmol","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAPackmol/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAPackmol/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAPackmol/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MDAnalysis","download_url":"https://codeload.github.com/MDAnalysis/MDAPackmol/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248031641,"owners_count":21036446,"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":[],"created_at":"2024-11-06T17:40:34.234Z","updated_at":"2025-04-09T11:32:00.955Z","avatar_url":"https://github.com/MDAnalysis.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"==========\nMDAPackmol\n==========\n\n.. |travis| image:: https://travis-ci.com/MDAnalysis/MDAPackmol.svg?branch=master\n    :target: https://travis-ci.com/MDAnalysis/MDAPackmol \n.. |coveralls| image:: https://coveralls.io/repos/github/MDAnalysis/MDAPackmol/badge.svg?branch=master\n    :target: https://coveralls.io/github/MDAnalysis/MDAPackmol?\n\n|travis| |coveralls|\n\n-----\n\nAn MDAnalysis_ wrapper around Packmol_\n\n* Allows combining MDAnalysis and Packmol\n\n* Preserves the topology information (bonds etc) of your system after Packmol\n\n* Free software: GNU General Public License v3\n\n.. _MDAnalysis: https://www.mdanalysis.org\n.. _Packmol: http://m3g.iqm.unicamp.br/packmol/home.shtml\n\nUsage Example\n-------------\n\n.. code-block:: python\n\n   import MDAnalysis as mda\n   import mdapackmol\n   \n   # load individual molecule files\n   water = mda.Universe('water.pdb')\n   urea = mda.Universe('urea.pdb')\n   \n   # call Packmol with MDAnalysis objects as arguments\n   # the 'instructions' allow for any valid Packmol commands\n   system = mdapackmol.packmol(\n       [mdapackmol.PackmolStructure(\n           water, number=1000,\n           instructions=['inside box 0. 0. 0. 40. 40. 40.']),\n        mdapackmol.PackmolStructure(\n           urea, number=400,\n           instructions=['inside box 0. 0. 0. 40. 40. 40.'])]\n   )\n   \n   # the returned system is a MDAnalysis Universe\n   # with all topology information from building blocks retained\n   # which can then be saved into any format\n   # eg to Lammps data file:\n   system.atoms.write('topology.data')\n\n\nCiting\n------\n\nIf you find mdapackmol useful for you, please cite the following sources:\n\n * L Martinez, R Andrade, E G Birgin, J M Martinez, \"Packmol: A package for building initial configurations for molecular dynamics simulations\". Journal of Computational Chemistry, 30, 2157-2164, 2009. \n \n * R J Gowers, M Linke, J Barnoud, T J E Reddy, M N Melo, S L Seyler, D L Dotson, J Domanski, S Buchoux, I M Kenney, and O Beckstein. \"MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations.\" In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102-109, Austin, TX, 2016.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fmdapackmol","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmdanalysis%2Fmdapackmol","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fmdapackmol/lists"}