From 31f33ccb127b659f5eebdcb81b6e65e2f9177783 Mon Sep 17 00:00:00 2001
From: Sergey O <krypton@uw.edu>
Date: Fri, 22 Dec 2023 13:34:23 -0500
Subject: [PATCH] fixing biopython 1.81

---
 AlphaFold2.ipynb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/AlphaFold2.ipynb b/AlphaFold2.ipynb
index de6d6d99..53fefa11 100644
--- a/AlphaFold2.ipynb
+++ b/AlphaFold2.ipynb
@@ -152,6 +152,7 @@
         "  os.system(\"ln -s /usr/local/lib/python3.*/dist-packages/alphafold alphafold\")\n",
         "  # patch for jax > 0.3.25\n",
         "  os.system(\"sed -i 's/weights = jax.nn.softmax(logits)/logits=jnp.clip(logits,-1e8,1e8);weights=jax.nn.softmax(logits)/g' alphafold/model/modules.py\")\n",
+        "  os.system(\"pip install -q biopython==1.81\")\n",
         "  os.system(\"touch COLABFOLD_READY\")\n",
         "\n",
         "if USE_AMBER or USE_TEMPLATES:\n",