{"id":15690397,"url":"https://github.com/michelml/chempp","last_synced_at":"2025-05-07T23:35:56.462Z","repository":{"id":51085705,"uuid":"367966758","full_name":"MichelML/chempp","owner":"MichelML","description":"[paused development] Large scale concurrent chemical search using RDKit cartridge, Oat++ and native Postgres \u0026 C++ features.","archived":false,"fork":false,"pushed_at":"2022-08-22T15:29:33.000Z","size":102,"stargazers_count":9,"open_issues_count":6,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-26T05:41:30.940Z","etag":null,"topics":["cheminformatics","cpp","oatpp","postgresql","rdkit"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MichelML.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-05-16T19:20:19.000Z","updated_at":"2024-09-13T00:09:57.000Z","dependencies_parsed_at":"2022-09-03T10:12:11.562Z","dependency_job_id":null,"html_url":"https://github.com/MichelML/chempp","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MichelML%2Fchempp","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MichelML%2Fchempp/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MichelML%2Fchempp/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MichelML%2Fchempp/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MichelML","download_url":"https://codeload.github.com/MichelML/chempp/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243042922,"owners_count":20226722,"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","cpp","oatpp","postgresql","rdkit"],"created_at":"2024-10-03T18:08:58.145Z","updated_at":"2025-03-11T13:32:02.196Z","avatar_url":"https://github.com/MichelML.png","language":"C++","readme":"**Paused Development** \n\n[![Contributors][contributors-shield]][contributors-url]\n[![Forks][forks-shield]][forks-url]\n[![Stargazers][stars-shield]][stars-url]\n[![Issues][issues-shield]][issues-url]\n[![Apache License][license-shield]][license-url]\n[![LinkedIn][linkedin-shield]][linkedin-url]\n\n\n\u003cbr /\u003e\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://github.com/michelml/chempp\"\u003e\n    \u003cimg src=\"chempp.png\" alt=\"Chempp - Project Logo\" width=\"200\" height=\"200\"\u003e\n  \u003c/a\u003e\n\n  \u003cp align=\"center\"\u003e\n    [Large scale] concurrent chemical search engine using RDKit cartridge, Oat++ and native Postgres \u0026 C++ features.\n    \u003cbr /\u003e\n    \u003ca href=\"https://github.com/michelml/chempp\"\u003e\u003cstrong\u003eExplore the docs »\u003c/strong\u003e\u003c/a\u003e\n    \u003cbr /\u003e\n    \u003cbr /\u003e\n    \u003ca href=\"https://github.com/michelml/chempp\"\u003eView Demo\u003c/a\u003e\n    ·\n    \u003ca href=\"https://github.com/michelml/chempp/issues\"\u003eReport Bug\u003c/a\u003e\n    ·\n    \u003ca href=\"https://github.com/michelml/chempp/issues\"\u003eRequest Feature\u003c/a\u003e\n  \u003c/p\u003e\n\u003c/p\u003e\n\n\n\n\u003c!-- TABLE OF CONTENTS --\u003e\n\u003cdetails open=\"open\"\u003e\n  \u003csummary\u003e\u003ch2 style=\"display: inline-block\"\u003eTable of Contents\u003c/h2\u003e\u003c/summary\u003e\n  \u003col\u003e\n    \u003cli\u003e\n      \u003ca href=\"#about-the-project\"\u003eAbout The Project\u003c/a\u003e\n      \u003cul\u003e\n        \u003cli\u003e\u003ca href=\"#built-with\"\u003eBuilt With\u003c/a\u003e\u003c/li\u003e\n      \u003c/ul\u003e\n    \u003c/li\u003e\n    \u003cli\u003e\n      \u003ca href=\"#getting-started\"\u003eInstallation\u003c/a\u003e\n      \u003cul\u003e\n        \u003cli\u003e\u003ca href=\"#prerequisites\"\u003ePrerequisites\u003c/a\u003e\u003c/li\u003e\n        \u003cli\u003e\u003ca href=\"#install-steps\"\u003eInstallation\u003c/a\u003e\u003c/li\u003e\n      \u003c/ul\u003e\n    \u003c/li\u003e\n    \u003cli\u003e\u003ca href=\"#usage\"\u003eUsage\u003c/a\u003e\u003c/li\u003e\n    \u003cli\u003e\u003ca href=\"#roadmap\"\u003eRoadmap\u003c/a\u003e\u003c/li\u003e\n    \u003cli\u003e\u003ca href=\"#contributing\"\u003eContributing\u003c/a\u003e\u003c/li\u003e\n    \u003cli\u003e\u003ca href=\"#license\"\u003eLicense\u003c/a\u003e\u003c/li\u003e\n    \u003cli\u003e\u003ca href=\"#contact\"\u003eContact\u003c/a\u003e\u003c/li\u003e\n    \u003cli\u003e\u003ca href=\"#acknowledgements\"\u003eAcknowledgements\u003c/a\u003e\u003c/li\u003e\n  \u003c/ol\u003e\n\u003c/details\u003e\n\n\u003c!-- ABOUT THE PROJECT --\u003e\n## About The Project\n\n**chempp** [kem-pee-pee], is a large scale concurrent chemical search engine using RDKit cartridge, Oat++ and native Postgres \u0026 C++ features.