Figure 2.

Illustration of molecular features and sinusoidal encoding. (a) Schematic representation of the PB model. The solute domain ${\mathrm{\Omega }}_{\mathrm{i}\mathrm{n}\mathrm{t}}$ and solvent domain ${\mathrm{\Omega }}_{\mathrm{e}\mathrm{x}\mathrm{t}}$ are separated by the solvent-excluded surface Γ. Atoms are depicted as spheres with “+” and “−” symbols indicating partial charges, and the probe sphere represents the solvent-accessible boundary. (b) Visualization of sinusoidal positional encoding applied to the atom charge feature $q^{\left(i\right)}$, illustrating how different charge values are mapped across the embedding dimensions.