AQME: Automated quantum mechanical environments for researchers and educators
AQME: Automated quantum mechanical environments for researchers and educators
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DOI：
10.1002/wcms.1663
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发表时间：
2023-02-26
影响因子：
11.4
通讯作者：
Paton, Robert S.
中科院分区：
文献类型：
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作者：
Alegre-Requena, Juan V.;Shree, Sowndarya S., V;Paton, Robert S.
AQME，自动化量子力学环境，是一个免费的开源Python包，用于使用化学信息学和量子化学快速部署自动化工作流程。AQME工作流程集成了跨多个计算化学包和数据格式执行的任务，保留了所有计算协议、数据和元数据，供机器和人类用户访问和重复使用。AQME具有独立模块的模块化结构，可以以任何顺序实现，允许用户使用程序的所有或仅使用所需部分。代码是为基本熟悉Python编程语言的研究人员开发的。CNOM模块与分子力学和半经验QM（SQM）构象生成工具（例如，RDKit和Conformer-Rotamer Encyclopedia Sampling Tool，CREST）。CMIN模块支持使用SQM和神经网络势（如ANI）进行几何细化。QPREP模块与多个QM程序接口，例如Gaussian、ORCA和PySCF。QCORR模块处理QM结果，存储结构、能量和属性数据，同时还实现自动错误处理（即，收敛误差、虚频数错误、异构化等）和工作重新提交。QDESCP模块提供了对QM整体平均分子描述符和计算性质（如NMR光谱）的轻松访问。总体而言，AQME提供自动化，透明和可重复的工作流程来生成，分析和存档计算化学结果。可以使用SMILES输入，并且可以避免许多繁琐的人工操作。在Windows、macOS和Linux平台上的安装和执行已经过测试，并且代码已经开发为支持通过Windows笔记本、命令行和作业提交（例如，Slurm）脚本。预配置的工作流程的例子有各种格式，和动手视频教程说明其使用.这篇文章分类下：数据科学>化学信息学数据科学>计算机算法和编程软件>量子化学
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.This article is categorized under:Data Science > ChemoinformaticsData Science > Computer Algorithms and ProgrammingSoftware > Quantum Chemistry