{"id":16466510,"url":"https://github.com/lukasturcani/atomlite","last_synced_at":"2025-07-07T19:34:43.603Z","repository":{"id":161081987,"uuid":"635415071","full_name":"lukasturcani/atomlite","owner":"lukasturcani","description":"Store your chemical data in a single file!","archived":false,"fork":false,"pushed_at":"2024-04-25T10:26:24.000Z","size":104,"stargazers_count":12,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-05-01T15:31:42.526Z","etag":null,"topics":["cheminformatics","chemistry","database"],"latest_commit_sha":null,"homepage":"https://atomlite.readthedocs.io","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/lukasturcani.png","metadata":{"files":{"readme":"README.rst","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-05-02T16:37:54.000Z","updated_at":"2024-04-25T10:26:26.000Z","dependencies_parsed_at":null,"dependency_job_id":"94a073c6-f217-40c4-9f34-70c169d41b82","html_url":"https://github.com/lukasturcani/atomlite","commit_stats":{"total_commits":43,"total_committers":1,"mean_commits":43.0,"dds":0.0,"last_synced_commit":"4ee29e38a84d7ba00f56c511bfb0844c6463b829"},"previous_names":[],"tags_count":25,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lukasturcani%2Fatomlite","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lukasturcani%2Fatomlite/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lukasturcani%2Fatomlite/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lukasturcani%2Fatomlite/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lukasturcani","download_url":"https://codeload.github.com/lukasturcani/atomlite/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243826788,"owners_count":20354220,"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":["cheminformatics","chemistry","database"],"created_at":"2024-10-11T11:43:55.940Z","updated_at":"2025-03-16T18:31:26.760Z","avatar_url":"https://github.com/lukasturcani.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":":Author: Lukas Turcani\n:Docs: https://atomlite.readthedocs.io\n\n========\nAtomLite\n========\n\nAtomLite is a Python library for simple molecular database on top of SQLite_.\n\nFor an alternative to AtomLite, which provides stronger integration with RDKit, and a\ngreater focus on cheminformatics, see chemicalite_.\n\n.. _SQLite: https://docs.python.org/3/library/sqlite3.html\n.. _chemicalite: https://github.com/rvianello/chemicalite\n\n\nInstallation\n============\n\n.. code-block:: bash\n\n  pip install atomlite\n\nQuickstart\n==========\n\nYou can see a lot more examples in our docs_ but here is a taste of using\nAtomLite:\n\n.. code-block:: python\n\n  import atomlite\n  import rdkit.Chem as rdkit\n  # Create a database.\n  db = atomlite.Database(\"molecules.db\")\n  # Create database entries.\n  entry1 = atomlite.Entry.from_rdkit(\"first\", rdkit.MolFromSmiles(\"C\"), {\"prop1\": \"hi\", \"prop2\": 100})\n  entry2 = atomlite.Entry.from_rdkit(\"second\", rdkit.MolFromSmiles(\"CN\"), {\"prop1\": \"thing\", \"prop2\": 203})\n  # Add entries to database.\n  db.add_entries([entry1, entry2])\n  # Retrieve entries from database.\n  for entry in db.get_entries([\"first\", \"second\"]):\n    molecule = atomlite.json_to_rdkit(entry.molecule)\n    print(entry.properties)\n\n::\n\n  {'prop1': 'hi', 'prop2': 100}\n  {'prop1': 'thing', 'prop2': 203}\n\n.. code-block:: python\n\n  db.get_property_df([\"$.prop1\", \"$.prop2\"])\n\n::\n\n  shape: (2, 3)\n  ┌────────┬─────────┬─────────┐\n  │ key    ┆ $.prop1 ┆ $.prop2 │\n  │ ---    ┆ ---     ┆ ---     │\n  │ str    ┆ str     ┆ i64     │\n  ╞════════╪═════════╪═════════╡\n  │ first  ┆ hi      ┆ 100     │\n  │ second ┆ thing   ┆ 203     │\n  └────────┴─────────┴─────────┘\n\n.. _docs: https://atomlite.readthedocs.io\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flukasturcani%2Fatomlite","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flukasturcani%2Fatomlite","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flukasturcani%2Fatomlite/lists"}