{"id":29656538,"url":"https://github.com/zincware/rdkit2ase","last_synced_at":"2025-07-22T08:35:58.652Z","repository":{"id":188657499,"uuid":"679169336","full_name":"zincware/rdkit2ase","owner":"zincware","description":"Create atomistic structures with ASE, rdkit and packmol","archived":false,"fork":false,"pushed_at":"2025-07-21T08:40:49.000Z","size":1513,"stargazers_count":12,"open_issues_count":6,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-07-21T10:12:18.450Z","etag":null,"topics":["ase","packmol","rdkit"],"latest_commit_sha":null,"homepage":"https://zincware.github.io/rdkit2ase/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/zincware.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","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}},"created_at":"2023-08-16T08:46:33.000Z","updated_at":"2025-07-16T18:25:02.000Z","dependencies_parsed_at":null,"dependency_job_id":"cc910e47-cf30-4104-8e17-a9f787374e68","html_url":"https://github.com/zincware/rdkit2ase","commit_stats":null,"previous_names":["zincware/rdkit2ase"],"tags_count":9,"template":false,"template_full_name":null,"purl":"pkg:github/zincware/rdkit2ase","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zincware%2Frdkit2ase","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zincware%2Frdkit2ase/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zincware%2Frdkit2ase/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zincware%2Frdkit2ase/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zincware","download_url":"https://codeload.github.com/zincware/rdkit2ase/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zincware%2Frdkit2ase/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266456405,"owners_count":23931404,"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":"2025-07-22T02:00:09.085Z","response_time":66,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"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":["ase","packmol","rdkit"],"created_at":"2025-07-22T08:35:52.571Z","updated_at":"2025-07-22T08:35:58.628Z","avatar_url":"https://github.com/zincware.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![zincware](https://img.shields.io/badge/Powered%20by-zincware-darkcyan)](https://github.com/zincware)\n[![codecov](https://codecov.io/gh/zincware/rdkit2ase/graph/badge.svg?token=Q0VIN03185)](https://codecov.io/gh/zincware/rdkit2ase)\n[![PyPI version](https://badge.fury.io/py/rdkit2ase.svg)](https://badge.fury.io/py/rdkit2ase)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15423477.svg)](https://doi.org/10.5281/zenodo.15423477)\n[![Docs](https://github.com/zincware/rdkit2ase/actions/workflows/pages.yaml/badge.svg)](https://zincware.github.io/rdkit2ase/)\n\n# rdkit2ase - Interface between the rdkit and ASE package.\n\nInstallation via `pip install rdkit2ase`.\n\n```py\nfrom rdkit2ase import rdkit2ase, ase2rdkit\n\natoms: ase.Atoms = rdkit2ase(mol)\nmol = ase2rdkit(atoms)\n```\n\n```py\nfrom rdkit2ase import smiles2atoms\n\natoms: ase.Atoms = smiles2atoms(\"O\")\n\nprint(atoms)\n\u003e\u003e\u003e Atoms(symbols='OH2', pbc=False)\n```\n\n## Packmol Interface\n\nIf you have [packmol](https://github.com/m3g/packmol) (at least `v20.15.0`) you\ncan use the rdkit2ase interface.\n\n```py\nfrom rdkit2ase import pack, smiles2conformers\n\nwater = smiles2conformers(\"O\", 2)\nethanol = smiles2conformers(\"CCO\", 5)\ndensity = 1000  # kg/m^3\nbox = pack([water, ethanol], [7, 5], density)\nprint(box)\n\u003e\u003e\u003e Atoms(symbols='C10H44O12', pbc=True, cell=[8.4, 8.4, 8.4])\n```\n\n### Limitations\n\n- `rdkit2ase.ase2rdkit` won't be able to detect higher order bonds.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzincware%2Frdkit2ase","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzincware%2Frdkit2ase","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzincware%2Frdkit2ase/lists"}