{"id":37610936,"url":"https://github.com/brsynth/rp3_dcache","last_synced_at":"2026-01-16T10:20:49.217Z","repository":{"id":57462782,"uuid":"211075178","full_name":"brsynth/rp3_dcache","owner":"brsynth","description":null,"archived":false,"fork":false,"pushed_at":"2021-04-28T06:16:15.000Z","size":18,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-09-09T20:14:08.353Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/brsynth.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}},"created_at":"2019-09-26T11:41:24.000Z","updated_at":"2023-05-04T19:56:31.000Z","dependencies_parsed_at":"2022-09-05T17:22:03.306Z","dependency_job_id":null,"html_url":"https://github.com/brsynth/rp3_dcache","commit_stats":null,"previous_names":["brsynth/rp3_cache"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/brsynth/rp3_dcache","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frp3_dcache","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frp3_dcache/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frp3_dcache/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frp3_dcache/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brsynth","download_url":"https://codeload.github.com/brsynth/rp3_dcache/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frp3_dcache/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478049,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"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":"2026-01-16T10:20:48.295Z","updated_at":"2026-01-16T10:20:49.202Z","avatar_url":"https://github.com/brsynth.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Database based cache to dope data retrieval for RetroPath RL\n\nHere it is a two components cache system to dope the result retrieval from reaction rules\nresults, to be used with RetroPath RL. The 2 components are:\n\n- A python module to be imported in RetroPath RL \n- A Mongo database, which should be started independently (see \"How to run the database in\nthe background\")\n\nNotice : at reading time, some of following information might be deprecated!\n\n## Needed components\n\n- docker : https://docs.docker.com/install/\n- docker-compose : https://docs.docker.com/compose/install/\n- conda : https://docs.conda.io/projects/conda/en/latest/user-guide/install/\n\n## Setting up python environment\n\nBasically: one needs a conda environment with following packages:\n- rdkit\n- pymongo\n- pytest\n\n```bash\nconda create --name myenv python=3.6\nsource activate myenv\nconda install --channel rdkit rdkit=2018.09.1.0\nconda install --channel conda-forge pytest\nconda install pytest\nconda install pymongo\nconda install pyyaml\n```\n\n## Install as a packages\n\n```bash\npip install -e .\n```\n\n\n## How to run the database service in the background\n \n```bash\ndocker-compose -f service/run/mongo.yml up  # Or 'up -d' to start in the background\n```\n \n## Q\u0026A\n\n- Where are stored the db files ? In a named docker data volume, see `service/run/*yml` file.\n\n\n## How to cite\n\nPlease cite: Koch M, Duigou T, Faulon JL. Reinforcement Learning for Bioretrosynthesis. ACS Synthetic Biology (2020). DOI: https://doi.org/10.1021/acssynbio.9b00447\n\n\n## License\n\nSee LICENSE file\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Frp3_dcache","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrsynth%2Frp3_dcache","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Frp3_dcache/lists"}