3DStructGen

3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal

Backgroud

 Nowadays, increasingly more organic as well as inorganic structures not only promote the development of “Big Data” in chemistry and material science, but also raise the demand for cross-platform and web-based tools to search, view, and edit these structures online. Many available web-based tools, which can show three-dimensional (3D) structures of specific materials, have been put forward 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.

Results

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.

Conclusions

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.

References

1.Chen, P., Wang, Y., Yan, H. et al. 3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal. J Cheminform 12, 7 (2020). https://doi.org/10.1186/s13321-020-0411-2