Changes to support `openfe` 1.0, `gufe` 1.0

OpenFreeEnergy / feflow

Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits

MIT License

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Changes to support `openfe` 1.0, `gufe` 1.0 #31

Closed dotsdl closed 4 months ago

dotsdl commented 9 months ago

There are changes in openfe and gufe for their respective 1.0 releases, in particular in Settings. These should be addressed in advance of a new feflow release.

@richardjgowers can give more insights into what has changed in these packages.

IAlibay commented 8 months ago

From an initial look, this is going to require a reasonably large amount of changes in the NEQ protocol, at least the way mappings are handled needs changing.

I've taken an initial test stab in #33 - happy to hand over as necessary @ijpulidos

ijpulidos commented 8 months ago

In order to keep things more modular and easier to understand I'm going to enumerate the things that will be needed for us to support 1.0 releases of gufe and openfe.

TODO:

[ ] Fix IntegratorSettings
- [ ] Make a new integrator settings class for NEQ integrator
[ ] Fix solvation settings
- [ ] should be just an import replacement
[ ] Deal with mapping changes
- [ ] SIngle mapping validation
- [ ] Make sure everything is now a list rather than a dictionary
- [ ] Remove dependency on "ligand" dictionary entry in mapping

dotsdl commented 4 months ago

Is this one now complete @ijpulidos?

ijpulidos commented 4 months ago

Yes, #38 should have taken care of this, closing!