Add SepTop BACE dataset#116
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| for edge in network.edges: | ||
| edge.annotations.update(network_provenance) |
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Unfortunately, annotations is a copy of the data so this doesn't get saved into the network, you can make a new set of edges using new_edge = edge.with_annotations(network_provenance) though.
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Thanks, fixed this!
jthorton
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jthorton
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Just one change needed for the lomap planning script to make sure the generation details are saved and then we just need to generate the network again and its good to go. Thanks for adding this one @hannahbaumann !
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Is it intentional that all systems have the tag "ross"? I'm assuming not. I would propose we update the CI so that if the first list is empty then none of the systems get that tag (opposite of current behavior where all of them do), and then add system names to the second list as exceptions to add the tag to those systems.
jaclark5
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jaclark5
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Other than a proper reference to exp.csv I think this is good to go!
| # tag each entry with the source, currently we link to the aggregated reference data but this should be changed if we refine it in future. | ||
| baumann_et_al_doi = "https://doi.org/10.1021/acs.jctc.3c00282" | ||
| # load the ref data from the industry benchmark results stored on github | ||
| ref_dg_data = pd.read_csv("/Users/hannahbaumann/test_septop/bace/exp.csv") |
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Instead of hard coding the path on your computer, maybe this should be (a) an input argument or (b) hardcode a wget from your GitHub repo
| ("cofactor", ["cofactors.sdf"], []), | ||
| ("bfe", ["experimental_binding_data.json"], []), | ||
| ("sfe", ["experimental_solvation_free_energy_data.json"], ["mnsol_neutral"]), | ||
| ("ross", [], []), |
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I double checked this, and this is correct. It acknowledges that the tag exists but doesn't have any rules on how it should be used. Thus, it can catch typos like accidentally manually writing the tag as roos for example
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