skip observables contained in particle groups

MDAnalysis · Jun 15, 2024 · f9c6ca1 · f9c6ca1
1 parent 347a0c0
commit f9c6ca1
Showing 1 changed file with 9 additions and 2 deletions.
diff --git a/package/MDAnalysis/coordinates/H5MD.py b/package/MDAnalysis/coordinates/H5MD.py
@@ -207,6 +207,7 @@
    :members:
 
 """
+import logging
 
 import numpy as np
 import MDAnalysis as mda
@@ -230,6 +231,8 @@ class MockH5pyFile:
 else:
     HAS_H5PY = True
 
+logger = logging.getLogger(__name__)
+
 
 class H5MDReader(base.ReaderBase):
     r"""Reader for the H5MD format.
@@ -675,8 +678,12 @@ def _copy_to_data(self):
 
         if 'observables' in self._file:
             for key in self._file['observables'].keys():
-                self.ts.data[key] = self._file['observables'][key][
-                    'value'][self._frame]
+                try:
+                    self.ts.data[key] = self._file['observables'][key][
+                        'value'][self._frame]
+                except KeyError:
+                    logger.warning(f"Unable to read '{key}' from 'observables'")
+
 
         # pulls 'time' and 'step' out of first available parent group
         for name, value in self._has.items():