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赛尔:用于原型算法和在分子模拟程序之间交换信息的互操作性引擎

Christopher J Woods^1,2,3, Lester O Hedges^1,3, Adrian J Mulholland²

¹Advanced Computing Research Centre, University of Bristol, Bristol, United Kingdom.

The Journal of chemical physics

|May 30, 2024

概括

Sire是一个多功能Python/C++库,可以作为分子模拟程序的互操作性引擎. 它简化了数据交换和算法原型设计,增强了研究工作流.

科学领域:

计算化学是一种计算化学.
生物信息学是一种生物信息学.
软件工程软件工程软件工程

背景情况:

分子仿真软件往往缺乏互操作性.
创建新算法的原型需要整合各种计算工具.
在复杂的研究中,模拟程序之间的高效数据交换至关重要.

研究的目的:

介绍Sire,一个作为互操作性引擎设计的Python/C++库.
为了促进各种分子模拟程序和库的集成.
使研究人员能够创建新算法的原型,并简化计算工作流程.

主要方法:

赛尔提供文件解析器和信息转换器,以实现无数据交换.
它可以与Gemini,RDKit,BioSimSpace,OpenMM和NGLView等工具进行集成.
包括用于分子信息搜索,轨迹操纵和能量评估的引擎.

主要成果:

允许研究人员从多个来源加载,搜索,编辑和结合分子信息.
促进了GPU加速分子动力学和复杂的工作流执行.
赛尔的引擎被BioSimSpace用来与GROMACS,NAMD,Amber和AmberTools进行互换.

结论:

赛尔显著提高了分子模拟研究的灵活性和效率.
它是开发新算法和复杂的计算管道的基础工具.
Sire 是开源的,可以通过 conda 和 Jupyter 笔记本服务器访问,并由 OpenBioSim.Sim 支持.

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