AQME: Automated quantum mechanical environments for researchers and educators
AQME, automated quantum mechanical environments, is a free and open-source Python package for the rapid deployment of automated workflows using cheminformatics and quantum chemistry. AQME workflows integrate tasks performed across multiple computational chemistry packages and data formats, preservin...
Published in: | WIREs Computational Molecular Science |
---|---|
Main Authors: | , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
2023
|
Subjects: | |
Online Access: | http://zaguan.unizar.es/record/125780 https://doi.org/10.1002/wcms.1663 |
id |
ftunivzaraaneto:oai:zaguan.unizar.es:125780 |
---|---|
record_format |
openpolar |
spelling |
ftunivzaraaneto:oai:zaguan.unizar.es:125780 2024-09-15T18:28:59+00:00 AQME: Automated quantum mechanical environments for researchers and educators Alegre-Requena, Juan V. S. V., Shree Sowndarya Pérez-Soto, Raúl Alturaifi, Turki M. Paton, Robert S. 2023 application/pdf http://zaguan.unizar.es/record/125780 https://doi.org/10.1002/wcms.1663 eng eng info:eu-repo/grantAgreement/ES/DGA-FSE/E07-20R info:eu-repo/grantAgreement/ES/MICINN/IJC-2020-044217-I http://zaguan.unizar.es/record/125780 doi:10.1002/wcms.1663 by http://creativecommons.org/licenses/by/3.0/es/ info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 2023 ftunivzaraaneto https://doi.org/10.1002/wcms.1663 2024-08-05T14:07:10Z AQME, automated quantum mechanical environments, is a free and open-source Python package for the rapid deployment of automated workflows using cheminformatics and quantum chemistry. AQME workflows integrate tasks performed across multiple computational chemistry packages and data formats, preserving all computational protocols, data, and metadata for machine and human users to access and reuse. AQME has a modular structure of independent modules that can be implemented in any sequence, allowing the users to use all or only the desired parts of the program. The code has been developed for researchers with basic familiarity with the Python programming language. The CSEARCH module interfaces to molecular mechanics and semi-empirical QM (SQM) conformer generation tools (e.g., RDKit and Conformer–Rotamer Ensemble Sampling Tool, CREST) starting from various initial structure formats. The CMIN module enables geometry refinement with SQM and neural network potentials, such as ANI. The QPREP module interfaces with multiple QM programs, such as Gaussian, ORCA, and PySCF. The QCORR module processes QM results, storing structural, energetic, and property data while also enabling automated error handling (i.e., convergence errors, wrong number of imaginary frequencies, isomerization, etc.) and job resubmission. The QDESCP module provides easy access to QM ensemble-averaged molecular descriptors and computed properties, such as NMR spectra. Overall, AQME provides automated, transparent, and reproducible workflows to produce, analyze and archive computational chemistry results. SMILES inputs can be used, and many aspects of tedious human manipulation can be avoided. Installation and execution on Windows, macOS, and Linux platforms have been tested, and the code has been developed to support access through Jupyter Notebooks, the command line, and job submission (e.g., Slurm) scripts. Examples of pre-configured workflows are available in various formats, and hands-on video tutorials illustrate their use. Article in Journal/Newspaper Orca Digital Repository of University of Zaragoza (ZAGUAN) WIREs Computational Molecular Science |
institution |
Open Polar |
collection |
Digital Repository of University of Zaragoza (ZAGUAN) |
op_collection_id |
ftunivzaraaneto |
language |
English |
description |
AQME, automated quantum mechanical environments, is a free and open-source Python package for the rapid deployment of automated workflows using cheminformatics and quantum chemistry. AQME workflows integrate tasks performed across multiple computational chemistry packages and data formats, preserving all computational protocols, data, and metadata for machine and human users to access and reuse. AQME has a modular structure of independent modules that can be implemented in any sequence, allowing the users to use all or only the desired parts of the program. The code has been developed for researchers with basic familiarity with the Python programming language. The CSEARCH module interfaces to molecular mechanics and semi-empirical QM (SQM) conformer generation tools (e.g., RDKit and Conformer–Rotamer Ensemble Sampling Tool, CREST) starting from various initial structure formats. The CMIN module enables geometry refinement with SQM and neural network potentials, such as ANI. The QPREP module interfaces with multiple QM programs, such as Gaussian, ORCA, and PySCF. The QCORR module processes QM results, storing structural, energetic, and property data while also enabling automated error handling (i.e., convergence errors, wrong number of imaginary frequencies, isomerization, etc.) and job resubmission. The QDESCP module provides easy access to QM ensemble-averaged molecular descriptors and computed properties, such as NMR spectra. Overall, AQME provides automated, transparent, and reproducible workflows to produce, analyze and archive computational chemistry results. SMILES inputs can be used, and many aspects of tedious human manipulation can be avoided. Installation and execution on Windows, macOS, and Linux platforms have been tested, and the code has been developed to support access through Jupyter Notebooks, the command line, and job submission (e.g., Slurm) scripts. Examples of pre-configured workflows are available in various formats, and hands-on video tutorials illustrate their use. |
format |
Article in Journal/Newspaper |
author |
Alegre-Requena, Juan V. S. V., Shree Sowndarya Pérez-Soto, Raúl Alturaifi, Turki M. Paton, Robert S. |
spellingShingle |
Alegre-Requena, Juan V. S. V., Shree Sowndarya Pérez-Soto, Raúl Alturaifi, Turki M. Paton, Robert S. AQME: Automated quantum mechanical environments for researchers and educators |
author_facet |
Alegre-Requena, Juan V. S. V., Shree Sowndarya Pérez-Soto, Raúl Alturaifi, Turki M. Paton, Robert S. |
author_sort |
Alegre-Requena, Juan V. |
title |
AQME: Automated quantum mechanical environments for researchers and educators |
title_short |
AQME: Automated quantum mechanical environments for researchers and educators |
title_full |
AQME: Automated quantum mechanical environments for researchers and educators |
title_fullStr |
AQME: Automated quantum mechanical environments for researchers and educators |
title_full_unstemmed |
AQME: Automated quantum mechanical environments for researchers and educators |
title_sort |
aqme: automated quantum mechanical environments for researchers and educators |
publishDate |
2023 |
url |
http://zaguan.unizar.es/record/125780 https://doi.org/10.1002/wcms.1663 |
genre |
Orca |
genre_facet |
Orca |
op_relation |
info:eu-repo/grantAgreement/ES/DGA-FSE/E07-20R info:eu-repo/grantAgreement/ES/MICINN/IJC-2020-044217-I http://zaguan.unizar.es/record/125780 doi:10.1002/wcms.1663 |
op_rights |
by http://creativecommons.org/licenses/by/3.0/es/ |
op_doi |
https://doi.org/10.1002/wcms.1663 |
container_title |
WIREs Computational Molecular Science |
_version_ |
1810470403351511040 |