Partial atomic charges are real numbers approximating the electron density in a molecule. They find applications in fields such as structural bioinformatics, computational chemistry or chemoinformatics. However, charges are only a theoretical concept, so their values cannot be determined by measurement but must be calculated. Standard calculation methods are based on quantum mechanical methods, but their computational complexity limits their application to small systems. Another way is to use significantly faster empirical methods that attempt to reproduce results from quantum mechanics using simple physical-chemical models.

At the National Center for Biomolecular Research, two applications have been developed to calculate partial atomic charges: the Atomic Charge Calculator II (ACC II) [1] and AlphaCharges. Both are web-based applications that allow rapid calculation of charges by empirical methods. They integrate charge visualization with LiteMol software [2], but this application is no longer supported. Its modern replacement is the Mol* Viewer [3], but it currently lacks support for charge visualization.

1. To study the minimum necessary theory on partial atomic charges (calculation of charges, chemical formats, types of visualizations of molecules).
2. Extend the Mol* Viewer to support charge visualization.
3. Integrate updated Mol* Viewer into ACC II and AlphaCharges.