mmtf-benchmark

Work in progres ...

Installation

1. Install Java 11
2. Download Maven
3. Clone this repo

git clone https://github.com/sbl-sdsc/mmtf-benchmark

4. Set environment variable to location of mmtf-benchmark

export MMTF_BENCHMARK=<path_to_repo>

5. Set environment variable to AF_YEAST_v4 directory

export AF_YEAST_v4=<path_to_directory>

6. Download Saccharomyces cerevisiae proteome from AlphaFold database version 4

wget https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000002311_559292_YEAST_v4.tar

7. Copy the .cif.gz files into the $AF_YEAST_v4/cif directory

8. Build the jar file with dependencies

mvn install

7. Run the benchmarks scripts in $MMTF_BENCHMARK/src/main/java/edu/sdsc/benchmark

 ./mmtf_lossless.sh
 ./mmtf_lossy.sh