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Updated: Nov 21, 2025

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

Pin Chen1, Yu Wang1,2, Hui Yan1

  • 1National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China.

Journal of Cheminformatics
|January 12, 2021
PubMed
Summary
This summary is machine-generated.

A new web-based tool, 3DStructGen, allows interactive visualization and editing of organic and crystal structures. It simplifies complex tasks like surface cleavage and supercell building for computational chemistry.

Keywords:
3DHTML5Structure editorVisualization

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Area of Science:

  • Chemistry
  • Material Science
  • Computational Science

Background:

  • The
  • Big Data
  • in chemistry and material science necessitates advanced tools for managing and analyzing chemical structures.
  • Existing web-based 3D structure tools often lack comprehensive support for crystal structures.

Purpose of the Study:

  • To develop a versatile, cross-platform web-based program for visualizing, building, and editing both organic molecules and crystal structures.
  • To provide cheminformatics algorithms specifically for crystal structure manipulation.
  • To facilitate the preparation of input files for computational chemistry software.

Main Methods:

  • Developed using standard web technologies: HTML5, CSS, and JavaScript.
  • Implemented interactive manipulation of atoms, bonds, angles, and dihedrals.
  • Integrated specialized algorithms for crystal structure analysis, including surface cleavage, vacuum layer creation, and supercell construction.

Main Results:

  • 3DStructGen enables interactive visualization and editing of organic and crystal structures.
  • Offers four distinct visualization styles for unit cells: "Primitive cell", "Original", "In-cell", and "Packing".
  • Generates input files for VASP and Gaussian through a user-friendly interface.

Conclusions:

  • 3DStructGen is a highly platform-independent, web-based tool requiring only an HTML5-compatible browser.
  • It can function as a standalone web service or be integrated into existing platforms.
  • The tool is valuable for online chemistry education and pre-processing quantum calculations, released under an MIT open-source license.