当前位置: X-MOL 学术J. Cheminfom. › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal
Journal of Cheminformatics ( IF 7.1 ) Pub Date : 2020-01-23 , DOI: 10.1186/s13321-020-0411-2
Pin Chen , Yu Wang , Hui Yan , Sen Gao , Zexin Xu , Yangzhong Li , Qing Mo , Junkang Huang , Jun Tao , GeChuanqi Pan , Jiahui Li , Yunfei Du

The increasing number of organic and inorganic structures promotes the development of the “Big Data” in chemistry and material science, and raises the need for cross-platform and web-based methods to search, view and edit structures. Many web-based three-dimensional (3D) structure tools have been developed for displaying existing models, building new models, and preparing initial input files for external calculations. But few of these tools can deal with crystal structures. We developed a user-friendly and versatile program based on standard web techniques, such as Hyper Text Markup Language 5 (HTML5), Cascade Style Sheet (CSS) and JavaScript. Both non-periodic organic molecule and crystal structure can be visualized, built and edited interactively. The atom, bond, angle and dihedral in a molecule can be viewed and modified using sample mouse operations. A wide range of cheminformatics algorithms for crystal structure are provided, including cleaving surfaces, establishing vacuum layers, and building supercells. Four displayed styles, namely “Primitive cell”, “Original”, “In-cell” and “Packing” can be used to visualize a unit cell. Additionally, the initial input files for Vienna Ab-initio Simulation Package (VASP) and Gaussian can be obtained by interacting with dialog boxes in 3DStructGen. 3DStructGen is a highly platform-independent program. It can provide web service independently or can be integrated into other web platforms. Other than local desktop software, it does not require any additional effort to install the system but a web browser supporting HTML5. 3DStructGen may play a valuable role in online chemistry education and pre-processing of quantum calculations. The program has been released under MIT open-source license and is available on: https://matgen.nscc-gz.cn/Tools.html.

中文翻译:

3DStructGen:用于非周期性分子和晶体的基于Web的交互式3D结构生成

越来越多的有机和无机结构促进了化学和材料科学中“大数据”的发展,并增加了对跨平台和基于Web的方法进行搜索,查看和编辑结构的需求。已经开发了许多基于Web的三维(3D)结构工具,用于显示现有模型,构建新模型以及准备用于外部计算的初始输入文件。但是这些工具很少能处理晶体结构。我们开发了基于标准Web技术的用户友好型通用程序,例如超文本标记语言5(HTML5),级联样式表(CSS)和JavaScript。非周期性有机分子和晶体结构都可以被可视化,建立和编辑。原子,键,可以使用示例鼠标操作查看和修改分子中的角度和二面角。提供了多种用于晶体结构的化学信息学算法,包括切割表面,建立真空层和构建超级单元。可以使用四种显示样式,即“原始单元格”,“原始”,“单元格内”和“包装”来可视化单元格。此外,可以通过与3DStructGen中的对话框进行交互来获取Vienna Ab-initio仿真包(VASP)和高斯的初始输入文件。3DStructGen是一个高度独立于平台的程序。它可以独立提供Web服务,也可以集成到其他Web平台中。除了本地桌面软件外,安装系统不需要任何额外的工作,而需要支持HTML5的Web浏览器。3DStructGen可能在在线化学教育和量子计算的预处理中发挥重要作用。该程序已根据MIT开源许可发布,可从以下网址获得:https://matgen.nscc-gz.cn/Tools.html。
更新日期:2020-01-23
down
wechat
bug