{"id":33175264,"url":"https://github.com/drorlab/atom3d","last_synced_at":"2026-03-17T23:13:09.349Z","repository":{"id":41194065,"uuid":"252859599","full_name":"drorlab/atom3d","owner":"drorlab","description":"ATOM3D: tasks on molecules in three dimensions","archived":false,"fork":false,"pushed_at":"2023-03-02T18:21:02.000Z","size":42689,"stargazers_count":315,"open_issues_count":22,"forks_count":35,"subscribers_count":14,"default_branch":"master","last_synced_at":"2025-11-20T20:03:01.789Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://www.atom3d.ai","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/drorlab.png","metadata":{"files":{"readme":"README.md","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":null}},"created_at":"2020-04-03T22:53:11.000Z","updated_at":"2025-11-18T12:13:02.000Z","dependencies_parsed_at":"2024-01-13T11:57:55.738Z","dependency_job_id":"f489ba17-ecc0-4670-acdf-cbf6950c8ed5","html_url":"https://github.com/drorlab/atom3d","commit_stats":null,"previous_names":[],"tags_count":16,"template":false,"template_full_name":null,"purl":"pkg:github/drorlab/atom3d","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drorlab%2Fatom3d","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drorlab%2Fatom3d/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drorlab%2Fatom3d/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drorlab%2Fatom3d/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/drorlab","download_url":"https://codeload.github.com/drorlab/atom3d/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drorlab%2Fatom3d/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30635157,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-17T22:38:22.569Z","status":"ssl_error","status_checked_at":"2026-03-17T22:38:11.804Z","response_time":56,"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":"2025-11-16T02:00:37.344Z","updated_at":"2026-03-17T23:13:09.332Z","avatar_url":"https://github.com/drorlab.png","language":"Python","funding_links":[],"categories":["Machine Learning"],"sub_categories":[],"readme":"# ATOM3D: Tasks On Molecules in 3 Dimensions\n\n[![Documentation\nStatus](https://readthedocs.org/projects/atom3d/badge/?version=latest)](http://atom3d.readthedocs.io/?badge=latest)\n![Package](https://github.com/drorlab/atom3d/workflows/package/badge.svg)\n[![codecov](https://codecov.io/gh/drorlab/atom3d/branch/master/graph/badge.svg?token=DHH78W45AB)](https://codecov.io/gh/drorlab/atom3d)\n[![PyPI version](https://badge.fury.io/py/atom3d.svg)](https://badge.fury.io/py/atom3d)\n\n[ATOM3D](https://www.atom3d.ai/) enables machine learning on three-dimensional molecular structure.\n\n## Features\n\n* Access to several datasets involving 3D molecular structure. \n* LMDB data format for storing lots of molecules (and associated metadata).\n* Utilities for splitting/filtering data based on many criteria.\n\nFor more detailed information, [read the documentation](https://atom3d.readthedocs.io/en/latest/).\n\n## Installation\n\nInstall with:\n\n```\npip install atom3d\n```\n    \nTo use rdkit functionality, please install within conda:\n\n```\nconda create -n atom3d python=3.6 pip rdkit\nconda activate atom3d\npip install atom3d\n```\n\n## Usage\n\n\n### Downloading a dataset\n\nFrom python:\n```\nimport atom3d.datasets as da\nda.download_dataset('lba', PATH_TO_DATASET) # Download LBA dataset.\n```\n\nOr, download and unzip from the [website](https://www.atom3d.ai/).\n\n### Loading a dataset\n\nFrom python:\n```\nimport atom3d.datasets as da\ndataset = da.load_dataset(PATH_TO_DATASET, {'lmdb','pdb','silent','sdf','xyz','xyz-gdb'})\nprint(len(dataset))  # Print length\nprint(dataset[0].keys())  # Print keys\n```\n\n### LMDB datasets\n\nLMDB allows for compressed, fast, random access to your structures, all within a\nsingle database.  Currently, we support creating LMDB datasets from PDB files, silent files, and xyz files.\n\n#### Creating an LMDB dataset\n\nFrom command line:\n```\npython -m atom3d.datasets PATH_TO_PDB_DIR PATH_TO_DATASET --filetype {pdb,silent,xyz,xyz-gdb} \n```\n\nFor more usage, please see the [documentation](https://atom3d.readthedocs.io/en/latest/).\n\n## Contribute\n\nAs a living repository, we welcome contributions of additional datasets, methods, and functionality!  See the [Contributing](https://atom3d.readthedocs.io/en/latest/contributing.html) section of the documentation for details.\n\n## Support\n\nFor support, please file an issue at https://github.com/drorlab/atom3d/issues.\n\n## License\n\nThe project is licensed under the [MIT license](https://github.com/drorlab/atom3d/blob/master/LICENSE).\n\n## Reference\n\nWe provide an overview on ATOM3D and details on the preparation of all datasets in our preprint:\n\n\u003e R. J. L. Townshend, M. Vögele, P. Suriana, A. Derry, A. Powers, Y. Laloudakis, S. Balachandar, B. Jing, B. Anderson, S. Eismann, R. Kondor, R. B. Altman, R. O. Dror \"ATOM3D: Tasks On Molecules in Three Dimensions\", [arXiv:2012.04035](https://arxiv.org/abs/2012.04035)\n  \nPlease cite this work if some of the ATOM3D code or datasets are helpful in your scientific endeavours. For specific datasets, please also cite the respective original source(s), given in the preprint.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdrorlab%2Fatom3d","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdrorlab%2Fatom3d","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdrorlab%2Fatom3d/lists"}