ENH: expose TPR box dimensions through timestep

package/AUTHORS

@@ -280,6 +280,7 @@ Chronological list of authors
   - Amarendra Mohan
   - Shubham Mittal  
   - Charity Grey
+  - Tanmay Baranwal
 
 External code
 -------------

package/CHANGELOG

@@ -18,10 +18,13 @@ The rules for this file:
          spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
          harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
          ollyfutur, Amarendra22, charity-g, ParthUppal523
-
+ 
  * 2.11.0
 
 Fixes
+ * TPRReader now exposes box dimensions when loading TPR files
+   as coordinates-only Universes, fixing missing `Universe.dimensions`
+   values. (Issue #5375, PR #5377)
  * `MDAnalysis.analysis.nucleicacids.WatsonCrickDist`, `MinorPairDist`,
    and `MajorPairDist` now match residue names against the full resname
    instead of only the first character, fixing incorrect behaviour with

package/MDAnalysis/coordinates/TPR.py

@@ -51,6 +51,7 @@
 
 """
 
+from ..lib.mdamath import triclinic_box
 from . import base
 from ..lib import util
 from .timestep import Timestep
@@ -110,7 +111,15 @@ def _read_first_frame(self):
 
         state_ngtc = th.ngtc  # done init_state() in src/gmxlib/tpxio.c
         if th.bBox:
-            tpr_utils.extract_box_info(data, th.fver)
+            box_info = tpr_utils.extract_box_info(data, th.fver)
+            # box vectors are stored in nm
+            box_angstrom = np.array(box_info.size) * 10.0
+
+            ts.dimensions = triclinic_box(
+                box_angstrom[0],
+                box_angstrom[1],
+                box_angstrom[2],
+            )
 
         if state_ngtc > 0:
             if th.fver < 69:  # redundancy due to  different versions

testsuite/MDAnalysisTests/coordinates/test_tpr.py

@@ -75,6 +75,7 @@
 import pytest
 import numpy as np
 from numpy.testing import assert_allclose, assert_equal
+from MDAnalysisTests.datafiles import TPR
 
 
 @pytest.mark.parametrize(
@@ -494,3 +495,35 @@ def test_different_versions():
     assert_allclose(u.atoms.velocities[-1, ...], exp_vel)
     assert_equal(u.atoms.positions.shape, exp_shape)
     assert_equal(u.atoms.velocities.shape, exp_shape)
+
+
+class TestTPRDimensions:
+    """Tests for TPR coordinate box dimensions."""
+
+    @pytest.mark.parametrize(
+        "tpr_file, expected_dims",
+        [
+            # cubic box - adk oplsaa system (tpx 58)
+            (
+                TPR,
+                [80.017006, 80.017006, 80.017, 60.0, 60.0, 90.0],
+            ),
+            # cubic box - same system different gromacs versions
+            (
+                TPR2024_4,
+                [79.1, 79.1, 37.9, 90.0, 90.0, 90.0],
+            ),
+            (
+                TPR2016,
+                [79.1, 79.1, 37.9, 90.0, 90.0, 90.0],
+            ),
+            # different box shape
+            (
+                TPR455Double,
+                [43.7388, 43.7388, 107.9261, 90.0, 90.0, 90.0],
+            ),
+        ],
+    )
+    def test_tpr_dimensions_values(self, tpr_file, expected_dims):
+        u = mda.Universe(tpr_file)
+        assert_allclose(u.dimensions, expected_dims, rtol=1e-3)

testsuite/MDAnalysisTests/topology/test_tprparser.py

@@ -23,6 +23,7 @@
 import functools
 
 import MDAnalysis as mda
+from numpy.testing import assert_allclose
 import MDAnalysis.topology.TPRParser
 import numpy as np
 import pytest