From b8d489508fe43f09126deb626d3ab2aff27fc06a Mon Sep 17 00:00:00 2001 From: Sergey O Date: Fri, 22 Dec 2023 13:35:22 -0500 Subject: [PATCH] fixing biopython 1.81 --- batch/AlphaFold2_batch.ipynb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/batch/AlphaFold2_batch.ipynb b/batch/AlphaFold2_batch.ipynb index 910d3858..092ba90a 100644 --- a/batch/AlphaFold2_batch.ipynb +++ b/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", @@ -261,7 +262,7 @@ "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", @@ -269,4 +270,4 @@ ] } ] -} +} \ No newline at end of file