Fix bond deletion

package/CHANGELOG

@@ -23,6 +23,9 @@ The rules for this file:
  * 2.8.0
 
 Fixes
+ * Fixes bug where multiple identical connection topologies could be
+   added to a _Connection TopologyAttr, and that deleting connections
+   by index would only delete one of them (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

@@ -3042,19 +3042,12 @@ class _Connection(AtomAttr, metaclass=_ConnectionTopologyAttrMeta):
 
     @_check_connection_values
     def __init__(self, values, types=None, guessed=False, order=None):
-        self.values = values
-        if types is None:
-            types = [None] * len(values)
-        self.types = types
-        if guessed in (True, False):
-            # if single value passed, multiply this across
-            # all bonds
-            guessed = [guessed] * len(values)
-        self._guessed = guessed
-        if order is None:
-            order = [None] * len(values)
-        self.order = order
+        self.values = []
+        self.types = []
+        self._guessed = []
+        self.order = []
         self._cache = dict()
+        self._add_bonds(values, types, guessed, order)
 
     def copy(self):
         """Return a deepcopy of this attribute"""
@@ -3118,9 +3111,8 @@ def _add_bonds(self, values, types=None, guessed=True, order=None):
         if order is None:
             order = itertools.cycle((None,))
 
-        existing = set(self.values)
         for v, t, g, o in zip(values, types, guessed, order):
-            if v not in existing:
+            if v not in self.values:
                 self.values.append(v)
                 self.types.append(t)
                 self._guessed.append(g)
@@ -3146,7 +3138,8 @@ 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
     )

testsuite/MDAnalysisTests/topology/test_pdb.py

@@ -146,7 +146,7 @@ def parse():
         struc = parse()
 
     assert hasattr(struc, 'bonds')
-    assert len(struc.bonds.values) == 4
+    assert len(struc.bonds.values) == 2
 
 
 def test_single_conect():
@@ -158,7 +158,7 @@ def parse():
     with pytest.warns(UserWarning):
         struc = parse()
     assert hasattr(struc, 'bonds')
-    assert len(struc.bonds.values) == 2
+    assert len(struc.bonds.values) == 1
 
 
 def test_new_chainid_new_res():