\n\n### Built With\n\n* [Oat++](https://oatpp.io/)\n* [PostgreSQL RDKit cartridge](https://rdkit.org/docs/Cartridge.html)\n* [PostgreSQL](https://www.postgresql.org/)\n* Special mention to Arthur Farias for his very well crafted [url encoding/decoding C++ gist](https://gist.github.com/arthurafarias/56fec2cd49a32f374c02d1df2b6c350f)\n\n## Installation\n\n### Prerequisites\n\n- Knowledge of what a [SMILES](https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system) is in chemistry\n- Knowledge of what a [SMARTS](https://en.wikipedia.org/wiki/SMILES_arbitrary_target_specification) is in chemistry\n- [Git](https://git-scm.com/)\n- [Docker and Docker-Compose](https://www.docker.com/)\n\n### Install steps\n\nClone the project\n\n```bash\ngit clone https://github.com/MichelML/chempp.git \u0026\u0026 \\\ncd chempp\n```\n\nThen, start the db and fill it with molecules. You have two options:\n\n#### Option 1 - Small Database of 1000 molecules\n\n```bash\ndocker-compose up -d db \u0026\u0026 \\\ndocker-compose exec db bash -c \"SMALLDB=1 /utility/populate_db.sh\"\n```\n\n#### Option 2 - Large database of ~3M compounds\n\n```bash\ndocker-compose up -d db \u0026\u0026 \\\ndocker-compose exec db bash -c \"/utility/populate_db.sh\"\n```\n\n\u003e **Warning:** This command will take a while because it inserts ~3M rows in the db and [creates indexes to perform efficient searches](https://rdkit.org/docs/Cartridge.html), a rough estimate being between 15 minutes and an hour.\n\nLastly, start the chempp service:\n\n```bash\ndocker-compose up service\n```\n\nOnce these commands are ran, you are ready to test the endpoints at http://localhost:8000/swagger/ui .\n\n\u003c!-- USAGE EXAMPLES --\u003e\n## Usage\n\nSee usage through Swagger demo here https://drive.google.com/file/d/1FKh3-N4KWvVEz7NPFmMDALWu-BzYbaHP/view?usp=sharing .\n\n\u003c!-- ROADMAP --\u003e\n## Roadmap\n\nSee the [open issues](https://github.com/michelml/chempp/issues) for a list of proposed features (and known issues).\n\n\u003c!-- CONTRIBUTING --\u003e\n## Contributing\n\nContributions are what make the open source community such an amazing place to be learn, inspire, and create. Any contributions you make are **greatly appreciated**.\n\n1. Fork the Project\n2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`)\n3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`)\n4. Push to the Branch (`git push origin feature/AmazingFeature`)\n5. Open a Pull Request\n\nMake sure to format your code properly with `make format`.\n\n\u003c!-- LICENSE --\u003e\n## License\n\nDistributed under the Apache-2.0 License. See `LICENSE` for more information.\n\n\n\n\u003c!-- CONTACT --\u003e\n## Contact\n\nMichel ML - [@michelml](https://github.com/MichelML) - michmoreau.l@gmail.com\n\nProject Link: [https://github.com/michelml/chempp](https://github.com/michelml/chempp)\n\n\u003c!-- ACKNOWLEDGEMENTS --\u003e\n## Acknowledgements\n\nThank you to all contributors of libraries and tools used in this project.\n\n\u003c!-- MARKDOWN LINKS \u0026 IMAGES --\u003e\n\u003c!-- https://www.markdownguide.org/basic-syntax/#reference-style-links --\u003e\n[contributors-shield]: https://img.shields.io/github/contributors/michelml/chempp.svg?style=for-the-badge\n[contributors-url]: https://github.com/michelml/chempp/graphs/contributors\n[forks-shield]: https://img.shields.io/github/forks/michelml/chempp.svg?style=for-the-badge\n[forks-url]: https://github.com/michelml/chempp/network/members\n[stars-shield]: https://img.shields.io/github/stars/michelml/chempp.svg?style=for-the-badge\n[stars-url]: https://github.com/michelml/chempp/stargazers\n[issues-shield]: https://img.shields.io/github/issues/michelml/chempp.svg?style=for-the-badge\n[issues-url]: https://github.com/michelml/chempp/issues\n[license-shield]: https://img.shields.io/github/license/michelml/chempp.svg?style=for-the-badge\n[license-url]: https://github.com/michelml/chempp/blob/master/LICENSE.txt\n[linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=for-the-badge\u0026logo=linkedin\u0026colorB=555\n[linkedin-url]: https://www.linkedin.com/in/michelmoreau1/\n[product-screenshot]: chempp.png\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmichelml%2Fchempp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmichelml%2Fchempp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmichelml%2Fchempp/lists"}