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update ligandnetwork generation notebooks #274

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@atravitz atravitz commented Dec 9, 2025

@atravitz atravitz self-assigned this Dec 9, 2025
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Colab 👈 Launch a Colab session on branch update_konnektor_notebooks

@atravitz atravitz force-pushed the update_konnektor_notebooks branch from 195fa0f to 4427ece Compare December 11, 2025 00:33
@atravitz atravitz mentioned this pull request Dec 11, 2025
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atravitz commented Dec 11, 2025

Some migration from OpenFreeEnergy/konnektor#200, but generally minor.

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atravitz commented Dec 11, 2025
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cookbook/generate_ligand_network.ipynb
"\n",
"[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html"
]
},
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@atravitz atravitz Dec 11, 2025 •
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It's my understanding that we want to phase out perses from tutorials.


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cookbook/generate_ligand_network.ipynb
"\n",
"[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html"
]
},
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@atravitz atravitz Dec 11, 2025 •
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do we want to drop perses_scorer here?


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cookbook/generate_ligand_network.ipynb
"\n",
"[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html"
]
},
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@atravitz atravitz Dec 11, 2025 •
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Here, as below, I'd like to execute all the code so our tests catch anything out of date.


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atravitz
atravitz commented Dec 11, 2025
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cookbook/generate_ligand_network.ipynb
"\n",
"[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html"
]
},
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@atravitz atravitz Dec 11, 2025 •
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It's my understanding that we want to phase out perses from tutorials.


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cookbook/generate_ligand_network.ipynb
"\n",
"[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html"
]
},
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@atravitz atravitz Dec 11, 2025 •
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do we want to drop perses_scorer here?


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cookbook/generate_ligand_network.ipynb
"\n",
"[Ligand Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.setup.LigandNetwork.html"
]
},
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@atravitz atravitz Dec 11, 2025 •
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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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@atravitz atravitz requested review from IAlibay and jthorton December 11, 2025 00:39
@atravitz atravitz changed the title update konnektor notebooks update ligand generation notebooks Dec 11, 2025
@atravitz atravitz changed the title update ligand generation notebooks update ligandnetwork generation notebooks Dec 11, 2025
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atravitz commented Dec 11, 2025 •
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related: OpenFreeEnergy/gufe#692 and OpenFreeEnergy/openfe#1750

@atravitz atravitz marked this pull request as ready for review December 11, 2025 03:28
@atravitz atravitz force-pushed the update_konnektor_notebooks branch from e4e3197 to 141cace Compare December 11, 2025 15:33
@atravitz atravitz force-pushed the update_konnektor_notebooks branch from f0b882c to 3ee90e0 Compare December 11, 2025 16:45
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