{"id":37079773,"url":"https://github.com/moltools/retromol","last_synced_at":"2026-01-14T09:39:09.055Z","repository":{"id":322891095,"uuid":"1080855888","full_name":"moltools/RetroMol","owner":"moltools","description":"RetroMol is retrosynthetic analysis tool for modular natural products.","archived":false,"fork":false,"pushed_at":"2026-01-11T00:43:44.000Z","size":282,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-01-11T00:58:16.426Z","etag":null,"topics":["biosynthesis","monomers","natural-products","retrobiosynthesis"],"latest_commit_sha":null,"homepage":"https://retromol.bioinformatics.nl/","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/moltools.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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-10-22T00:55:33.000Z","updated_at":"2026-01-08T21:35:36.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/moltools/RetroMol","commit_stats":null,"previous_names":["moltools/retromol"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/moltools/RetroMol","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moltools%2FRetroMol","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moltools%2FRetroMol/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moltools%2FRetroMol/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moltools%2FRetroMol/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/moltools","download_url":"https://codeload.github.com/moltools/RetroMol/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moltools%2FRetroMol/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28416120,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-14T08:38:59.149Z","status":"ssl_error","status_checked_at":"2026-01-14T08:38:43.588Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":["biosynthesis","monomers","natural-products","retrobiosynthesis"],"created_at":"2026-01-14T09:39:08.478Z","updated_at":"2026-01-14T09:39:09.048Z","avatar_url":"https://github.com/moltools.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cp align=\"center\"\u003e\n  \u003cimg\n    src=\"https://raw.githubusercontent.com/moltools/RetroMol/main/logo.png\"\n    height=\"150\"\n    alt=\"RetroMol logo\"\n  \u003e\n\u003c/p\u003e\n\n\u003ch1 align=\"center\"\u003e\n  RetroMol\n\u003c/h1\u003e\n\n\u003cp align=\"center\"\u003e\n    \u003ca href=\"https://github.com/MolTools/RetroMol/actions/workflows/tests.yml\"\u003e\n      \u003cimg alt=\"testing \u0026 quality\" src=\"https://github.com/MolTools/RetroMol/actions/workflows/tests.yml/badge.svg\" /\u003e\u003c/a\u003e\n    \u003ca href=\"https://pypi.org/project/retromol\"\u003e\n      \u003cimg alt=\"PyPI\" src=\"https://img.shields.io/pypi/v/retromol\" /\u003e\u003c/a\u003e\n    \u003ca href=\"https://pypi.org/project/retromol\"\u003e\n      \u003cimg alt=\"PyPI - Python Version\" src=\"https://img.shields.io/pypi/pyversions/retromol\" /\u003e\u003c/a\u003e\n     \u003ca href=\"https://doi.org/10.5281/zenodo.17555655\"\u003e\n      \u003cimg src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.17555655.svg\" alt=\"DOI\" /\u003e\u003c/a\u003e\n\u003c/p\u003e\n\nRetroMol is retrosynthetic parsing and fingerprinting tool for modular natural products. \n\nRetroMol is designed to facilitate clustering modular natural products based on biosynthetic similarity, and to enable cross-modal retrieval between modular natural products and their coding biosynthetic gene clusters.\n\nRetroMol powers the RetroMol webapp, available at [here](https://retromol.bioinformatics.nl/). The webapp can be used to query NPAtlas, MIBiG, and antiSMASH database entries for modular natural products based on biosynthetic similarity.\n\n## Installation\n\nThe most recent code and data can be installed directly from GitHub with:\n\n```shell\npip install git+https://github.com/MolTools/RetroMol.git\n```\n\nThe latest stable release can be installed from PyPI with:\n\n```shell\npip install retromol\n```\n\nRetroMol has been developed for Linux and MacOS.\n\n## Getting started\n\nThe retromol command line tool is automatically installed alongside installation of the package. The command line tool can be used from the shell with the `--help` flag to show all subcommands:\n\n```shell\npython3 -m retromol --help\n```\n\nThe RetroMol CLI has two modes, single and batch:\n* `single`: process a single compound at a time.\n* `batch`: process multiple compounds in a single command.\n\nIn either case a the output folder will contain a log file together with the results in either JSON or JSONL format. JSONL is standard output mode for batch mode to allow for easy parsing of large result sets. Batch mode also supports parallel processing.\n\nAny column, field, or property in the input file, either CSV, TSV, SDF, or JSON, is preserved as props in the output JSON or JSONL.\n\nStereochemistry parsing is supported by supplying the `-c` flag.\n\nResult JSONs or lines from a JSONL file can be loaded into Python using RetroMol's `Result` class for further downstream analyses.\n\nCheck out the [examples](https://github.com/moltools/RetroMol/tree/main/examples) folder for example scripts demonstrating how to use RetroMol as a library.\n\n### Using custom rules\n\nRetroMol comes with a default set of retrosynthetic rules for modular natural products. See [the default rules](src/retromol/data/) for examples of the included rules.\n\n## Attribution\n\n### License\n\nThe code in this package is licensed under the MIT License.\n\n## For Developers\n\nThe final section of the README is for if you want to get involved by making a code contribution.\n\n### Development installation\n\nFirst fork the repository on GitHub, then clone your fork locally and install the package\nin \"editable\" mode with the development dependencies:\n\n```bash\ngit clone git+https://github.com/MolTools/RetroMol.git\ncd RetroMol\npip install -e .[dev]\n```\n\nYou can now make code changes locally and have them immediately available for testing.\n\nAfter testing your changes, you can commit and push them to your fork, and then open a pull request\non the main repository explaining your changes.\n\n### Testing\n\nAfter cloning the repository, the unit tests in the `tests/` folder can be run\nreproducibly with:\n\n```shell\npytest tests\n```\n\nAdditionally, these tests are automatically re-run with each push and pull request on `main` in a\n[GitHub Action](https://github.com/MolTools/RetroMol/actions?query=workflow%3ATests).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoltools%2Fretromol","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmoltools%2Fretromol","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoltools%2Fretromol/lists"}