This repository contains the benchmarking code and results for the paper, "Foldcomp: a library and format for compressing and indexing large protein structure sets".
- benchmark
- result: Benchmark results for each tool. For each tool, compression and decompression was run 5 times.
- scripts: Scripts for running the benchmark
- bcif: ciftools-java
- foldcomp: foldcomp
- gzip
- mmtf
- pic: PIC
- pulchra: pulchra
- visualization: Scripts for visualizing the benchmark results
- plotting_script.r
- data
- benchmark_result.txt: Summary of the benchmark results
- rmsd.txt: RMSD values for each tool
- size.txt: Compressed sizes (bytes) for each tool
Special thanks to @pwrose for the help with benchmarking MMTF in Java.