Perses benchmarks

This subdirectory exposes a CLI tool for running automated benchmarks from OpenFF's protein ligand benchmark dataset using perses.

Running benchmarks

Assuming you have a clone of the perses code repository and you are standing in the benchmarks subdirectory (where this file lives). Then the benchmarks can be run using the following command syntax:

python run_benchmarks.py --target [protein-name] --edge [edge-index]

For example, for running the seventh edge (zero-based, according to plbenchmark data ) for tyk2 protein, you would run:

# Set up and run edge 6
python run_benchmarks.py --target tyk2 --edge 6

Should the calculation for an edge fail, you can simply re-run the same command-line and the calculation will resume:

# Resume failed edge 6
python run_benchmarks.py --target tyk2 --edge 6

For more information on how to use the tool, you can run python run_benchmarks.py -h.

Analyzing benchmarks

To analyze the simulations a script called benchmark_analysis.py is used as follows:

python benchmark_analysis.py --target [protein-name]

For example, for tyk2 results:

python benchmark_analysis.py --target tyk2

This will generate an output CSV file for arsenic and corresponding absolute and relative free energy plots as PNG files produced according to best practices.)

For more information on how to use the cli analysis tool use python benchmark_analysis.py -h.