{"id":13684484,"url":"https://github.com/chembl/ChEMBL_Structure_Pipeline","last_synced_at":"2025-04-30T21:30:39.385Z","repository":{"id":40757499,"uuid":"169412514","full_name":"chembl/ChEMBL_Structure_Pipeline","owner":"chembl","description":"ChEMBL database structure pipelines","archived":false,"fork":false,"pushed_at":"2024-09-03T22:48:17.000Z","size":228,"stargazers_count":200,"open_issues_count":7,"forks_count":37,"subscribers_count":15,"default_branch":"master","last_synced_at":"2025-04-21T13:04:15.971Z","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/chembl.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}},"created_at":"2019-02-06T13:43:57.000Z","updated_at":"2025-04-05T12:27:57.000Z","dependencies_parsed_at":"2023-01-24T06:15:17.429Z","dependency_job_id":"1a35a91c-ab8e-42fa-a0b0-5742d4ed4520","html_url":"https://github.com/chembl/ChEMBL_Structure_Pipeline","commit_stats":{"total_commits":120,"total_committers":4,"mean_commits":30.0,"dds":"0.23333333333333328","last_synced_commit":"02fae41903d35e6bb853ee56cf6b799d774bfe92"},"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chembl%2FChEMBL_Structure_Pipeline","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chembl%2FChEMBL_Structure_Pipeline/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chembl%2FChEMBL_Structure_Pipeline/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chembl%2FChEMBL_Structure_Pipeline/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/chembl","download_url":"https://codeload.github.com/chembl/ChEMBL_Structure_Pipeline/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251785344,"owners_count":21643458,"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":[],"created_at":"2024-08-02T14:00:34.053Z","updated_at":"2025-04-30T21:30:39.046Z","avatar_url":"https://github.com/chembl.png","language":"Python","funding_links":[],"categories":["Cheminformatics","Ranked by starred repositories","Libraries"],"sub_categories":["Format Checking"],"readme":"[![CI Testing](https://github.com/chembl/ChEMBL_Structure_Pipeline/workflows/CI/badge.svg)](https://github.com/chembl/ChEMBL_Structure_Pipeline/actions?query=workflow%3ACI+branch%3Amaster)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n\n\n# ChEMBL Structure Pipeline\n\nChEMBL protocols used to standardise and salt strip molecules. First used in ChEMBL 26.\n\nCheck the [wiki](https://github.com/chembl/ChEMBL_Structure_Pipeline/wiki) and paper[[1]](#1) for a detailed description of the different processes.\n\n## Installation\n\nFrom source:\n\n    git clone https://github.com/chembl/ChEMBL_Structure_Pipeline.git\n    pip install ./ChEMBL_Structure_Pipeline\n\nwith pip:\n\n```bash\npip install chembl_structure_pipeline\n```\n\nwith conda:\n\n```bash\nconda install -c conda-forge chembl_structure_pipeline\n```\n\n## Usage\n\n### Standardise a compound [(info)](https://github.com/chembl/ChEMBL_Structure_Pipeline/wiki/Work-done-by-each-step#standardize_molblock)\n\n\n```python\nfrom chembl_structure_pipeline import standardizer\n\no_molblock = \"\"\"\n  Mrv1810 07121910172D          \n\n  4  3  0  0  0  0            999 V2000\n   -2.5038    0.4060    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0\n   -2.5038    1.2310    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n   -3.2182   -0.0065    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0\n   -1.7893   -0.0065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  1  3  1  0  0  0  0\n  1  4  1  4  0  0  0\nM  CHG  2   2  -1   3   1\nM  END\n\"\"\"\n\nstd_molblock = standardizer.standardize_molblock(o_molblock)\n```\n\n### Get the parent compound [(info)](https://github.com/chembl/ChEMBL_Structure_Pipeline/wiki/Work-done-by-each-step#get_parent_molblock)\n\n\n```python\nfrom chembl_structure_pipeline import standardizer\n\no_molblock = \"\"\"\n  Mrv1810 07121910262D          \n\n  3  1  0  0  0  0            999 V2000\n   -5.2331    1.1053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.5186    1.5178    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0\n   -2.8647    1.5789    0.0000 Cl  0  5  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\nM  CHG  2   2   1   3  -1\nM  END\n\"\"\"\n\nparent_molblock, _ = standardizer.get_parent_molblock(o_molblock)\n```\n\n### Check a compound [(info)](https://github.com/chembl/ChEMBL_Structure_Pipeline/wiki/Work-done-by-each-step#checkmolecule)\n\nThe checker assesses the quality of a structure. It highlights specific features or issues in the structure that may need to be revised. Together with the description of the issue, the checker process returns a penalty score (between 0-9) which reflects the seriousness of the issue (the higher the score, the more critical is the issue)\n\n```python\nfrom chembl_structure_pipeline import checker\n\no_molblock = \"\"\" \n  Mrv1810 02151908462D           \n \n  4  3  0  0  0  0            999 V2000 \n    2.2321    4.4196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0 \n    3.0023    4.7153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0 \n    1.4117    4.5059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0 \n    1.9568    3.6420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0 \n  1  2  1  1  0  0  0 \n  1  3  1  0  0  0  0 \n  1  4  1  0  0  0  0 \nM  END \n\"\"\"\n\nissues = checker.check_molblock(o_molblock)\n```\n\n## References\n\u003ca id=\"1\"\u003e[1]\u003c/a\u003e \nBento, A.P., Hersey, A., Félix, E. et al. An open source chemical structure curation pipeline using RDKit. J Cheminform 12, 51 (2020). https://doi.org/10.1186/s13321-020-00456-1\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchembl%2FChEMBL_Structure_Pipeline","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchembl%2FChEMBL_Structure_Pipeline","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchembl%2FChEMBL_Structure_Pipeline/lists"}