# Patch-Based Ray Tracing in NanoShaper Boosts Molecular Surface Computation

## TL;DR

NanoShaper's new patch-based ray tracing method significantly improves speed and memory efficiency for computing molecular surfaces.

## Contribution

A novel patch-based ray tracing algorithm that boosts performance and reduces memory usage in molecular surface computation.

## Key findings

- The new method achieves up to 12.5× performance gains and 8× memory reductions.
- It enables triangulation of multimillion-atom complexes on modest hardware.
- Results on over 1500 structures and the H1N1 virus confirm improved speed and accuracy.

## Abstract

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 12.5× and memory
reductions of up to 8×, 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.