Sphinx

usage: sphinx [options] pdbfile > spheres.pdb

Sphinx generates a complete, optimal set of 1,000 - 10,000 overlapping, variable radius spheres tangent to macromolecule atoms in 30 - 90 seconds using Yeates' inversive geometry algorithm.

Reference

T. Yeates, J. Mol. Bio., 249, 804-814, (1995).