2022-06-13 Core Developers meeting notes

General updates

• JW and DN will leave at the 30 minute mark for gov board meeting.

• DD will be offline Tues - Tues

• JW will be offline Fri

• DN will be offline Thursday

Individual updates

• DN

  • Last week I asked for help with annual report. On Friday, Katharina Meier asked for annual report. Bayer makes their budget decisions in July. I said we’d sent the report after the annual meeting (June 28). So I’ve started the report but I still have a shallow understanding of the technical stuff.

    • JW – As we work on the annual meeting presentation, I can work with you to propagate relevant info the the annual report.

    • DD – DN, do you think this will be enough for your needs?

    • DN – Yes, I see the material as largely overlapping.

• MT

  • Not much to say - Covered below in JW’s update and some stuff not of general interest

  • Made a new version (0.0.3) of amber-ff-porting. This fixes the fractional_bondorder_method on BondHandler, and removes all sterochemistry. I verified that the files are still loadable, and that T4 lysozyme is correctly processed (compared to AMBER).

• DD

  • Most of my time went toward reaching the 0.3.0 release of PLBenchmarks. Big blocking PR is #52, with protein structure prep. Did some iterations with bobym and now it’s in a nice state. So I’ve asked IA and JC to give it an independent review. This PR will knock out a lot of the remaining issues that need to be cleared for 0.3.0

  • Continued optimizing approach to using Max Planck Institute cluster (MPI cluster), and now we’re getting a lot of throughput. It has a lot of compute and somewhat limited memory, so this is well suited for chapin’s sets - Looks like it’s finishing ~10k optimizations per day. I saw a throughput problem over the weekend that may be due to straining QCA’s bandwidth.

  • Working on the S3 component for F@H. Had to make decisions about what’s hosted where. I’m going to use OMSF’s account for CI and continuous deployment. Basically, I need to be able to run unit tests with a live S3 instance. This should load-balance with the hosting that JC is going for other parts of this project.

    • includes alchemlyb#97

• JW –

  • Merged PDB loading with RDKit backend, should be much faster. I’m working on PDB loading with OE backend. Right now OE-only loading won’t work, you should use an older commit if you need that.

  • Reviewed Lorenzo’s small molecule benchmarking manuscript. It looks pretty good, you can check it out on #benchmarks-partners.

  • Following up with MT about interchange regression tests. Partial charge changes seem limited to a small number of molecules, and the differences in assignment are also small. I think this is unlikely to be a regression introduced by interchange, the release is already months delayed, and debugging will get harder since OE code i closed source, so we’re going to put this on the backburner and move forward with Interchange.

  • Worked with DN and LW last week to start defining our strategy/direction. Having a clear map will help us justify our value to pharma partners.

  • Worked with MShirts and CDavel on defining CD’s summer project. Difficult because this is a chicken-and-egg problem where we’re also finding deficiencies in using tagged SMARTS as our substructure specification and networkx for graph matching.

  •