Fix parsing of box vector in H5MD reader

package/AUTHORS

@@ -211,6 +211,7 @@ Chronological list of authors
   - Xu Hong Chen
   - Domenico Marson
   - Ahmed Salah Ghoneim
+  - Alexander Schlaich
 
 External code
 -------------

package/CHANGELOG

@@ -16,10 +16,11 @@ The rules for this file:
 
 ??/??/?? IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae, 
          ooprathamm, MeetB7, BFedder, v-parmar, MoSchaeffler, jbarnoud, jandom,
-         xhgchen, jaclark5, DrDomenicoMarson, AHMED-salah00
+         xhgchen, jaclark5, DrDomenicoMarson, AHMED-salah00, schlaicha
  * 2.5.0
 
 Fixes
+  * Fix parsing of box vector in H5MD reader (Issue #4076)
   * Fix the misleading 'AtomGroup.guess_bonds()' docs and passed missing
     arguments (PR #4059)
   * Fix for NetCDF trajectories without `time` variable (Issue #4073)

package/MDAnalysis/coordinates/H5MD.py

@@ -332,6 +332,8 @@ class H5MDReader(base.ReaderBase):
        Adds :meth:`parse_n_atoms` method to obtain the number of atoms directly
        from the trajectory by evaluating the shape of the ``position``,
        ``velocity``, or ``force`` groups.
+    .. versionchanged:: 2.5.0
+       Add correct handling of simple cuboid boxes
 
     """
 
@@ -640,8 +642,17 @@ def _read_frame(self, frame):
 
         # Sets frame box dimensions
         # Note: H5MD files must contain 'box' group in each 'particles' group
-        if 'edges' in particle_group['box']:
-            ts.dimensions = core.triclinic_box(*particle_group['box/edges/value'][frame, :])
+        if "edges" in particle_group["box"]:
+            edges = particle_group["box/edges/value"][frame, :]
+            # A D-dimensional vector or a D × D matrix, depending on the
+            # geometry of the box, of Float or Integer type. If edges is a
+            # vector, it specifies the space diagonal of a cuboid-shaped box.
+            # If edges is a matrix, the box is of triclinic shape with the edge
+            # vectors given by the rows of the matrix.
+            if edges.shape == (3,):
+                ts.dimensions = [*edges, 90, 90, 90]
+            else:
+                ts.dimensions = core.triclinic_box(*edges)
         else:
             ts.dimensions = None
 

testsuite/MDAnalysisTests/coordinates/test_h5md.py

@@ -341,6 +341,18 @@ def test_2D_box(self, h5md_file, outfile):
                            match="MDAnalysis only supports 3-dimensional"):
             u = mda.Universe(TPR_xvf, outfile)
 
+    def test_box_vector(self, h5md_file, outfile):
+        with h5md_file as f:
+            with h5py.File(outfile, 'w') as g:
+                f.copy(source='particles', dest=g)
+                f.copy(source='h5md', dest=g)
+                vector = [1, 2, 3]
+                del g['particles/trajectory/box/edges']
+                g['particles/trajectory/box/edges/value'] = [vector, vector, vector]
+        u = mda.Universe(TPR_xvf, outfile)
+        # values in vector are conveted from nm -> Angstrom
+        assert_equal(u.trajectory.ts.dimensions, [10, 20, 30, 90, 90, 90])
+
     def test_no_box(self, h5md_file, outfile):
         with h5md_file as f:
             with h5py.File(outfile, 'w') as g: