v2.3.6 - Fix BioPython deprecated SCOPData import & Fix NaN

steineggerlab · Dec 28, 2023 · 9c3ec6e · 9c3ec6e
1 parent 2febbbd
commit 9c3ec6e
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/alphafold/data/mmcif_parsing.py b/alphafold/data/mmcif_parsing.py
@@ -21,7 +21,10 @@
 
 from absl import logging
 from Bio import PDB
-from Bio.Data import SCOPData
+try:
+  from Bio.Data import PDBData
+except ImportError:
+  from Bio.Data import SCOPData as PDBData
 
 # Type aliases:
 ChainId = str
@@ -258,7 +261,7 @@ def parse(*,
       author_chain = mmcif_to_author_chain_id[chain_id]
       seq = []
       for monomer in seq_info:
-        code = SCOPData.protein_letters_3to1.get(monomer.id, 'X')
+        code = PDBData.protein_letters_3to1.get(monomer.id, 'X')
         seq.append(code if len(code) == 1 else 'X')
       seq = ''.join(seq)
       author_chain_to_sequence[author_chain] = seq

diff --git a/setup.py b/setup.py
@@ -18,7 +18,7 @@
 
 setup(
     name='alphafold-colabfold',
-    version='2.3.5',
+    version='2.3.6',
     long_description_content_type='text/markdown',
     description='An implementation of the inference pipeline of AlphaFold v2.3.1. '
     'This is a completely new model that was entered as AlphaFold2 in CASP14 '