feat: disulfide bonding

PaddlePaddle · Aug 24, 2024 · e4d6821 · e4d6821
1 parent db42183
commit e4d6821
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Showing 2 changed files with 15 additions and 1 deletion.
diff --git a/apps/protein_folding/helixfold3/data/demo_disulf.json b/apps/protein_folding/helixfold3/data/demo_disulf.json
@@ -0,0 +1,14 @@
+{
+    "entities": [
+        {
+            "type": "protein",
+            "sequence": "MASVKSSSSSSSSSFISLLLLILLVIVLQSQVIECQPQQSCTASLTGLNVCAPFLVPGSPTASTECCNAVQSINHDCMCNTMRIAAQIPAQCNLPPLSCSAN",
+            "count": 1
+        },
+        {
+            "type": "bond",
+            "bond": "A,CYS,41,SG,A,CYS,77,SG,disulf,2.2;A,CYS,51,SG,A,CYS,66,SG,disulf,2.2;A,CYS,67,SG,A,CYS,92,SG,disulf,2.2;A,CYS,79,SG,A,CYS,99,SG,disulf,2.2",
+            "_case_from": "https://www.uniprot.org/uniprotkb/Q43495/entry#ptm_processing"
+        }
+    ]
+}
diff --git a/apps/protein_folding/helixfold3/helixfold/data/pipeline_conf_bonds.py b/apps/protein_folding/helixfold3/helixfold/data/pipeline_conf_bonds.py
@@ -116,7 +116,7 @@ def parse_covalent_bond_input(input_string: str) -> List[CovalentBond]:
 
         # Append the CovalentBond instance to the list
         covalent_bonds.append(covalent_bond)
-        logging.info(f"Added {len(covalent_bonds)} bonds: {covalent_bonds}")
+    logging.info(f"Added {len(covalent_bonds)} bonds: {covalent_bonds}")
 
     return covalent_bonds