{"id":21721364,"url":"https://github.com/informaticsmatters/standardize-molecule","last_synced_at":"2025-08-12T18:34:36.076Z","repository":{"id":62570802,"uuid":"349095559","full_name":"InformaticsMatters/standardize-molecule","owner":"InformaticsMatters","description":"Utilities for SMILES analysis","archived":false,"fork":false,"pushed_at":"2021-03-18T17:32:59.000Z","size":48,"stargazers_count":5,"open_issues_count":1,"forks_count":2,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-11T09:59:49.502Z","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":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/InformaticsMatters.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":"2021-03-18T14:02:41.000Z","updated_at":"2023-12-22T01:55:17.000Z","dependencies_parsed_at":"2022-11-04T00:28:44.984Z","dependency_job_id":null,"html_url":"https://github.com/InformaticsMatters/standardize-molecule","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/InformaticsMatters%2Fstandardize-molecule","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/InformaticsMatters%2Fstandardize-molecule/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/InformaticsMatters%2Fstandardize-molecule/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/InformaticsMatters%2Fstandardize-molecule/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/InformaticsMatters","download_url":"https://codeload.github.com/InformaticsMatters/standardize-molecule/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248636825,"owners_count":21137527,"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":"2024-11-26T02:16:03.482Z","updated_at":"2025-04-12T21:33:52.776Z","avatar_url":"https://github.com/InformaticsMatters.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Informatics Matters Standardize Molecule Utility\n\n[![build](https://github.com/InformaticsMatters/standardize-molecule/actions/workflows/build.yaml/badge.svg)](https://github.com/InformaticsMatters/standardize-molecule/actions/workflows/build.yaml)\n[![publish](https://github.com/InformaticsMatters/standardize-molecule/actions/workflows/publish.yaml/badge.svg)](https://github.com/InformaticsMatters/standardize-molecule/actions/workflows/publish.yaml)\n\n[![PyPI version](https://badge.fury.io/py/im-standardize-molecule.svg)](https://badge.fury.io/py/im-standardize-molecule)\n![PyPI - License](https://img.shields.io/pypi/l/im-standardize-molecule)\n\nThe *im-standardize-molecule* module is a utility provided by Informatics Matters\n\nIt contains a Python module to:\n1. Take an original SMILES (*Simple Molecule Input Line rESpresentation*) and\nconvert it to an Isomeric or Nonisomeric canonical SMILES representation in a consistent way.\n2. Convert an *rdkit.Chem.rdchem.Mol* object to a standard format.\n\nFor installation and testing, see the associated README.rst file.\n\n## Usage\n\n**standardize_to_noniso_smiles** *(osmiles:str)*\n\n**standardize_to_iso_smiles** *(osmiles:str)*\n\nTakes a smiles and returns the converted smiles and standardized molecule as an *rdkit.Chem.rdchem.Mol*\n\nExample::\n\n    from standardize_molecule import standardize_to_noniso_smiles\n    noniso = standardize_to_noniso_smiles('N[C@@H](C[C@@H]1CCNC1O)[C@@H](O)CO')\n    [17:30:44] Initializing MetalDisconnector\n    [17:30:44] Running MetalDisconnector\n    [17:30:44] Initializing Normalizer\n    [17:30:44] Running Normalizer\n    [17:30:44] Running Uncharger\n    print(noniso[0])\n    NC(CC1CCNC1O)C(O)CO\n\n\n**standardize_molecule** *(molecule: object, osmiles:str = 'NotProvided')*\n\nTakes an rdkit.Chem.rdchem.Mol object and (optionally) a smiles string for logging and returns\na standardized molecule.\n\nExample::\n\n    from rdkit import Chem\n    from standardize_molecule import standardize_molecule\n    mol = Chem.MolFromSmiles('C1=CC=CC=C1')\n    std = standardize_molecule(mol, 'C1=CC=CC=C1')\n    [17:37:40] Initializing MetalDisconnector\n    [17:37:40] Running MetalDisconnector\n    [17:37:40] Initializing Normalizer\n    [17:37:40] Running Normalizer\n    [17:37:40] Running Uncharger\n    print(std)\n    \u003crdkit.Chem.rdchem.Mol object at 0x7f18ca2a93f0\u003e\n    print(noniso[1].GetNumHeavyAtoms())\n    13\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finformaticsmatters%2Fstandardize-molecule","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finformaticsmatters%2Fstandardize-molecule","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finformaticsmatters%2Fstandardize-molecule/lists"}