{"id":26356533,"url":"https://github.com/ds4sd/molannotator","last_synced_at":"2025-08-04T08:38:34.366Z","repository":{"id":222861589,"uuid":"758574875","full_name":"DS4SD/MolAnnotator","owner":"DS4SD","description":null,"archived":false,"fork":false,"pushed_at":"2024-07-08T16:00:44.000Z","size":50,"stargazers_count":7,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-16T13:35:40.604Z","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/DS4SD.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-02-16T16:02:36.000Z","updated_at":"2025-01-04T19:15:47.000Z","dependencies_parsed_at":"2024-07-08T20:04:26.818Z","dependency_job_id":null,"html_url":"https://github.com/DS4SD/MolAnnotator","commit_stats":null,"previous_names":["ds4sd/molannotator"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/DS4SD/MolAnnotator","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DS4SD%2FMolAnnotator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DS4SD%2FMolAnnotator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DS4SD%2FMolAnnotator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DS4SD%2FMolAnnotator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DS4SD","download_url":"https://codeload.github.com/DS4SD/MolAnnotator/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DS4SD%2FMolAnnotator/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268671954,"owners_count":24288241,"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":"2025-08-04T02:00:09.867Z","response_time":79,"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":"2025-03-16T13:30:56.195Z","updated_at":"2025-08-04T08:38:34.307Z","avatar_url":"https://github.com/DS4SD.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MolAnnotator\n\nThis repository implements applications to ease manual annotation of chemical images. \n\n## Installation\n\n```\nconda create -n molannotator python=3.11\nconda activate molannotator\npip install -e .\n```\n\n## Classification\nThe classification application allows to assign to an image one of the following categories: `standard_molecule` (Molecular Structure), `markush_structure` (Markush Structure), `miscellaneous` (Background), `polymer` (Markush Structure), and `segmentation_annotation_error`.\n\nTo run the application:\n1. Move the images to be annotated to `./data/classfication/default/images/*.png`,\n2. (optional) Move pre-annotations to `./data/classfication/default/classes/*.json`,\n3. Run `bash ./molannotator/apps/run_classification_app.sh`.\n\nAnnotations are saved in `./data/classfication/default/classes/*.json`.\n\n## Recognition\nThe recognition application allows to annotate the molecular graph of a chemical-structure image.\n\nTo run the application:\n1. Move the images to be annotated to `./data/recognition/default/images/*.png`,\n2. (optional) Create pre-annotations by running `python3 ./molannotator/molscribe_pre_annotate.py` (see [MolScribe](https://github.com/thomas0809/MolScribe) for installation steps),\n3. (optional) Move pre-annotations to `./data/recognition/default/predictions/*.mol`,\n3. Run `bash ./molannotator/apps/run_recognition_app.sh`.\n\nAnnotations are saved in `./data/recognition/default/molfiles/*.mol`.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fds4sd%2Fmolannotator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fds4sd%2Fmolannotator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fds4sd%2Fmolannotator/lists"}