3DStructGen

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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

Based on standard web techniques, such as HyperText Markup Language 5 (HTML 5), Cascade Style Sheet (CSS), and JavaScript, we have developed a versatile and user-friendly program called 3DStructGen. In this program, the structure of the non-periodic organic molecules and long-range order crystal materials can both be visualized, built, and edited interactively. Users can view and modify the atoms, bonds, angles, and dihedrals in any molecule or material by some simple mouse operations. Especially, equipped with cheminformatics algorithms for crystal structures, including cleaving surfaces, establishing vacuum layers, and building supercells, four displayed styles, “Primitive cell”, “Original”, “In-cell” and “Packing” can be used to visualize a unit cell in this program. Moreover, the initial input files of Vienna Ab-initio Simulation Package (VASP) and Gaussian can also be obtained through interacting with dialog boxes in 3DStructGen.

Conclusions

Other than local desktop software, this program 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