foldcomp-analysis

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
      • mmtf-python
      • mmtf-java
    • 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.