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https://github.com/jvalegre/aqme

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
https://github.com/jvalegre/aqme

automation cheminformatics jupyter-notebooks python quantum-chemistry reproducibility workflows

Last synced: 1 day ago
JSON representation

Host: GitHub
URL: https://github.com/jvalegre/aqme
Owner: jvalegre
License: mit
Created: 2020-01-07T19:37:33.000Z (almost 5 years ago)
Default Branch: master
Last Pushed: 2024-10-27T10:49:34.000Z (about 2 months ago)
Last Synced: 2024-10-30T09:16:26.311Z (about 1 month ago)
Topics: automation, cheminformatics, jupyter-notebooks, python, quantum-chemistry, reproducibility, workflows
Language: Python
Homepage:
Size: 82.5 MB
Stars: 98
Watchers: 5
Forks: 23
Open Issues: 14
Metadata Files:
- Readme: README.md
- License: LICENSE
- Support: SUPPORT.md

Awesome Lists containing this project

awesome-python-chemistry - AQME - Ensemble of automated QM workflows that can be run through jupyter notebooks, command lines and yaml files. (General Chemistry)

README

        ![](Logos/AQME_logo.jpg)

#

## 
 AQME (Automated Quantum Mechanical Environments)


[![CircleCI](https://img.shields.io/circleci/build/github/jvalegre/aqme?label=Circle%20CI&logo=circleci)](https://app.circleci.com/pipelines/github/jvalegre/aqme)

[![Codecov](https://img.shields.io/codecov/c/github/jvalegre/aqme?label=Codecov&logo=codecov)](https://codecov.io/gh/jvalegre/aqme)

[![Downloads](https://img.shields.io/pepy/dt/aqme?label=Downloads&logo=pypi)](https://www.pepy.tech/projects/aqme)

[![Read the Docs](https://img.shields.io/readthedocs/aqme?label=Read%20the%20Docs&logo=readthedocs)](https://aqme.readthedocs.io/)

[![PyPI](https://img.shields.io/pypi/v/aqme)](https://pypi.org/project/aqme/)

## Documentation  

Full documentation with installation instructions, technical details and examples can be found in [Read the Docs](https://aqme.readthedocs.io).  

Don't miss out the latest hands-on tutorials from our [YouTube channel](https://www.youtube.com/channel/UCHRqI8N61bYxWV9BjbUI4Xw)!  

## Recommended installation

1. (Only once) Create new conda environment: `conda create -n aqme python=3.10`  

2. Activate conda environment: `conda activate aqme`  

3. Install AQME using pip: `pip install aqme`  

4. Install Open Babel: `conda install -y -c conda-forge openbabel=3.1.1`  

* Inexperienced users should visit the *Users with no Python experience* section in our [Read the Docs](https://aqme.readthedocs.io).

## Update the program

1. Update to the latest version: `pip install aqme --upgrade`  

## Developers and help desk

List of main developers and contact emails:  

  - [ ] [Juan V. Alegre-Requena](https://orcid.org/0000-0002-0769-7168), main developer of the CSEARCH, QCORR, QPREP and QDESCP modules. Contact: [[email protected]](mailto:[email protected])  

  - [ ] [Shree Sowndarya S. V.](https://orcid.org/0000-0002-4568-5854), main developer of the CSEARCH, CMIN and QDESCP modules. Contact: [[email protected]](mailto:[email protected])  

  - [ ] [Brenda Manzanilla](https://orcid.org/0000-0001-5955-6079), developer of the QDESCP module. Contact: [[email protected]](mailto:[email protected])  

  - [ ] [Turki Alturaifi](https://www.chem.pitt.edu/person/turki-alturaifi), worked in benchmarking the parameters for RDKit-based conformer generation. Contact: [[email protected]](mailto:[email protected])  

  - [ ] [Raúl Pérez-Soto](https://orcid.org/0000-0002-6237-2155), worked in refactoring the code and creating the documentation. Contact: [[email protected]](mailto:[email protected])  

  - [ ] [Robert S. Paton](https://orcid.org/0000-0002-0104-4166), research group supervisor and code advisor. Contact: [[email protected]](mailto:[email protected])  

For suggestions and improvements of the code (greatly appreciated!), please reach out through the issues and pull requests options of Github.  

## License

AQME is freely available under an [MIT](https://opensource.org/licenses/MIT) License  

## Reference

If you use any of the AQME modules, please include this citation:  

Alegre-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).  

  

Additionally, please include the corresponding references for the following programs:  

  * If you used CSEARCH with RDKit methods or from SMILES: [RDKit](https://www.rdkit.org)  

  * If you used CSEARCH with CREST methods: [CREST](https://crest-lab.github.io/crest-docs)  

  * If you used CMIN with xTB: [xTB](https://xtb-docs.readthedocs.io/en/latest/contents.html)  

  * If you used CMIN with ANI: [ANI](https://github.com/isayev/ASE_ANI)  

  * If you used QCORR: [cclib](https://cclib.github.io/)  

  * If you used QDESCP with xTB: [xTB](https://xtb-docs.readthedocs.io/en/latest/contents.html)