fixup to_openmm_positions

OpenFreeEnergy · Dec 20, 2023 · 8658083 · 8658083
1 parent 4e91467
commit 8658083
Showing 1 changed file with 2 additions and 5 deletions.
diff --git a/gufe/components/proteincomponent.py b/gufe/components/proteincomponent.py
@@ -231,12 +231,9 @@ def to_openmm_positions(self) -> "openmm.app.unit.Quantity":
         """
         from openmm import unit as omm_unit
 
-        np_pos = deserialize_numpy(self.to_dict()["conformers"][0])
-        openmm_pos = (
-            list(map(lambda x: np.array(x), np_pos)) * omm_unit.angstrom
-        )
+        np_pos = self._rdkit.GetConformer().GetPositions()
 
-        return openmm_pos
+        return np_pos * omm_unit.angstrom
 
     def to_pdb_file(self, out_path: Union[str, bytes, PathLike[str], PathLike[bytes], io.TextIOBase]) -> str:
         """Write protein to pdb file.