added tests for residues

package/MDAnalysis/core/groups.py

@@ -415,7 +415,11 @@ def get_connections(self, typename, outside=False):
         if not len(ugroup):
             return ugroup
         func = np.any if outside else np.all
-        seen = [np.in1d(col, self.ix_array) for col in ugroup._bix.T]
+        try:
+            indices = self.atoms.ix_array
+        except AttributeError:  # if self is an Atom
+            indices = self.ix_array
+        seen = [np.in1d(col, indices) for col in ugroup._bix.T]
         mask = func(seen, axis=0)
         return ugroup[mask]
 

testsuite/MDAnalysisTests/core/test_groups.py

@@ -1473,8 +1473,8 @@ def tpr():
     return mda.Universe(TPR)
 
 
-class TestGetConnections(object):
-    """Test _MutableBase.get_connections"""
+class TestGetConnectionsAtoms(object):
+    """Test Atom and AtomGroup.get_connections"""
 
     @pytest.mark.parametrize("typename",
                             ["bonds", "angles", "dihedrals", "impropers"])
@@ -1530,6 +1530,67 @@ def test_get_empty_group(self, tpr, outside):
         assert len(cxns) == 0
 
 
+class TestGetConnectionsResidues(object):
+    """Test Residue and ResidueGroup.get_connections"""
+
+    @pytest.mark.parametrize("typename, n_atoms", [
+        ("bonds", 9),
+        ("angles", 14),
+        ("dihedrals", 9),
+        ("impropers", 0),
+    ])
+    def test_connection_from_res_not_outside(self, tpr, typename, n_atoms):
+        cxns = tpr.residues[10].get_connections(typename, outside=False)
+        assert len(cxns) == n_atoms
+
+    @pytest.mark.parametrize("typename, n_atoms", [
+        ("bonds", 11),
+        ("angles", 22),
+        ("dihedrals", 27),
+        ("impropers", 0),
+    ])
+    def test_connection_from_res_outside(self, tpr, typename, n_atoms):
+        cxns = tpr.residues[10].get_connections(typename, outside=True)
+        assert len(cxns) == n_atoms
+
+    @pytest.mark.parametrize("typename, n_atoms", [
+        ("bonds", 157),
+        ("angles", 290),
+        ("dihedrals", 351),
+    ])
+    def test_connection_from_residues_not_outside(self, tpr, typename,
+                                                  n_atoms):
+        ag = tpr.residues[:10]
+        cxns = ag.get_connections(typename, outside=False)
+        assert len(cxns) == n_atoms
+        indices = np.ravel(cxns.to_indices())
+        assert np.all(np.in1d(indices, ag.atoms.indices))
+
+    @pytest.mark.parametrize("typename, n_atoms", [
+        ("bonds", 158),
+        ("angles", 294),
+        ("dihedrals", 360),
+    ])
+    def test_connection_from_residues_outside(self, tpr, typename, n_atoms):
+        ag = tpr.residues[:10]
+        cxns = ag.get_connections(typename, outside=True)
+        assert len(cxns) == n_atoms
+        indices = np.ravel(cxns.to_indices())
+        assert not np.all(np.in1d(indices, ag.indices))
+
+    def test_invalid_connection_error(self, tpr):
+        with pytest.raises(AttributeError, match="does not contain"):
+            ag = tpr.residues[:10]
+            ag.get_connections("ureybradleys")
+
+    @pytest.mark.parametrize("outside", [True, False])
+    def test_get_empty_group(self, tpr, outside):
+        imp = tpr.impropers
+        ag = tpr.residues[:10]
+        cxns = ag.get_connections("impropers", outside=outside)
+        assert len(imp) == 0
+        assert len(cxns) == 0
+
 @pytest.mark.parametrize("typename, n_atoms", [
     ("bonds", 13),
     ("angles", 27),