2020-08-06 PLBenchmark update notes

Keep code and data separate?

Yes, but how?

• If 2 repos, need to include some minimal test data in code repo

How to distribute data?

• Can put them in release tarballs, as PDBs can get quite large

• Used to push data to github, got too big and now storing on google drive

Current structure

• targets.yml contains metadata, for each target

  • /data/: metadata for each ligand (edges.yml, ligands.yml, and protein.yaml)

  • /protein/ (PDB for structure, GROMACS TOP for topology, and FF file - a modified 99sb now, could be others/multiple in the future)

  • /ligands/, (similar structure for each, coordinates using SDF, force field parsley)

  • /hybrid/, defines which atoms are converted into others

  • not stored, could could also add things like combined systems, solvated boxes

Data needs

• Avoid redundancy (i.e. only one coordinate file, convert on the fly as needed)

  • A single master ligand SDF would be useful for somebody looking through, but that would be redundant data

• It would be nice to be able to easily access without using the command line (MT disagrees/is unsure)

• Current directory structure is good for DH’s work, may not be the most accessible for users

• Most important need here is getting ligand data out, with structures, since the force fields are accessible

  • Maybe topologies should not be provided, only the tools required to generate them?

    • Upside: Lighter data, better fit to the principle of this data

    • Downside: partial charges will be inconsistent, and probably something else will cause different topologies to be generated

• MT: How significantly does data change regularly?

  • DH: Often, i.e. changing ligand or protein structure, adding in more t, even more targets, especially if user contributions in the future.

Code needs

DH: Could use a review on current code. Also would like to add some features to it

MT will review code

DH also built a workflow in his fork of pmx

Rename

PLBenchmarks needs a better name, John suggested Beryllium