Patch-Based Ray Tracing in NanoShaper Boosts Molecular Surface Computation

NanoShaper (NS) is a widely used tool that leverages ray tracing for molecular surface triangulation, pocket detection, and supports Poisson-Boltzmann equation solvers. By retaining the established methodological framework and implementing a targeted redesign, our approach achieves performance gains of up to 12.5x and memory reductions of up to 8x, enabling the triangulation of complexes containing millions of atoms on relatively modest computational architectures in a short time. The key innovation is a patch-based ray tracing algorithm that replaces the traditional ray-sweeping approach. By iterating over surface patches rather than rays, this method enhances cache performance and removes the need for memory-intensive grids for patch localization, yielding major reductions in memory usage. Further optimizations include the parallelization of the analytical solvent-excluded surface (SES) construction and the replacement of uniform grids and octrees with bilevel grids and/or compressed buffers. We also introduce an analytical ray-torus intersection scheme based on an exact quartic solution, which improves both accuracy and computational efficiency. The updated version (v1.5) additionally provides a public C++ API for seamless integration with external tools. The tool is available at https://gitlab.iit.it/SDecherchi/nanoshaper. Results on more than 1500 structures and on a multimillion atom complex (e.g., the H1N1 virus) confirm speed and accuracy achievements.