update ligandnetwork generation notebooks #274
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atravitz
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Some migration from OpenFreeEnergy/konnektor#200, but generally minor changes. |
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| "[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html" | ||
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| "[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html" | ||
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Yes I don't think anyone uses it.
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| "[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html" | ||
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Here, as below, I'd like to execute all the code so our tests catch anything out of date.
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| "[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html" | ||
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| "[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html" | ||
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| "[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html" | ||
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Here, as below, I'd like to execute all the code so our tests catch anything out of date.
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related: OpenFreeEnergy/gufe#692 and OpenFreeEnergy/openfe#1750 |
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| "id": "5da95fa6-c9a7-48a2-9d8e-e35b3b6818f6", |
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This makes edge scoring sound like an exact science, which we know it's not, maybe make it clear that the scorer returns an estimate of the difficulty of the edge and is well known to get this wrong!
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Line #12. mappers=[openfe.setup.LomapAtomMapper()],
nit I would consider using kartograf as the mapper with map_hydrogens_on_hydrogens_only set to True if the ligands are well aligned, this will lead to a more representative edge visualisation below as OpenFE doesn't allow transformations between hydrogens and heavy atoms.
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See above, while this is what the 3D mapping shows this is not what OpenFE actually does.
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More a question for me: can we use this to visualise the ligands with the receptor as well?
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-01-08T11:38:30Z Do we want some more details on what we are trying to show in the notebook, it might be good so users can quickly tell if this is relevent to them, we also might want to point to the konnector docs for more examples and details on the networks available. |
related to: OpenFreeEnergy/konnektor#169
and OpenFreeEnergy/konnektor#200