{"id":37610890,"url":"https://github.com/brsynth/rpchemtools","last_synced_at":"2026-01-16T10:20:41.493Z","repository":{"id":109125253,"uuid":"281713658","full_name":"brsynth/rpchemtools","owner":"brsynth","description":"Minimalist toolbox to deal with chemicals","archived":false,"fork":false,"pushed_at":"2020-07-24T10:09:21.000Z","size":41,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-09-09T20:14:20.346Z","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,"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":"2020-07-22T15:24:40.000Z","updated_at":"2023-03-06T16:04:16.000Z","dependencies_parsed_at":"2023-06-14T21:30:50.409Z","dependency_job_id":null,"html_url":"https://github.com/brsynth/rpchemtools","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/brsynth/rpchemtools","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frpchemtools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frpchemtools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frpchemtools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frpchemtools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brsynth","download_url":"https://codeload.github.com/brsynth/rpchemtools/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frpchemtools/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":"2026-01-16T10:20:40.723Z","updated_at":"2026-01-16T10:20:41.485Z","avatar_url":"https://github.com/brsynth.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Anaconda-Server Badge](https://anaconda.org/brsynth/rpchemtools/badges/version.svg)](https://anaconda.org/brsynth/rpchemtools)\n[![Anaconda-Server Badge](https://anaconda.org/brsynth/rpchemtools/badges/license.svg)](https://anaconda.org/brsynth/rpchemtools)\n\n# rpchemtools\n\nMinimalist toolbox to deal with chemicals\n\n## Installation\n\n```bash\nconda create --name myenv python=3\nconda activate myenv\nconda install --channel rdkit --channel tduigou rpchemtools\n```\n\n## Use\n\n### Standardise chemical following several filters\n```\nfrom rpchemtools.Standardizer import Standardizer\nfrom rdkit.Chem import MolFromInchi\n\ninchi = 'InChI=1S/C20H13N3O3/c24-10-5-6-15-12(7-10)14(9-21-15)17-8-13(19(25)23-17)18-11-3-1-2-4-16(11)22-20(18)26/h1-9,21,24H,(H,22,26)(H,23,25)/b18-13+'\n\nparams = {\n    'OP_REMOVE_ISOTOPE': True,\n    'OP_NEUTRALISE_CHARGE': True,\n    'OP_REMOVE_STEREO': True,\n    'OP_COMMUTE_INCHI': True,\n    'OP_KEEP_BIGGEST': True,\n    'OP_ADD_HYDROGEN': False,\n    'OP_KEKULIZE': False,\n    'OP_NEUTRALISE_CHARGE_LATE': True\n}\n\nmol = MolFromInchi(inchi, sanitize=False)\nsmol = Standardizer(sequence_fun='sequence_tunable', params=params).compute(mol)\n```\n\n## Build\n```bash\nconda create --name build_env python=3\nconda install conda-build\nconda build recipe --channel rdkit\n```\n\n## Bugs\n\n### TD201904.01 -- stereochemistry assignment from MolToSmiles(sanitize=True) is not the same as MolToSmiles + SanitizeMol \n\nSource (april 2019): https://github.com/rdkit/rdkit/issues/2361\n\nIn the second case the stereo assignment is not made:\n\n```\nIn [44]: m = AllChem.MolFromSmiles('[O-][n+]1onc2cc(/C=C/c3ccc(Cl)cc3)ccc21', sanitize=True)\n\nIn [45]: AllChem.MolToInchiKey(m)\nOut[45]: 'AALOGNDNCMFSSI-OWOJBTEDSA-N'\n\nIn [46]: m = AllChem.MolFromSmiles('[O-][n+]1onc2cc(/C=C/c3ccc(Cl)cc3)ccc21', sanitize=False)\n\nIn [47]: AllChem.SanitizeMol(m, Chem.rdmolops.SanitizeFlags.SANITIZE_ALL)\nOut[47]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE\n\nIn [48]: AllChem.MolToInchiKey(m)\nOut[48]: 'AALOGNDNCMFSSI-UHFFFAOYSA-N'\n```\n\nFor the case of calling SanitizeMol after MolFromSmiles you can\nforce rdkit to calculate the correct InChI key by calling \nAllChem.AssignStereochemistry(m1, cleanIt=True, force=True) \nbefore calculating the key.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Frpchemtools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrsynth%2Frpchemtools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Frpchemtools/lists"}