{"id":13869929,"url":"https://github.com/choderalab/gimlet","last_synced_at":"2026-02-04T18:10:21.304Z","repository":{"id":39736891,"uuid":"182863502","full_name":"choderalab/gimlet","owner":"choderalab","description":"Graph Inference on MoLEcular Topology","archived":false,"fork":false,"pushed_at":"2023-03-25T00:21:46.000Z","size":28690,"stargazers_count":26,"open_issues_count":3,"forks_count":9,"subscribers_count":10,"default_branch":"master","last_synced_at":"2025-09-10T02:30:03.666Z","etag":null,"topics":["graph-theory","molecular-modeling","tensorflow-gpu"],"latest_commit_sha":null,"homepage":"","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/choderalab.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,"governance":null}},"created_at":"2019-04-22T20:33:12.000Z","updated_at":"2024-11-27T06:57:55.000Z","dependencies_parsed_at":"2022-08-28T23:32:50.776Z","dependency_job_id":"fb8454db-8682-4797-a0a2-59f555674f9c","html_url":"https://github.com/choderalab/gimlet","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/choderalab/gimlet","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/choderalab%2Fgimlet","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/choderalab%2Fgimlet/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/choderalab%2Fgimlet/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/choderalab%2Fgimlet/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/choderalab","download_url":"https://codeload.github.com/choderalab/gimlet/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/choderalab%2Fgimlet/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29092908,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-04T03:31:03.593Z","status":"ssl_error","status_checked_at":"2026-02-04T03:29:50.742Z","response_time":62,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: 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":["graph-theory","molecular-modeling","tensorflow-gpu"],"created_at":"2024-08-05T20:01:22.304Z","updated_at":"2026-02-04T18:10:18.880Z","avatar_url":"https://github.com/choderalab.png","language":"Python","funding_links":[],"categories":["Python"],"sub_categories":[],"readme":"\u003cdiv align=\"center\"\u003e\n   \u003cimg src=\"logo.png\" width=\"600\"\u003e\n\u003c/div\u003e\n\n\n# gimlet\nGraph Inference on MoLEcular Topology. A package for modelling, learning, and inference on molecular topological space written in Python and TensorFlow.\n\n## Dependencies\n`gimlet` doesn't depend on _any_ packages except `TensorFlow 2.0 `, and `pandas` and `pytest`, if you must.\n\n## Examples\nhttps://github.com/choderalab/gimlet/blob/master/lime/scripts/notebooks/190728_yuanqing_gn_with_gru_on_sereina_riniker_dataset.ipynb\n\n## Authors\n- yuanqing wang `\u003cyuanqing.wang@choderalab.org\u003e\u003cwangyq@wangyq.net\u003e` (while at Chodera Lab at Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, and the City College of the City University of New York.)\n\n## Manifest\n* `gin/` the core (and fun) part of the package.\n    * `i_o/` reading and writing popular molecule embedding/representing structures.\n    * `deterministic/` property predictions, conformer and charge generations. \n    * `probabilistic/` molecular machine learning through graph networks.\n* `lime/` auxiliary scripts.\n    * `for_biologists/` ready-to-use modules and scripts.\n    * `architectures/` off-the-shelf model architectures developed elsewhere.\n    * `scripts/` fun scripts we used to generate data and hypothesis.\n    * `trained_models/` _Nomen est omen_.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchoderalab%2Fgimlet","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchoderalab%2Fgimlet","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchoderalab%2Fgimlet/lists"}