Fix bond guessing with mixed-case atomtypes (#5343)

Guessing with atom types that were mixed case ('Au' vs 'AU') errored. Atomtypes are now converted to uppercase during comparison with the vdwradii table which is all uppercase.

Author: hejamu

package/CHANGELOG

@@ -22,6 +22,7 @@ The rules for this file:
  * 2.11.0
 
 Fixes
+ * Fix mixed-case atom types in guess_bonds (Issue #5342, PR #5343)
  * Fixes msd for non-linear frames, when non_linear is not explicitly
    provided (Issue #5100, PR #5254)
  * Fixes TypeError with np.int64 indexing in GSD Reader (Issue #5224)

package/MDAnalysis/guesser/default_guesser.py

@@ -433,6 +433,9 @@ def guess_bonds(self, atoms=None, coords=None):
         else:
             atomtypes = self.guess_types(atom_types=atoms.names)
 
+        # vdwradii keys are uppercase, so normalize atomtypes to match
+        atomtypes = np.char.upper(np.asarray(atomtypes, dtype=str))
+
         # check that all types have a defined vdw
         if not all(val in vdwradii for val in set(atomtypes)):
             raise ValueError(

testsuite/MDAnalysisTests/guesser/test_default_guesser.py

@@ -280,6 +280,19 @@ def test_guess_bonds_peptide():
     assert_equal(np.sort(u.bonds.indices, axis=0), np.sort(bonds, axis=0))
 
 
+def test_guess_bonds_mixed_case_types():
+    """Test that the guesser can handle mixed-case types"""
+    n_atoms = 2
+    # Actual positions don't matter for this test
+    positions = np.array([[0.0, 0.0, 0.0], [2.5, 0.0, 0.0]])
+    # Use mixed-case types
+    topology = Topology(n_atoms, attrs=[Atomtypes(["Au", "h"])])
+    u = mda.Universe(topology)
+    guesser = DefaultGuesser(None)
+    # This should not raise an error due to the mixed-case types
+    bonds = guesser.guess_bonds(u.atoms, positions)
+
+
 @pytest.mark.parametrize(
     "smi",
     [