{"id":18718021,"url":"https://github.com/rdkit/mongo-rdkit","last_synced_at":"2025-10-14T04:14:40.713Z","repository":{"id":52687179,"uuid":"267522173","full_name":"rdkit/mongo-rdkit","owner":"rdkit","description":"GSoC 2020 project to integrate the RDKit and MongoDb","archived":false,"fork":false,"pushed_at":"2024-04-08T15:45:22.000Z","size":266,"stargazers_count":16,"open_issues_count":1,"forks_count":7,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-08-11T23:34:34.556Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/rdkit.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2020-05-28T07:25:40.000Z","updated_at":"2024-02-26T02:15:25.000Z","dependencies_parsed_at":"2025-04-12T13:49:28.996Z","dependency_job_id":"85ffd2df-73a5-4ba0-b798-6d356df7ab8e","html_url":"https://github.com/rdkit/mongo-rdkit","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/rdkit/mongo-rdkit","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rdkit%2Fmongo-rdkit","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rdkit%2Fmongo-rdkit/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rdkit%2Fmongo-rdkit/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rdkit%2Fmongo-rdkit/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rdkit","download_url":"https://codeload.github.com/rdkit/mongo-rdkit/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rdkit%2Fmongo-rdkit/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279017984,"owners_count":26086213,"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","status":"online","status_checked_at":"2025-10-14T02:00:06.444Z","response_time":60,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":"2024-11-07T13:19:07.508Z","updated_at":"2025-10-14T04:14:40.685Z","avatar_url":"https://github.com/rdkit.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# mongo-rdkit\n[![Build Status](https://dev.azure.com/cwzou/mongo-rdkit/_apis/build/status/rdkit.mongo-rdkit?branchName=master)](https://dev.azure.com/cwzou/mongo-rdkit/_build/latest?definitionId=1\u0026branchName=master)\n\n\u003ca href=\"https://github.com/rdkit/mongo-rdkit\"\u003eMongo-rdkit\u003c/a\u003e is an integration between MongoDB, \na NoSQL database platform, and RDKit, a collection of cheminformatics and machine-learning software.\nThis package contains tools to create and manipulate a chemically-intelligent database, as well as\nmethods for high-performance searches on the database that leverage native MongoDB features.\n\nUseful links: \n* [BSD License](https://github.com/rdkit/mongo-rdkit/blob/master/LICENSE) - a business friendly license for open-source.\n* [Jupyter Notebooks](https://github.com/rdkit/mongo-rdkit/tree/master/docs) - walkthroughs for main functionality.\n* [Testing Guide](https://github.com/rdkit/mongo-rdkit/blob/master/docs/testing.md) - walkthrough of running `mongordkit` tests.\n\n## Documentation\nJupyter Notebooks and resources for getting started in the [docs](https://github.com/rdkit/mongo-rdkit/tree/master/docs) \nfolder on GitHub.\n\n## Installation\n\n### macOS and Linux:\nEnsure that you have either Anaconda or Miniconda installed and that `conda` has been added to `PATH`.\n\nClone the repository into your desired directory.\n\nNavigate so that your current working directory is `mongo-rdkit`.\n\nCreate a conda environment called mongo_rdkit that includes all dependencies needed for this package: \n```\nconda env create --quiet --force --file env.yml\n```\nActivate said conda environment:\n```\nsource activate mongo_rdkit\n```\nInstall a local copy of mongo-rdkit by running this from the same directory as `setup.py` (`mongo-rdkit` is not yet published to PyPI):\n```\npip install -e .\n```\n\nYou can now `import mongordkit` in your Python interpreter or run all tests using the `pytest` command.\n\n### Windows:\nSimilarly, ensure that `conda` has been added to `PATH`.\n\nClone the repository into your desired directory and navigate into it.\n\nCreate a conda environment called mongo_rdkit that includes dependencies:\n```\nconda env create --quiet --force --file env.yml\n```\nActivate this conda environment: \n```\ncall activate mongo_rdkit\n```\nCheck that you are able to import mongordkit:\n```\npython -c \"import mongordkit\"\n```\nIf this fails, you may need to add the current directory manually to `PYTHONPATH`:\n```\nset PYTHONPATH=%PYTHONPATH%;C:.\n```\nYou can now use `mongordkit` in your interpreter and run tests using `python -m pytest`.\n## Package Contents\n### Modules\n`mongordkit` contains two main modules, each of which contains a variety of importable methods and classes.\n`Database` contains functionality for writing and registering data. `Search` contains functionality for setting up and performing\nsubstructure and similarity search. Detailed walkthroughs can be found in the notebooks, listed below.\n\n### Notebooks\n- **Creating and Writing to MongoDB**: documentation and demos for creating and modifying mongo-rdkit databases.\n- **Similarity and Substructure Search**: documentation and demos for similarity and substructure search.\n- **Similarity Benchmarking**: documentation for reproducing similarity benchmarking.\n- **Substructure Benchmarking**: documentation for reproducing substructure benchmarking.\n\n### Configuration\n- **azure_pipelines.yml**: CI/CD pipeline configurations.\n- **conftest.py**: `pytest` configurations.\n- **env.yml**: required dependencies.\n- **setup.py**: python package setup including pip dependencies\n\n## License\nCode released under the BSD License.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frdkit%2Fmongo-rdkit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frdkit%2Fmongo-rdkit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frdkit%2Fmongo-rdkit/lists"}