Fix missing chainIDs in XYZ files

cnpem · Jun 27, 2024 · 6bc43b3 · 6bc43b3
1 parent d2c1462
commit 6bc43b3
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/AtomPacker/core/io/xyz/file.py b/AtomPacker/core/io/xyz/file.py
@@ -30,6 +30,12 @@ def load_xyz(filename: str) -> Universe:
     # Read XYZ file in MDAnalysis.Universe
     universe = Universe(filename)
 
+    # if chainIDs not provided, set them to 'X'
+    if "chainIDs" not in universe.atoms._SETATTR_WHITELIST:
+        universe.add_TopologyAttr(
+            "chainIDs", ["X"] * universe.atoms.n_atoms
+        )  # chainIDs
+
     # Add radii to topology
     universe.add_TopologyAttr(
         "radii",