Accept bond lists

package/CHANGELOG

@@ -25,6 +25,7 @@ Fixes
 
 Enhancements
   * Expanded selection wildcards to the start and middle of strings (Issue #2370)
+  * Added type checking and conversion to Connection TopologyAttrs (Issue #2373)
 
 
 09/05/19 IAlibay, richardjgowers

package/MDAnalysis/core/topologyattrs.py

@@ -1642,7 +1642,14 @@ def _get_named_segment(group, segid):
 class _Connection(AtomAttr):
     """Base class for connectivity between atoms"""
     def __init__(self, values, types=None, guessed=False, order=None):
-        self.values = list(values)
+        values = [tuple(x) for x in values]
+        if not all(len(x) == self._n_atoms 
+                   and all(isinstance(y, (int, np.integer)) for y in x)
+                   for x in values):
+            raise ValueError(("{} must be an iterable of tuples with {}"
+                              " atom indices").format(self.attrname,
+                              self._n_atoms))
+        self.values = values
         if types is None:
             types = [None] * len(values)
         self.types = types
@@ -1743,6 +1750,7 @@ class Bonds(_Connection):
     # many bonds, so still asks for "bonds" in the plural
     singular = 'bonds'
     transplants = defaultdict(list)
+    _n_atoms = 2
 
     def bonded_atoms(self):
         """An :class:`~MDAnalysis.core.groups.AtomGroup` of all
@@ -1891,17 +1899,20 @@ class Angles(_Connection):
     attrname = 'angles'
     singular = 'angles'
     transplants = defaultdict(list)
+    _n_atoms = 3
 
 
 class Dihedrals(_Connection):
     """A connection between four sequential atoms"""
     attrname = 'dihedrals'
     singular = 'dihedrals'
     transplants = defaultdict(list)
+    _n_atoms = 4
 
 
 class Impropers(_Connection):
     """An imaginary dihedral between four atoms"""
     attrname = 'impropers'
     singular = 'impropers'
     transplants = defaultdict(list)
+    _n_atoms = 4

testsuite/MDAnalysisTests/core/test_universe.py

@@ -628,6 +628,42 @@ def test_add_charges(self, universe, toadd, attrname, default):
 
         assert hasattr(universe.atoms, attrname)
         assert getattr(universe.atoms, attrname)[0] == default
+
+    @pytest.mark.parametrize(
+        'attr,values', (
+            ('bonds', [(1, 0), (1, 2)]),
+            ('bonds', [[1, 0], [1, 2]]),
+            ('bonds', set([(1, 0), (1, 2)])),
+            ('angles', [(1, 0, 2), (1, 2, 3), (2, 1, 4)]),
+            ('dihedrals', [[1, 2, 3, 1], (3, 1, 5, 2)]),
+            ('impropers', [[1, 2, 3, 1], (3, 1, 5, 2)]),
+        )
+    )
+    def test_add_connection(self, universe, attr, values):
+        universe.add_TopologyAttr(attr, values)
+        assert hasattr(universe, attr)
+        attrgroup = getattr(universe, attr)
+        assert len(attrgroup) == len(values)
+        for x in attrgroup:
+            ix = x.indices
+            assert ix[0] <= ix[-1]
+
+    @pytest.mark.parametrize(
+        'attr,values', (
+            ('bonds', [(1, 0, 0), (1, 2)]),
+            ('bonds', [['x', 'y'], [1, 2]]),
+            ('bonds', 'rubbish'),
+            ('bonds', [[1.01, 2.0]]),
+            ('angles', [(1, 0), (1, 2)]),
+            ('angles', 'rubbish'),
+            ('dihedrals', [[1, 1, 1, 0.1]]),
+            ('impropers', [(1, 2, 3)]),
+        )
+    )
+    def add_connection_error(self, universe, attr, values):
+        with pytest.raises(ValueError):
+            universe.add_TopologyAttr(attr, values)
+
 
 
 class TestAllCoordinatesKwarg(object):