Fix bond deletion (#4763)

* Fix issue where duplicate bonds were not being adequately deleted.
---------

Co-authored-by: Irfan Alibay <[email protected]>

package/CHANGELOG

@@ -23,6 +23,8 @@ The rules for this file:
  * 2.8.0
 
 Fixes
+ * Fixes bug where deleting connections by index would only delete
+   one of multiple, if multiple are present (Issue #4762, PR #4763)
  * Changes error to warning on Universe creation if guessing fails
    due to missing information (Issue #4750, PR #4754)
  * Adds guessed attributes documentation back to each parser page

package/MDAnalysis/core/topologyattrs.py

@@ -3146,7 +3146,8 @@ def _delete_bonds(self, values):
                               '{attrname} with atom indices:'
                               '{indices}').format(attrname=self.attrname,
                                                   indices=indices))
-        idx = [self.values.index(v) for v in to_check]
+        # allow multiple matches
+        idx = [i for i, x in enumerate(self.values) if x in to_check]
         for i in sorted(idx, reverse=True):
             del self.values[i]
 

testsuite/MDAnalysisTests/core/test_universe.py

@@ -48,6 +48,7 @@
     two_water_gro, two_water_gro_nonames,
     TRZ, TRZ_psf,
     PDB, MMTF, CONECT,
+    PDB_conect
 )
 
 import MDAnalysis as mda
@@ -1247,6 +1248,16 @@ def test_delete_bonds_refresh_fragments(self, universe):
         universe.delete_bonds([universe.atoms[[2, 3]]])
         assert len(universe.atoms.fragments) == n_fragments + 1
 
+    @pytest.mark.parametrize("filename, n_bonds", [
+        (CONECT, 72),
+        (PDB_conect, 8)
+    ])
+    def test_delete_all_bonds(self, filename, n_bonds):
+        u = mda.Universe(filename)
+        assert len(u.bonds) == n_bonds
+        u.delete_bonds(u.bonds)
+        assert len(u.bonds) == 0
+
     @pytest.mark.parametrize(
         'attr,values', existing_atom_indices
     )