{"id":13772550,"url":"https://github.com/jvalegre/aqme","last_synced_at":"2025-04-13T00:47:57.905Z","repository":{"id":37433189,"uuid":"232402350","full_name":"jvalegre/aqme","owner":"jvalegre","description":"Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and command lines, including: 1) RDKit- and CREST-based conformer generation, 2) QM input file creation, 3) post-processing of QM output files, 4) generation of xTB, DFT and RDKit descriptors. https://aqme.readthedocs.io","archived":false,"fork":false,"pushed_at":"2025-04-11T16:45:04.000Z","size":86909,"stargazers_count":107,"open_issues_count":14,"forks_count":26,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-11T16:55:47.771Z","etag":null,"topics":["automation","cheminformatics","jupyter-notebooks","python","quantum-chemistry","reproducibility","workflows"],"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/jvalegre.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":"SUPPORT.md","governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-01-07T19:37:33.000Z","updated_at":"2025-04-11T16:45:09.000Z","dependencies_parsed_at":"2023-10-13T12:47:55.011Z","dependency_job_id":"ab54c6d2-aa7f-479e-af09-110cb0a238f3","html_url":"https://github.com/jvalegre/aqme","commit_stats":{"total_commits":818,"total_committers":14,"mean_commits":58.42857142857143,"dds":0.5268948655256724,"last_synced_commit":"a31cd25a217a1aebc8a3a3d48ff1908b99bf3e8d"},"previous_names":[],"tags_count":21,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jvalegre%2Faqme","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jvalegre%2Faqme/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jvalegre%2Faqme/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jvalegre%2Faqme/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jvalegre","download_url":"https://codeload.github.com/jvalegre/aqme/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248447550,"owners_count":21105137,"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":["automation","cheminformatics","jupyter-notebooks","python","quantum-chemistry","reproducibility","workflows"],"created_at":"2024-08-03T17:01:05.295Z","updated_at":"2025-04-13T00:47:57.882Z","avatar_url":"https://github.com/jvalegre.png","language":"Python","funding_links":[],"categories":["General Chemistry"],"sub_categories":[],"readme":"![](Logos/AQME_logo.jpg)\r\n#\r\n## \u003cp align=\"center\"\u003e AQME (Automated Quantum Mechanical Environments)\u003c/p\u003e\r\n\r\n\r\n\r\n[![CircleCI](https://img.shields.io/circleci/build/github/jvalegre/aqme?label=Circle%20CI\u0026logo=circleci)](https://app.circleci.com/pipelines/github/jvalegre/aqme)\r\n[![Codecov](https://img.shields.io/codecov/c/github/jvalegre/aqme?label=Codecov\u0026logo=codecov)](https://codecov.io/gh/jvalegre/aqme)\r\n[![Downloads](https://img.shields.io/pepy/dt/aqme?label=Downloads\u0026logo=pypi)](https://www.pepy.tech/projects/aqme)\r\n[![Read the Docs](https://img.shields.io/readthedocs/aqme?label=Read%20the%20Docs\u0026logo=readthedocs)](https://aqme.readthedocs.io/)\r\n[![PyPI](https://img.shields.io/pypi/v/aqme)](https://pypi.org/project/aqme/)\r\n\r\n## Documentation  \r\nFull documentation with installation instructions, technical details and examples can be found in [Read the Docs](https://aqme.readthedocs.io).  \r\n\r\nDon't miss out the latest hands-on tutorials from our [YouTube channel](https://www.youtube.com/channel/UCHRqI8N61bYxWV9BjbUI4Xw)!  \r\n\r\n## Recommended installation\r\n1. (Only once) Create new conda environment: `conda create -n aqme python=3.10`  \r\n2. Activate conda environment: `conda activate aqme`  \r\n3. Install AQME using pip: `pip install aqme`  \r\n4. Install Open Babel: `conda install -y -c conda-forge openbabel=3.1.1`  \r\n\r\n* Inexperienced users should visit the *Users with no Python experience* section in our [Read the Docs](https://aqme.readthedocs.io).\r\n\r\n## Update the program\r\n1. Update to the latest version: `pip install aqme --upgrade`  \r\n\r\n## Developers and help desk\r\nList of main developers and contact emails:  \r\n  - [ ] [Juan V. Alegre-Requena](https://orcid.org/0000-0002-0769-7168), main developer of the CSEARCH, QCORR, QPREP and QDESCP modules. Contact: [jv.alegre@csic.es](mailto:jv.alegre@csic.es)  \r\n  - [ ] [Shree Sowndarya S. V.](https://orcid.org/0000-0002-4568-5854), main developer of the CSEARCH, CMIN and QDESCP modules. Contact: [svss@colostate.edu](mailto:svss@colostate.edu)  \r\n  - [ ] [Brenda Manzanilla](https://orcid.org/0000-0001-5955-6079), developer of the QDESCP module. Contact: [iqmanzanilla@gmail.com](mailto:iqmanzanilla@gmail.com)\r\n  - [ ] [David Dalmau](https://orcid.org/0000-0002-2506-6546), developer of the QDESCP module. Contact: [ddalmau@unizar.es](mailto:ddalmau@unizar.es)  \r\n  - [ ] [Turki Alturaifi](https://www.chem.pitt.edu/person/turki-alturaifi), worked in benchmarking the parameters for RDKit-based conformer generation. Contact: [tma53@pitt.edu](mailto:tma53@pitt.edu)  \r\n  - [ ] [Raúl Pérez-Soto](https://orcid.org/0000-0002-6237-2155), worked in refactoring the code and creating the documentation. Contact: [Raul.Perez_Soto@colostate.edu](mailto:Raul.Perez_Soto@colostate.edu)  \r\n  - [ ] [Robert S. Paton](https://orcid.org/0000-0002-0104-4166), code advisor and feedback. Contact: [robert.paton@colostate.edu](mailto:robert.paton@colostate.edu)  \r\n\r\nFor suggestions and improvements of the code (greatly appreciated!), please reach out through the issues and pull requests options of Github.  \r\n\r\n## License\r\nAQME is freely available under an [MIT](https://opensource.org/licenses/MIT) License  \r\n\r\n## Reference\r\nIf you use any of the AQME modules, please include this citation:  \r\nAlegre-Requena, J. V.; Sowndarya, S.; Pérez-Soto, R.; Alturaifi, T.; Paton, R. AQME: Automated Quantum Mechanical Environments for Researchers and Educators. *Wiley Interdiscip. Rev. Comput. Mol. Sci.* **2023**, *13*, e1663. (DOI: 10.1002/wcms.1663).  \r\n  \r\nAdditionally, please include the corresponding references for the following programs:  \r\n  * If you used CSEARCH with RDKit methods or from SMILES: [RDKit](https://www.rdkit.org)  \r\n  * If you used CSEARCH with CREST methods: [CREST](https://crest-lab.github.io/crest-docs)  \r\n  * If you used CMIN with xTB: [xTB](https://xtb-docs.readthedocs.io/en/latest/contents.html)  \r\n  * If you used CMIN with ANI: [ANI](https://github.com/isayev/ASE_ANI)  \r\n  * If you used QCORR: [cclib](https://cclib.github.io/)  \r\n  * If you used QDESCP with xTB: [xTB](https://xtb-docs.readthedocs.io/en/latest/contents.html)\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjvalegre%2Faqme","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjvalegre%2Faqme","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjvalegre%2Faqme/lists"}