fixing biopython 1.81

batch/AlphaFold2_batch.ipynb

@@ -41,7 +41,7 @@
         "Easy to use AlphaFold2 protein structure [(Jumper et al. 2021)](https://www.nature.com/articles/s41586-021-03819-2) and complex [(Evans et al. 2021)](https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1) prediction using multiple sequence alignments generated through MMseqs2. For details, refer to our manuscript:\n",
         "\n",
         "[Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: Making protein folding accessible to all.\n",
-        "*Nature Methods*, 2022](https://www.nature.com/articles/s41592-022-01488-1) \n",
+        "*Nature Methods*, 2022](https://www.nature.com/articles/s41592-022-01488-1)\n",
         "\n",
         "**Usage**\n",
         "\n",
@@ -71,7 +71,7 @@
         "#@title Mount google drive\n",
         "from google.colab import drive\n",
         "drive.mount('/content/drive')\n",
-        "from sys import version_info \n",
+        "from sys import version_info\n",
         "python_version = f\"{version_info.major}.{version_info.minor}\""
       ],
       "execution_count": null,
@@ -132,6 +132,7 @@
         "  ln -s /usr/local/lib/python3.*/dist-packages/colabfold colabfold\n",
         "  ln -s /usr/local/lib/python3.*/dist-packages/alphafold alphafold\n",
         "  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",
+        "  pip install -q biopython==1.81\n",
         "  touch COLABFOLD_READY\n",
         "fi\n",
         "\n",
@@ -261,12 +262,12 @@
         "The source code of ColabFold is licensed under [MIT](https://raw.githubusercontent.com/sokrypton/ColabFold/main/LICENSE). Additionally, this notebook uses AlphaFold2 source code and its parameters licensed under [Apache 2.0](https://raw.githubusercontent.com/deepmind/alphafold/main/LICENSE) and  [CC BY 4.0](https://creativecommons.org/licenses/by-sa/4.0/) respectively. Read more about the AlphaFold license [here](https://github.com/deepmind/alphafold).\n",
         "\n",
         "**Acknowledgments**\n",
-        "- We thank the AlphaFold team for developing an excellent model and open sourcing the software. \n",
+        "- We thank the AlphaFold team for developing an excellent model and open sourcing the software.\n",
         "\n",
         "- Do-Yoon Kim for creating the ColabFold logo.\n",
         "\n",
         "- A colab by Sergey Ovchinnikov ([@sokrypton](https://twitter.com/sokrypton)), Milot Mirdita ([@milot_mirdita](https://twitter.com/milot_mirdita)) and Martin Steinegger ([@thesteinegger](https://twitter.com/thesteinegger)).\n"
       ]
     }
   ]
-}
+}