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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

Jan Busa Jr., Jan Busa, Shura Hayryan, Chin-Kun Hu, Ming-Chya Wu
Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
Computer Physics Communications, 2015

@article{buvsa2015cave,

   title={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},

   author={Bu{v{s}}a, J{‘a}n and Hayryan, Shura and Hu, Chin-Kun and Wu, Ming-Chya},

   journal={Computer Physics Communications},

   year={2015},

   publisher={Elsevier}

}

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Here we present the revised and newly rewritten version of our earlier published CAVE package [J. Busa et al., Comput. Phys. Commun. 181 (2010) 2116] 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.
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