Adding multimer support to OpenFold notebook

d4acbe6e · jnwei · 81d817fe · d4acbe6e · d4acbe6e
Commit d4acbe6e authored Jan 30, 2024 by jnwei
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Showing with 319 additions and 176 deletions

notebooks/OpenFold.ipynb notebooks/OpenFold.ipynb +313 -170

notebooks/environment.yml notebooks/environment.yml +6 -6

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--- a/notebooks/OpenFold.ipynb
+++ b/notebooks/OpenFold.ipynb
--- a/notebooks/environment.yml
+++ b/notebooks/environment.yml
@@ -3,15 +3,15 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
-  - conda-forge::openmm=7.5.1
-  - conda-forge::pdbfixer
+  - openmm=7.7
+  - pdbfixer
+  - ml-collections 
+  - PyYAML==5.4.1
+  - requests
+  - typing-extensions
  - bioconda::hmmer==3.3.2
  - bioconda::hhsuite==3.3.0
  - bioconda::kalign2==2.04
  - pip:
      - biopython==1.79
      - dm-tree==0.1.6
-      - ml-collections==0.1.0
-      - PyYAML==5.4.1
-      - requests==2.26.0
-      - typing-extensions==3.10.0.2