DH – Worked on benchmark datasets. Contributing to Lim paper by adding OPLS3e and new openff versions. Could use some support/recommendations for versioning protein-ligand benchmark datasets.
JRG – OpenMM Conda-forge migration. Working with Anthony Scopatz. Kickoff meeting this coming Friday. This overlaps with some other work that Scopatz is doing, and may mean that he GPU CI infrastructure will be built with our needs in mind. Looking at OpenMM on C-F by october.
SB – Mostly writing papers. Close-to-first-pass at recharge implemented in ForceBalance. Separates normal parameters from “mathematical parameters”. Need input from Lee-Ping. Need to package Recharge – Would like to build it on conda-forge, but it requires psi4 and openforcefield.
SB – Can I do “alpha” or “prerelease” versions? (eg 0.0.1a3)
JRG – Yes, just have a consistent semantically/lexically-ordered system. They may only accept certain patterns. May be possible to add to build string if they don’t like your naming pattern. Could ask at their gitter.im room.
MT – Started working on conformer generation CLI tool. Most test cases work, some ambiguity about molecule interpretation and output file naming. Needs feedback. Made openforcefield.cli module, which currently only has the python file. Basing this script off conformer energy one. Have the choice to either run the script top-to-bottom with lots of comments, or refactor into functions. I think the latter is more readable. Not sure where those functions should live (in toolkit vs. somewhere else).
JW – I think all the running code should stay in the script, since it’s
SB – Think we shouldn’t try to teach people to interact with the code this way, since it’ll be hard for pharma people to debug. Having scripts call refactored functions in the toolkit itself would be better. People who want to modify the CLI could access an equivalent notebook.
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