CAVE-CL: An OpenCL version of the package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins

Abstract

Here we present the revised and newly rewritten version of our earlier published CAVE package (Busa et al., 2010) which was originally written in FORTRAN. The package has been rewritten in C language, the algorithm has been parallelized and implemented using OpenCL. This makes the program convenient to run on platforms with Graphical Processing Units (GPUs). Improvements include also some modifications/optimizations of the original algorithm. A considerable improvement in the performance of the code has been achieved. A new tool called input_structure has been added which helps the user to make the data input and conversion more easier and universal.