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| benchmark_sys.ligands[PARTIAL_CHARGE], return_dict=False | ||
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| # apply new partial charges |
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Probably left over from example in meeting?
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Yes but I thought it would be good to leave for a future OpenFF person
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IAlibay
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Base on our meeting today, this seems fine. I did have the one question re: the pytest helper function, but it's fully up to you.
| # __________________________ Pytest Validation Function ________________________________ | ||
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| def validate_rbfe_network(script_dir, config): |
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I think this is something that came from Josh's review?
Just checking that this makes sense for you - i.e. it's not confusing to folks that might look at this example file.
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It did come from Josh's review. I do like it because it's a check to make sure you have what you think you have. At OpenFF we decided to keep it, but have main call validation, I'll be making these changes shortly.
| BENCHMARK_SET = "mcs_docking_set" | ||
| BENCHMARK_SYS = "hne" | ||
| PARTIAL_CHARGE = "nagl_openff-gnn-am1bcc-1.0.0.pt" # for the ligand and cofactors | ||
| FORCEFIELD = "openff-2.3.0" # available in openff-forcefields |
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Is the comment referring to openff-forcefields, or openmmforcefields (where one can find all the supported forcefields)?
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Thanks @jaclark5 , LGTM, just the two small comments.
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* Simple plan_rbfe * Add example script testing * pin gufe Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> * Update plan_rbfe script to include validation without pytest complexity --------- Co-authored-by: jaclark5 <jennifer.clark@openforcefield.org> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
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Close #89
Close #54
BenchmarkSystemand derived classRBFEBenchmarkSystemopenfe_benchmarks.dataPlease feel free to be nitpicky about naming and terminology.