From 2b01c47f1a87d2e041f6d67c6e17df01c20b0f5b Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 24 Oct 2025 08:26:14 -0700 Subject: [PATCH] pull data for septop when running in Colab --- openmm_septop/septop_tutorial.ipynb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/openmm_septop/septop_tutorial.ipynb b/openmm_septop/septop_tutorial.ipynb index e995c2e..6dd8297 100644 --- a/openmm_septop/septop_tutorial.ipynb +++ b/openmm_septop/septop_tutorial.ipynb @@ -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",