{"id":37610805,"url":"https://github.com/adicksonlab/csnanalysis","last_synced_at":"2026-01-16T10:20:23.244Z","repository":{"id":88374348,"uuid":"123935042","full_name":"ADicksonLab/CSNAnalysis","owner":"ADicksonLab","description":"Tools for creating, analyzing and visualizing Conformation Space Networks","archived":false,"fork":false,"pushed_at":"2022-08-31T20:29:59.000Z","size":712,"stargazers_count":16,"open_issues_count":2,"forks_count":3,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-09-27T14:13:17.624Z","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ADicksonLab.png","metadata":{"files":{"readme":"README.org","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-03-05T14:55:15.000Z","updated_at":"2024-09-07T15:18:08.000Z","dependencies_parsed_at":"2023-10-20T16:20:56.587Z","dependency_job_id":null,"html_url":"https://github.com/ADicksonLab/CSNAnalysis","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/ADicksonLab/CSNAnalysis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ADicksonLab%2FCSNAnalysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ADicksonLab%2FCSNAnalysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ADicksonLab%2FCSNAnalysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ADicksonLab%2FCSNAnalysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ADicksonLab","download_url":"https://codeload.github.com/ADicksonLab/CSNAnalysis/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ADicksonLab%2FCSNAnalysis/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478049,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2026-01-16T10:20:23.137Z","updated_at":"2026-01-16T10:20:23.231Z","avatar_url":"https://github.com/ADicksonLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"* CSNAnalysis: Tools for creating, analyzing and visualizing Conformation Space Networks.\n\nCSNAnalysis is a set of tools for network-based analysis of molecular dynamics trajectories.\nTo use, initialize a `CSN` object using a matrix of transition counts.\nThe \"killer app\" of CSNAnalysis is an easy interface between enhanced sampling algorithms \n(e.g. WExplore), molecular clustering programs (e.g. MSMBuilder), graph analysis packages (e.g. networkX) \nand graph visualization programs (e.g. Gephi).\n\nCSNAnalysis is currently in beta.\n\n* Installation\n\nTo install CSNAnalysis, you can get the latest:\n\n#+begin_src bash\n  pip install git+https://github.com/ADicksonLab/CSNAnalysis\n#+end_src\n\nOr one of the releases:\n\n#+begin_src bash\n  pip install git+https://github.com/ADicksonLab/CSNAnalysis@v0.3\n#+end_src\n\n* Dependencies\n- numpy\n- scipy\n- networkx\n\n* Features\nCSNAnalysis has the following capabilities:\n\n- constructing transition probability matrices\n- trimming CSNs using a variety of criteria\n- computing committor probabilities with an arbitrary number of basins\n- export gexf files with custom node colorings\n\n* Tutorial\nSee the Jupyter Notebook in examples/examples.ipynb\n\n* Misc\n** Versioning\n\nSee [[http://semver.org/]] for version number meanings.\n\nVersion 1.0.0 will be released whenever the abstract layer API is stable. Subsequent 1.X.y releases will be made as applied and porcelain layer features are added.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadicksonlab%2Fcsnanalysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fadicksonlab%2Fcsnanalysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadicksonlab%2Fcsnanalysis/lists"}