update for new cinnabar API#311
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# Conflicts: # environment.yaml
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| "id": "ddae61fd-fa15-4be9-9160-ba3e195c67dc", | |||
| "metadata": {}, | |||
| "source": [ | |||
| "# Plotting OpenFE DG results against experiment using Cinnabar v0.4\n", | |||
| "# Plotting OpenFE DG results against experiment using Cinnabar v0.6.0\n", | |||
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This notebook is not included in the current docs do we still want this?
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It might be useful for people who run ABFEs not having to go throught he RBFE related content in the general plotting notebook, but maybe it's also not super important? If we keep it, we should definitely add it to the docs!
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Note: Personally I'm in support of merging the notebooks.
I think this notebook was necessary because some folks were asking how they could plot their absolute results and they didn't know how. We just need to make sure that's got a proper example somewhere.
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| "id": "ddae61fd-fa15-4be9-9160-ba3e195c67dc", | |||
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Maybe we could also add here or gathered with gather_abfe and refer to the ABFE CLI tutorial?
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| "id": "ddae61fd-fa15-4be9-9160-ba3e195c67dc", | |||
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We probably need to make it clearer that this tutorial is geared solely towards relative free energies.
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| "id": "ddae61fd-fa15-4be9-9160-ba3e195c67dc", | |||
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"gather the experiemtnal" -> typo
"to have units" -> Can you expand and mention OpenFF units here?
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| "id": "ddae61fd-fa15-4be9-9160-ba3e195c67dc", | |||
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Line #8. value=row["DDG(i->j) (kcal/mol)"] * unit.kilocalories_per_mole, # the computed relative free energy change for the transformation
[nit] I like these inline comments, but it might be easier for folks to read them if you put the comment on the line before the kwargs rather than trying to have it all on the same line.
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| "id": "ddae61fd-fa15-4be9-9160-ba3e195c67dc", | |||
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IAlibay
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IAlibay
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Couple of typos, otherwise the content changes look good.
I would advocate for merging post content fix and then opening a follow-up PR / issue to deal with the absolute cookbook (my suggestion would be to try to merge if possible, otherwise maybe breaking down the one tutorial into more cookbooks).
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