Benchmarks¶
Epock Benchmarks are a set of control and test-case systems which aims at providing some standards for benchmarking pocket volume measurement / pore profile calculation software.
The material is public and available at the Epock benchmark package page.
The repository is contains two subdirectories:
controlcontains artificial systems in which the pocket volume is knowtest_casescontains biological system trajectories
Control systems¶
Epock benchmarks thus far contains a single control system, namely sphere. This system is made of a multitude of pseudo-atoms distributed in space in order to create a spherical void at in the middle of the set of pseudo-atoms.
As the equation of the points on a sphere is known and the pseudo-atoms are very closely located, the surface of the resulting void is expected to be as close as possible from a perfect sphere with known radius, therefore known surface.
Test cases¶
Test cases gather together “real” biological systems containing pockets or channels.
They are useful to evaluate a software performances on real-life problems and to compare raw data provided by different programs.