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pull data for septop when running in Colab #256

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pull data for septop when running in Colab #256

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pull data for septop when running in Colab
atravitz Oct 24, 2025
cb0e0e6
Merge branch 'main' into fix/septop-colab-data
mikemhenry Oct 30, 2025
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5 changes: 4 additions & 1 deletion openmm_septop/septop_tutorial.ipynb
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Expand Up @@ -69,11 +69,14 @@
" import condacolab\n",
" import locale\n",
" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
"\n",
" # quick fix for https://github.com/conda-incubator/condacolab/issues/75\n",
" # if deprecation warnings persist, rerun this cell\n",
" import warnings\n",
" warnings.filterwarnings(action=\"ignore\", message=r\"datetime.datetime.utcnow\") \n",
" \n",
" ! curl -L --remote-name https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/openmm_septop/tyk2_ligands.sdf\n",
" ! curl -L --remote-name https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/openmm_septop/tyk2_protein.pdb\n",
" for _ in range(3):\n",
" # Sometimes we have to re-run the check\n",
" try:\n",
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