parallelAC - A CUDA library for parallel computation of the 3D alpha complex for large biomolecules.
The alpha complex has been extensively used as the underlying representation for biomolecular structures. parallelAC is a CUDA library that implements a GPU-based parallel algorithm for the computation of the alpha complex. The algorithm exploits the knowledge of typical spatial distribution and sizes of atoms in a biomolecule. The alpha complex is a subset of the delaunay triangulation. Unlike existing methods, this algorithm does not require prior construction of the delaunay triangulation. Computational experiments on several biomolecules demonstrate the superior performance of the algorithm, up to a factor of 50 when compared to existing methods that are optimized for biomolecules.
Source code and instructions on bitbucket here.
- Talha Bin Masood, Tathagata Ray and Vijay Natarajan.
Parallel Computation of Alpha Complexes for Biomolecules
Computational Geometry : Theory and Applications, 90, 2020, 1 - 17.
SoCG 2020: Symposium on Computational Geometry 2020, 17:1 - 17:16.