moved imports and more direct check

nomad-coe · Feb 8, 2024 · 05ec8ef · 05ec8ef
1 parent dfe4adf
commit 05ec8ef
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Showing 2 changed files with 10 additions and 12 deletions.
diff --git a/atomisticparsers/gromacs/parser.py b/atomisticparsers/gromacs/parser.py
@@ -30,7 +30,7 @@
 except Exception:
     logging.warning("Required module MDAnalysis not found.")
     MDAnalysis = False
-
+from ase.symbols import symbols2numbers
 from nomad.units import ureg
 from nomad.parsing.file_parser import TextParser, Quantity, FileParser
 from runschema.run import Run, Program, TimeRun
@@ -837,12 +837,11 @@ def get_composition(children_names):
                 )
 
             atom_labels = self.traj_parser.get_atom_labels(n)
-            try:
-                from ase import Atoms as ase_atoms
-
-                _ = ase_atoms(symbols=atom_labels)
-            except Exception:  # TODO this check should be moved to the system normalizer in the new schema
-                atom_labels = ["X" for _ in atom_labels]
+            if atom_labels is not None:
+                try:
+                    symbols2numbers(atom_labels)
+                except KeyError:
+                    atom_labels = ["X"] * len(atom_labels)
 
             self.parse_trajectory_step(
                 {

diff --git a/atomisticparsers/h5md/parser.py b/atomisticparsers/h5md/parser.py
@@ -52,6 +52,7 @@
 from atomisticparsers.utils import MDParser, MOL
 from .metainfo.h5md import ParamEntry, CalcEntry, Author
 from nomad.units import ureg
+from ase.symbols import symbols2numbers
 
 
 class HDF5Parser(FileParser):
@@ -583,11 +584,9 @@ def parse_system(self):
             atom_labels = atoms_dict.get("labels")
             if atom_labels is not None:
                 try:
-                    from ase import Atoms as ase_atoms
-
-                    _ = ase_atoms(symbols=atom_labels)
-                except Exception:  # TODO this check should be moved to the system normalizer in the new schema
-                    atoms_dict["labels"] = ["X" for _ in atom_labels]
+                    symbols2numbers(atom_labels)
+                except KeyError:  # TODO this check should be moved to the system normalizer in the new schema
+                    atoms_dict["labels"] = ["X"] * len(atom_labels)
 
             topology = None
             if i_step == 0:  # TODO extend to time-dependent bond lists and topologies