Adding guards to index assignment in Universe creation

package/AUTHORS

@@ -270,6 +270,7 @@ Chronological list of authors
 2026
   - Mohammad Ayaan
   - Khushi Phougat
+  - Akshat Raj
 
 External code
 -------------

package/CHANGELOG

@@ -17,6 +17,13 @@ The rules for this file:
 ??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
          spyke7, talagayev, tanii1125, BradyAJohnston
 
+Fixes
+ * Universe.empty now raises a ValueError if atom_resindex or residue_segindex
+   contains out-of-bounds indices (Issue #5223)
+
+02/11/2026 IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
+         spyke7, talagayev, tanii1125, BradyAJohnston, Akshat Raj
+
  * 2.11.0
 
 Fixes
@@ -3610,4 +3617,4 @@ Testsuite
     licenses
 
 11/12/07 naveen
-  * prepared for release outside lab
+  * prepared for release outside lab

package/MDAnalysis/core/universe.py

@@ -745,6 +745,26 @@ def empty(
                 UserWarning,
             )
 
+        if atom_resindex is not None:
+            atom_resindex = np.asarray(atom_resindex)
+            if np.any(atom_resindex >= n_residues) or np.any(
+                atom_resindex < 0
+            ):
+                raise ValueError(
+                    "atom_resindex contains invalid residue indices."
+                    "All values must be between 0 and n_residues-1."
+                )
+
+        if residue_segindex is not None:
+            residue_segindex = np.asarray(residue_segindex)
+            if np.any(residue_segindex >= n_segments) or np.any(
+                residue_segindex < 0
+            ):
+                raise ValueError(
+                    "residue_segindex contains invalid segment indices. "
+                    "All values must be between 0 and n_segments-1."
+                )
+
         if residue_segindex is None and n_segments > 1:
             warnings.warn(
                 "Segments specified but no segment_resindex given.  "

testsuite/MDAnalysisTests/analysis/test_helix_analysis.py

@@ -247,7 +247,10 @@ def zigzag():
     """
     n_atoms = 100
     u = mda.Universe.empty(
-        100, atom_resindex=np.arange(n_atoms), trajectory=True
+        100,
+        atom_resindex=np.arange(n_atoms),
+        n_residues=n_atoms,
+        trajectory=True,
     )
     xyz = np.array(
         list(

testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py

@@ -440,6 +440,7 @@ def universe():
             n_residues=n_residues,
             atom_resindex=[0, 0, 0, 1, 1, 1, 2, 2, 3, 3],
             residue_segindex=[0, 0, 1, 1],
+            n_segments=2,
             trajectory=True,  # necessary for adding coordinates
         )
 

testsuite/MDAnalysisTests/core/test_universe.py

@@ -1867,3 +1867,23 @@ def test_no_affect_custom_attrs(self, good):
             sorted([each.attrname for each in original_attrs]),
             sorted([each.attrname for each in good._topology.attrs]),
         )
+
+    def test_empty_universe_bounds(self):
+        with pytest.raises(
+            ValueError, match="atom_resindex contains invalid residue indices."
+        ):
+            mda.Universe.empty(
+                n_atoms=2, n_residues=2, atom_resindex=[0, 2], trajectory=True
+            )
+
+        with pytest.raises(
+            ValueError,
+            match="residue_segindex contains invalid segment indices.",
+        ):
+            mda.Universe.empty(
+                n_atoms=2,
+                n_residues=2,
+                n_segments=2,
+                atom_resindex=[0, 1],
+                residue_segindex=[0, 2],
+            )