{"id":23280296,"url":"https://github.com/moldyn/hp35-benchmark","last_synced_at":"2025-04-06T13:30:46.094Z","repository":{"id":53699597,"uuid":"241328376","full_name":"moldyn/HP35-Benchmark","owner":"moldyn","description":"Benchmarking dimensionality reduction methods and clustering on HP35-DESRES","archived":false,"fork":false,"pushed_at":"2022-08-05T06:50:12.000Z","size":30,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-12T19:45:47.799Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/moldyn.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-02-18T10:04:23.000Z","updated_at":"2022-08-05T06:47:34.000Z","dependencies_parsed_at":"2022-08-28T19:30:26.944Z","dependency_job_id":null,"html_url":"https://github.com/moldyn/HP35-Benchmark","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FHP35-Benchmark","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FHP35-Benchmark/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FHP35-Benchmark/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FHP35-Benchmark/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/moldyn","download_url":"https://codeload.github.com/moldyn/HP35-Benchmark/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247488281,"owners_count":20946913,"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":"2024-12-19T23:31:43.807Z","updated_at":"2025-04-06T13:30:46.057Z","avatar_url":"https://github.com/moldyn.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![wemake-python-styleguide](https://img.shields.io/badge/style-wemake-000000.svg)](https://github.com/wemake-services/wemake-python-styleguide)\n# HP35-Benchmark\nBenchmarking dimensionality reduction methods and clustering on [HP35-DESRES](https://github.com/moldyn/HP35-DESRES).\n\nThis is package automatizes the comparison of  different clustring and dimensionality reduction methods and its effects on the resulting Markov state models. So far, only the result of Nagel et al. 19 are reproduced. Comparison methods will follow soon.\n\nIf the provided scripts are used, please cite:\n- D. Nagel, A. Weber, B. Lickert and G. Stock, *Dynamical coring of Markov state models*, J. Chem. Phys., 150, 094111, 2019; DOI: [10.1063/1.5081767](https://aip.scitation.org/doi/10.1063/1.5081767)\n\n## Getting ready\nSimply clone this repository with\n```bash\ngit clone --recurse-submodules git://github.com/moldyn/HP35-Benchmark.git\ncd HP35-Benchmark\n```\n\nReproducing the published state trajectory can be achieved with\n```bash\ncd clustering \u0026\u0026 bash robust_clustering\n```\nUntil our python package [msmhelper](https://moldyn.github.io/msmhelper) is available, the states are not renamed by their population.\n\n## Add Own Routine\nFor an example take a look at [robust_clustering](https://github.com/moldyn/HP35-Benchmark/blob/master/clustering/robust_clustering)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoldyn%2Fhp35-benchmark","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmoldyn%2Fhp35-benchmark","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoldyn%2Fhp35-benchmark/lists"}